Index % CPU Time:Total CPU Time:Self CPU Time:Children Name Index
------ ---------------- ------------- ----------------- ------------------------------------------------------------------------------- ------
[0] 100.0 34.697 26607.203 <spontaneous> [0]
34.697 19703.603 clone [1]
0.0 6903.6 __libc_start_main [13]
34.697 19703.603 <spontaneous> [0]
[1] 74.09 34.697 19703.603 clone [1]
0.0 9531.4 fillUpGraph.omp_fn.4 [5]
0.0 8311.5 fillUpGraph.omp_fn.3 [10]
0.0 1164.2 connectPreNodes.omp_fn.2 [26]
0.0 232.5 computeReadToNodeMappings.omp_fn.1 [74]
0.0 202.8 orderInsertionMarkers.omp_fn.0 [78]
0.0 176.1 computeNodeToNodeMappings.omp_fn.3 [89]
0.0 83.2 computeReadToNodeCounts.omp_fn.0 [117]
0.0 1.2 computeNodeToNodeMappings.omp_fn.5 [636]
0.0 0.501 createNodeLocks.omp_fn.1 [764]
0.0 0.2 createNodeLocks.omp_fn.2 [868]
1226.9 6502.198 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
1283.603 6323.198 threadSequenceThroughGraph [7]
[2] 57.56 2510.503 12825.396 findKmerInKmerOccurenceTable [2]
450.4 12317.196 [Loop@0x435cf0 at line 84 in findKmerInKmerOccurenceTable] [3]
1.4 56.4 keyInAccelerationTable [175]
450.4 12317.196 findKmerInKmerOccurenceTable [2]
[3] 47.92 450.4 12317.196 [Loop@0x435cf0 at line 84 in findKmerInKmerOccurenceTable] [3]
12317.196 0.0 compareKmers [4]
12317.196 0.0 [Loop@0x435cf0 at line 84 in findKmerInKmerOccurenceTable] [3]
17.9 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
15.495 0.0 qsort_r [43]
12.5 0.0 threadSequenceThroughGraph [7]
0.9 0.0 compareKmerOccurences [674]
0.1 0.0 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
[4] 46.41 12364.091 0.0 compareKmers [4]
0.0 9531.4 clone [1]
0.0 744.399 fillUpGraph [25]
[5] 38.57 0.0 10275.8 fillUpGraph.omp_fn.4 [5]
6.0 10269.8 [Loop@0x42ccd5 at line 1141 in fillUpGraph.omp_fn.4] [6]
6.0 10269.8 fillUpGraph.omp_fn.4 [5]
[6] 38.57 6.0 10269.8 [Loop@0x42ccd5 at line 1141 in fillUpGraph.omp_fn.4] [6]
0.0 10203.3 [Loop@0x42cf80 at line 863 in fillUpGraph.omp_fn.4] [8]
3.0 61.4 threadSequenceThroughGraph [7]
2.1 0.0 isSecondInPair [466]
146.3 10057.0 [Loop@0x42cf80 at line 863 in fillUpGraph.omp_fn.4] [8]
3.0 61.4 [Loop@0x42ccd5 at line 1141 in fillUpGraph.omp_fn.4] [6]
[7] 38.54 149.3 10118.4 threadSequenceThroughGraph [7]
1283.603 6323.198 findKmerInKmerOccurenceTable [2]
309.9 577.8 createArc [35]
330.4 2.4 addReadStart [56]
9.8 317.399 lockTwoNodes [58]
25.1 192.3 lockNode [80]
207.8 0.0 getNodeInGraph [47]
12.1 60.6 unLockNode [145]
66.2 0.0 getNodeLength [148]
2.0 62.0 memorizeNode [165]
7.6 47.9 unLockTwoNodes [181]
0.9 38.4 isNodeMemorized [209]
6.0 31.7 [Loop@0x42d820 at line 848 in threadSequenceThroughGraph] [218]
30.9 0.0 getKmerOccurenceNodeID [177]
29.4 0.0 incrementVirtualCoverage [240]
27.5 0.5 reversePushNucleotide [114]
24.6 0.0 getNucleotide [107]
22.6 0.0 getKmerOccurencePosition [264]
0.7 20.5 unMemorizeNodes [280]
16.3 0.0 incrementOriginalVirtualCoverage [322]
13.2 0.0 pushNucleotide [185]
12.5 0.0 compareKmers [4]
3.2 0.0 getLength [381]
0.5 0.0 getWordLength [727]
0.4 0.1 blurLastShortReadMarker [783]
0.3 0.0 findReferenceMapping [825]
0.1 0.0 clearKmer [824]
0.0 10203.3 [Loop@0x42ccd5 at line 1141 in fillUpGraph.omp_fn.4] [6]
[8] 38.3 0.0 10203.3 [Loop@0x42cf80 at line 863 in fillUpGraph.omp_fn.4] [8]
146.3 10057.0 threadSequenceThroughGraph [7]
4.8 8752.4 fillUpGraph.omp_fn.3 [10]
[9] 32.87 4.8 8752.4 [Loop@0x42df3f at line 1101 in fillUpGraph.omp_fn.3] [9]
2.0 8747.7 ghostThreadSequenceThroughGraph [11]
2.2 0.0 isSecondInPair [466]
0.5 0.0 getTightStringInArray [722]
0.0 8311.5 clone [1]
0.0 445.7 fillUpGraph [25]
[10] 32.87 0.0 8757.2 fillUpGraph.omp_fn.3 [10]
4.8 8752.4 [Loop@0x42df3f at line 1101 in fillUpGraph.omp_fn.3] [9]
2.0 8747.7 [Loop@0x42df3f at line 1101 in fillUpGraph.omp_fn.3] [9]
[11] 32.84 2.0 8747.7 ghostThreadSequenceThroughGraph [11]
103.4 8585.9 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
6.8 31.4 [Loop@0x42de10 at line 683 in ghostThreadSequenceThroughGraph] [217]
0.4 19.6 unMemorizeNodes [290]
0.2 0.0 clearKmer [824]
103.4 8585.9 ghostThreadSequenceThroughGraph [11]
[12] 32.62 103.4 8585.9 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
1226.9 6502.198 findKmerInKmerOccurenceTable [2]
17.6 254.2 lockNode [68]
251.201 0.0 getNodeInGraph [47]
8.0 53.5 isNodeMemorized [168]
0.7 55.4 memorizeNode [178]
55.7 0.0 getNucleotide [107]
38.7 0.0 incrementReadStartCount [214]
30.5 1.6 reversePushNucleotide [114]
25.7 0.0 getKmerOccurenceNodeID [177]
2.4 19.8 unLockNode [270]
19.1 0.0 pushNucleotide [185]
17.9 0.0 compareKmers [4]
4.6 0.0 getLength [381]
0.2 0.0 getWordLength [727]
0.0 6903.6 <spontaneous> [0]
[13] 25.91 0.0 6903.6 __libc_start_main [13]
0.0 6902.9 main [14]
0.7 0.0 _IO_vfprintf [19]
0.0 6902.9 __libc_start_main [13]
[14] 25.91 0.0 6902.9 main [14]
0.0 1693.3 correctGraph [15]
0.0 1616.5 importPreGraph [16]
0.1 1572.4 exportGraph [18]
0.1 731.4 newPreGraph_pg [37]
0.0 308.6 importRoadMapArray [62]
0.0 281.0 removeLowCoverageNodesAndDenounceDubiousReads [66]
0.0 170.1 importReadSet [98]
0.0 157.1 [Loop@0x40b8d0 at line 619 in main] [102]
0.0 70.3 exportPreGraph_pg [152]
0.0 60.4 exportLongNodeSequences [171]
0.0 60.3 concatenatePreGraph_pg [127]
0.0 44.1 convertSequences [198]
0.0 44.1 clipTips_pg [200]
0.0 36.4 clipTipsHard [144]
0.0 18.7 concatenateGraph [59]
0.0 17.7 displayGeneralStatistics [310]
0.0 9.6 logFinalStats [370]
0.1 2.8 destroyPreGraph_pg [525]
2.6 0.0 _IO_fclose [538]
0.0 1.6 destroyGraph [603]
0.0 1.4 getSequenceLengths [533]
0.0 0.8 removeHighCoverageNodes [706]
0.0 0.6 createReadPairingArray [753]
0.0 0.3 pairedCategories [840]
0.0 0.3 detachDubiousReads [841]
0.0 0.1 cleanUpRedundancy [40]
0.0 0.1 readCoherentGraph [994]
0.0 1693.3 main [14]
[15] 6.36 0.0 1693.3 correctGraph [15]
0.0 1483.4 [Loop@0x41a4bf at line 2568 in correctGraph] [22]
0.0 90.5 determineEligibleStartingPoints [122]
0.0 49.5 activateArcLookupTable [190]
0.0 37.0 clipTipsHard [144]
0.0 22.4 [Loop@0x41a3a6 at line 2565 in correctGraph] [266]
0.0 8.4 concatenateGraph [59]
0.0 1.2 resetNodeStatus [539]
0.8 0.0 [Loop@0x41a04d at line 2541 in correctGraph] [701]
0.0 0.1 callocOrExit3 [221]
0.0 1616.5 main [14]
[16] 6.07 0.0 1616.5 importPreGraph [16]
0.0 1370.5 fillUpGraph [25]
0.0 207.0 referenceGraphKmers [83]
0.0 39.0 readPreGraphFile [212]
15.4 1473.8 [Loop@0x407c50 at line 2016 in exportGraph] [21]
5.3 53.9 exportPreNode_pg [150]
0.9 19.1 exportNode [210]
1.2 11.6 [Loop@0x4076f4 at line 548 in exportNode] [324]
0.1 5.6 [Loop@0x413330 at line 927 in exportLongNodeSequence] [419]
0.0 3.2 [Loop@0x407c00 at line 2007 in exportGraph] [20]
0.1 2.8 exportArc [485]
0.0 1.7 exportArc [454]
0.0 0.4 [Loop@0x4128ec at line 432 in displayGeneralStatistics] [311]
0.0 0.1 exportLongNodeSequence [170]
[17] 5.99 23.0 1572.2 velvetFprintf [17]
1566.8 4.1 _IO_vfprintf [19]
1.3 0.0 [Import thunk vfprintf] [633]
0.1 1572.4 main [14]
[18] 5.9 0.1 1572.4 exportGraph [18]
0.1 1515.9 [Loop@0x407c00 at line 2007 in exportGraph] [20]
1.5 37.8 exportNode [210]
0.5 4.3 sortNodeArcs [450]
0.0 4.7 [Loop@0x407cf1 at line 1716 in exportGraph] [453]
0.1 3.9 [Loop@0x407c80 at line 1987 in exportGraph] [481]
0.2 3.0 sortNodeArcs [509]
0.4 0.0 [Loop@0x407b90 at line 1995 in exportGraph] [785]
1566.8 4.1 velvetFprintf [17]
0.7 0.0 __libc_start_main [13]
0.1 0.0 [Loop@0x407c50 at line 2016 in exportGraph] [21]
[19] 5.9 1567.6 4.1 _IO_vfprintf [19]
4.1 0.0 [Import thunk free] [470]
0.1 1515.9 exportGraph [18]
[20] 5.69 0.1 1515.9 [Loop@0x407c00 at line 2007 in exportGraph] [20]
23.4 1489.3 [Loop@0x407c50 at line 2016 in exportGraph] [21]
0.0 3.2 velvetFprintf [17]
23.4 1489.3 [Loop@0x407c00 at line 2007 in exportGraph] [20]
[21] 5.68 23.4 1489.3 [Loop@0x407c50 at line 2016 in exportGraph] [21]
15.4 1473.8 velvetFprintf [17]
0.1 0.0 _IO_vfprintf [19]
0.0 1483.4 correctGraph [15]
[22] 5.57 0.0 1483.4 [Loop@0x41a4bf at line 2568 in correctGraph] [22]
0.0 1456.8 [Loop@0x41a640 at line 2570 in correctGraph] [23]
0.0 21.0 updateNodeStatus [283]
0.1 5.3 nextStartingPoint [434]
0.1 0.1 tourBus [24]
0.0 1456.8 [Loop@0x41a4bf at line 2568 in correctGraph] [22]
[23] 5.47 0.0 1456.8 [Loop@0x41a640 at line 2570 in correctGraph] [23]
0.0 1228.71 [Loop@0x41a71f at line 2296 in correctGraph] [32]
0.2 227.89 tourBus [24]
0.0 1217.51 [Loop@0x41a71f at line 2296 in correctGraph] [32]
0.2 227.89 [Loop@0x41a640 at line 2570 in correctGraph] [23]
0.1 0.1 [Loop@0x41a4bf at line 2568 in correctGraph] [22]
[24] 5.43 0.3 1445.5 tourBus [24]
0.1 1217.41 tourBusNode [31]
0.2 216.39 dfh_extractmin [81]
11.3 0.0 getNodeID [49]
0.1 0.0 removeNextNodeFromDHeap [946]
0.0 1370.5 importPreGraph [16]
[25] 5.14 0.0 1370.5 fillUpGraph [25]
0.0 744.399 fillUpGraph.omp_fn.4 [5]
0.0 445.7 fillUpGraph.omp_fn.3 [10]
0.0 172.5 orderNodeReadStartArrays [96]
0.0 6.201 createNodeReadStartArrays [421]
0.0 1.4 resetNodeStatus [539]
0.2 0.0 [libgomp.so.1.0.0] [94]
0.0 0.1 activateReadStarts [989]
0.0 1164.2 clone [1]
0.0 167.2 connectPreNodes [99]
[26] 5.0 0.0 1331.4 connectPreNodes.omp_fn.2 [26]
2.0 1329.4 [Loop@0x4321b0 at line 867 in connectPreNodes.omp_fn.2] [27]
2.0 1329.4 connectPreNodes.omp_fn.2 [26]
[27] 5.0 2.0 1329.4 [Loop@0x4321b0 at line 867 in connectPreNodes.omp_fn.2] [27]
1.2 1327.0 [Loop@0x432270 at line 699 in connectPreNodes.omp_fn.2] [28]
0.5 0.3 chooseNextInternalPreNode [717]
0.4 0.0 getAnnotationCount [681]
1.2 1327.0 [Loop@0x4321b0 at line 867 in connectPreNodes.omp_fn.2] [27]
[28] 4.99 1.2 1327.0 [Loop@0x432270 at line 699 in connectPreNodes.omp_fn.2] [28]
1.0 1307.7 connectAnnotation [30]
0.4 17.7 [Loop@0x43227f at line 891 in connectPreNodes.omp_fn.2] [307]
0.2 0.0 getNextAnnotation [682]
43.9 1012.2 [Loop@0x432390 at line 705 in connectAnnotation] [34]
3.3 236.0 connectAnnotation [30]
0.6 16.3 [Loop@0x43227f at line 891 in connectPreNodes.omp_fn.2] [307]
[29] 4.93 47.8 1264.5 connectPreNodeToTheNext [29]
29.6 704.101 createPreArc_pg [36]
13.1 229.7 lockTwoNodes [75]
13.5 166.0 unLockTwoNodes [92]
108.5 0.0 getPreNodeLength_pg [111]
1.0 1307.7 [Loop@0x432270 at line 699 in connectPreNodes.omp_fn.2] [28]
[30] 4.91 1.0 1307.7 connectAnnotation [30]
8.0 1059.5 [Loop@0x432390 at line 705 in connectAnnotation] [34]
3.3 236.0 connectPreNodeToTheNext [29]
0.9 0.0 getStartID [600]
0.1 1217.41 tourBus [24]
9.5 1.7 [Loop@0x41a71f at line 2296 in correctGraph] [32]
[31] 4.61 9.6 1219.11 tourBusNode [31]
9.499 1106.015 tourBusArc [33]
52.098 3.999 getArcBetweenNodes [179]
34.199 0.0 nextTodoTicket [229]
11.6 0.0 getNodeInGraph [47]
0.7 0.1 getNodeTime [711]
0.0 0.5 freeDoneTickets [770]
0.2 0.0 _IO_fflush [547]
0.0 0.2 velvetLog [891]
0.0 1228.71 [Loop@0x41a640 at line 2570 in correctGraph] [23]
[32] 4.61 0.0 1228.71 [Loop@0x41a71f at line 2296 in correctGraph] [32]
0.0 1217.51 tourBus [24]
9.5 1.7 tourBusNode [31]
9.499 1106.015 tourBusNode [31]
[33] 4.19 9.499 1106.015 tourBusArc [33]
0.0 619.031 cleanUpRedundancy [40]
0.1 452.887 comparePaths [50]
0.0 30.497 destroyPaths [236]
1.4 0.0 getNodeStatus [365]
0.4 0.9 dfh_replacekey [629]
0.1 0.4 dfh_insertkey [784]
0.1 0.0 getMultiplicity [346]
0.1 0.0 setNodeTime [1006]
0.1 0.0 insertNodeIntoDHeap [1009]
8.0 1059.5 connectAnnotation [30]
[34] 4.01 8.0 1059.5 [Loop@0x432390 at line 705 in connectAnnotation] [34]
43.9 1012.2 connectPreNodeToTheNext [29]
3.4 0.0 getFinishID [490]
309.9 577.8 threadSequenceThroughGraph [7]
[35] 3.33 309.9 577.8 createArc [35]
53.6 374.1 getArcBetweenNodes [52]
114.799 0.0 [libgomp.so.1.0.0] [94]
2.9 12.606 allocatePointer [109]
12.299 0.0 GOMP_critical_start [334]
7.396 0.0 GOMP_critical_end [364]
0.1 0.0 allocateArc [878]
29.6 704.101 connectPreNodeToTheNext [29]
[36] 2.75 29.6 704.101 createPreArc_pg [36]
0.0 650.6 [Loop@0x431967 at line 83 in createPreArc_pg] [38]
23.8 0.0 getPreArcBetweenPreNodes_pg [39]
0.0 19.7 allocatePreArc_pg [291]
4.7 0.3 addPreArcToPreNode_pg [442]
4.5 0.0 PREARC_FI2P [462]
0.5 0.0 addPreArcToPreNode_pg [772]
0.1 731.4 main [14]
[37] 2.75 0.1 731.4 newPreGraph_pg [37]
20.401 423.399 createPreNodes [51]
0.0 168.0 connectPreNodes [99]
0.0 77.9 setInsertionMarkers [139]
0.0 22.3 [Loop@0x4337dd at line 341 in newPreGraph_pg] [268]
0.0 19.4 countPreNodes [295]
0.0 650.6 createPreArc_pg [36]
[38] 2.44 0.0 650.6 [Loop@0x431967 at line 83 in createPreArc_pg] [38]
17.5 595.7 getPreArcBetweenPreNodes_pg [39]
37.4 0.0 getPreArc_pg [219]
17.5 595.7 [Loop@0x431967 at line 83 in createPreArc_pg] [38]
23.8 0.0 createPreArc_pg [36]
[39] 2.39 41.3 595.7 getPreArcBetweenPreNodes_pg [39]
524.0 67.6 getDestination_pg [42]
4.1 0.0 getNextPreArc_pg [472]
0.0 619.031 tourBusArc [33]
0.0 0.1 main [14]
[40] 2.32 0.0 619.131 cleanUpRedundancy [40]
0.0 546.132 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
0.0 70.899 concatenatePathNodes [147]
0.1 2.0 destroyPaths [479]
2.1 176.828 remapBackOfNodeMarkersOntoNeighbour [61]
1.0 166.042 concatenateReadStarts [77]
0.9 118.798 remapNodeMarkersOntoNeighbour [104]
0.7 114.558 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
0.0 25.0 pushNeighbours [142]
0.4 11.6 concatenateNodesAndVaccinate [169]
[41] 2.32 5.1 612.826 injectShortReads [41]
209.319 119.604 [Loop@0x403556 at line 3776 in injectShortReads] [57]
0.199 243.005 mallocOrExit3 [67]
10.398 20.7 [Loop@0x403668 at line 3540 in injectShortReads] [234]
7.5 0.0 _int_free [227]
0.5 0.8 [Loop@0x403610 at line 3776 in injectShortReads] [627]
0.8 0.0 free [497]
524.0 67.6 getPreArcBetweenPreNodes_pg [39]
[42] 2.22 524.0 67.6 getDestination_pg [42]
67.6 0.0 PREARC_FI2P [158]
84.4 138.5 [Loop@0x4320d0 at line 154 in orderInsertionMarkers.omp_fn.0] [79]
124.6 47.9 [Loop@0x40449b at line 2881 in orderNodeReadStartArrays] [95]
118.505 19.495 sortKmerOccurenceTable [105]
11.9 7.1 sortCoords [300]
9.9 7.0 sortCoords [318]
[43] 2.14 349.306 219.995 qsort_r [43]
28.6 109.8 compareInsertionMarkers [106]
47.9 0.0 compareShortReadMarkers [192]
15.495 0.0 compareKmers [4]
14.1 0.0 compareCoords [336]
4.0 0.0 compareKmerOccurences [482]
0.1 0.0 [Import thunk free] [470]
213.0 0.0 lockTwoNodes [75]
124.499 0.0 lockTwoNodes [58]
122.4 0.0 lockNode [80]
69.7 0.0 lockNode [68]
14.9 0.0 lockTwoNodes [281]
11.5 0.0 lockRead [237]
[44] 2.09 555.998 0.0 omp_set_lock [44]
0.0 546.132 cleanUpRedundancy [40]
[45] 2.05 0.0 546.132 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
0.3 539.632 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.1 2.8 mapDistancesOntoPaths [526]
0.0 2.0 destroyPaths [479]
0.2 0.8 mapSlowOntoFast [673]
0.0 0.2 [Loop@0x418ba4 at line 2161 in cleanUpRedundancy] [911]
0.0 0.1 getNextInSequence [347]
0.3 539.632 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
[46] 2.03 0.3 539.632 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.4 337.321 remapBackOfNodeOntoNeighbour [55]
0.0 172.096 remapNodeOntoNeighbour [97]
0.0 19.316 remapEmptyPathOntoMiddlePath [298]
0.0 3.6 markerLeadsToNode [491]
2.1 0.0 _IO_fflush [547]
1.8 0.3 getNextInSequence [347]
0.0 1.1 markerLeadsToNode [661]
0.3 0.6 getPassageMarkerFinish [616]
0.0 0.3 getNode [360]
0.0 0.3 destroyNode [276]
0.1 0.0 isTerminal [392]
251.201 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
207.8 0.0 threadSequenceThroughGraph [7]
11.6 0.0 tourBusNode [31]
2.4 0.0 nextStartingPoint [434]
2.2 0.0 projectFromReadPair [184]
0.8 0.0 projectFromSingleRead [203]
0.5 0.0 createConnection [162]
0.5 0.0 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
0.2 0.0 [Loop@0x41a20d at line 473 in determineEligibleStartingPoints] [325]
0.2 0.0 initializeTodoLists [267]
0.1 0.0 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
0.1 0.0 [Loop@0x414ada at line 1184 in removeLowCoverageNodesAndDenounceDubiousReads] [233]
0.1 0.0 createNewConnection [990]
[47] 1.79 477.7 0.0 getNodeInGraph [47]
182.381 0.0 unLockRead [86]
148.6 0.0 unLockTwoNodes [92]
54.8 0.0 unLockNode [145]
41.7 0.0 unLockTwoNodes [181]
18.6 0.0 unLockNode [270]
5.498 0.0 unLockTwoNodes [383]
1.0 0.0 [Loop@0x429a08 at line 1442 in projectFromShortRead] [156]
1.0 0.0 projectFromSingleRead [203]
0.2 0.0 projectFromReadPair [184]
[48] 1.7 453.779 0.0 omp_unset_lock [48]
183.801 0.0 lockNode [68]
79.797 0.0 getNodeTime [137]
69.6 0.0 lockNode [80]
51.8 0.0 getNodeTime [112]
12.8 0.0 [Loop@0x41a326 at line 497 in determineEligibleStartingPoints] [140]
11.3 0.0 initializeTodoLists [267]
11.3 0.0 tourBus [24]
5.0 0.0 [Loop@0x4286e4 at line 882 in splayConnection] [312]
4.8 0.0 lockTwoNodes [58]
4.6 0.0 getNodeTime [455]
3.4 0.0 unLockNode [145]
3.399 0.0 getNodeTime [496]
2.7 0.0 unLockTwoNodes [181]
1.8 0.0 projectFromReadPair [184]
1.2 0.0 unLockNode [270]
1.2 0.0 getNodePrevious [640]
0.7 0.0 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
0.699 0.0 getNodePrevious [594]
0.5 0.0 getNodePrevious [779]
0.4 0.0 getNodePrevious [804]
0.4 0.0 findOrCreateConnection [257]
0.3 0.0 getNodePrevious [743]
0.3 0.0 getNodePrevious [789]
0.3 0.0 getNodePrevious [808]
0.3 0.0 [Loop@0x42bab8 at line 513 in correctGraphLocally] [677]
0.2 0.0 getNodeTime [561]
0.2 0.0 popNodeRecord [807]
0.2 0.0 getNodePrevious [834]
0.1 0.0 markInterestingNodes [512]
0.1 0.0 setNodePrevious [773]
0.1 0.0 getNodePrevious [363]
0.1 0.0 getNodeTime [711]
[49] 1.7 453.395 0.0 getNodeID [49]
0.1 452.887 tourBusArc [33]
[50] 1.7 0.1 452.887 comparePaths [50]
48.2 222.294 [Loop@0x4196cb at line 2210 in comparePaths] [69]
0.0 87.998 [Loop@0x419dab at line 589 in comparePaths] [131]
1.399 32.699 [Loop@0x419ae0 at line 2246 in comparePaths] [231]
0.8 23.698 [Loop@0x419bb0 at line 2264 in comparePaths] [256]
0.2 23.799 extractSequence [258]
0.0 7.0 pathContainsReference [407]
0.4 3.4 addUncertainPassageMarker [202]
0.3 0.5 setPassageMarkerStatus [403]
0.0 0.2 compareSequences [130]
20.401 423.399 newPreGraph_pg [37]
[51] 1.67 20.401 423.399 createPreNodes [51]
5.2 197.404 [Loop@0x432850 at line 390 in createPreNodes] [84]
201.595 0.0 _IO_getc [53]
3.8 2.8 [Loop@0x432ee1 at line 565 in createPreNodes] [415]
4.6 0.0 [Import thunk _IO_getc] [416]
4.6 0.0 __ctype_b_loc [448]
3.4 0.0 [Import thunk __ctype_b_loc] [503]
53.6 374.1 createArc [35]
[52] 1.61 53.6 374.1 getArcBetweenNodes [52]
338.0 0.0 [Loop@0x40553c at line 351 in getArcBetweenNodes] [54]
36.1 0.0 [Loop@0x40559d at line 357 in getArcBetweenNodes] [222]
201.595 0.0 createPreNodes [51]
87.0 0.0 [Loop@0x432a08 at line 461 in createPreNodes] [128]
26.0 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
24.7 0.0 [Loop@0x42c13c at line 502 in referenceGraphKmers] [251]
15.7 0.0 [Loop@0x42c4a0 at line 543 in referenceGraphKmers] [293]
9.3 0.0 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
7.799 0.0 newDescriptor_pg [232]
2.8 0.0 [Loop@0x432ee1 at line 565 in createPreNodes] [415]
0.2 0.0 [Loop@0x42ff74 at line 1025 in newDescriptor_pg] [856]
[53] 1.41 375.094 0.0 _IO_getc [53]
338.0 0.0 getArcBetweenNodes [52]
[54] 1.27 338.0 0.0 [Loop@0x40553c at line 351 in getArcBetweenNodes] [54]
0.4 337.321 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
[55] 1.27 0.4 337.321 remapBackOfNodeOntoNeighbour [55]
1.3 299.222 remapBackOfNodeMarkersOntoNeighbour [61]
0.0 17.7 remapBackOfNodeArcsOntoNeighbour [313]
0.0 9.4 [Loop@0x416850 at line 894 in remapBackOfNodeOntoNeighbour] [374]
0.3 5.1 remapBackOfNodeTimesOntoNeighbour [436]
1.0 1.3 remapNodeFibHeapReferencesOntoNode [437]
0.0 1.8 remapBackOfNodeDescriptorOntoNeighbour [587]
0.2 0.0 getTwinNode [228]
330.4 2.4 threadSequenceThroughGraph [7]
[56] 1.25 330.4 2.4 addReadStart [56]
2.4 0.0 getNodeID [544]
209.319 119.604 injectShortReads [41]
[57] 1.23 209.319 119.604 [Loop@0x403556 at line 3776 in injectShortReads] [57]
57.601 0.0 setShortReadMarkerOffset [176]
28.799 0.0 setShortReadMarkerPosition [242]
12.803 0.0 setShortReadMarkerOffset [341]
5.7 0.0 setShortReadMarkerPosition [429]
5.0 0.0 setShortReadMarkerPosition [443]
2.7 0.0 setShortReadMarkerPosition [535]
2.1 0.0 setShortReadMarkerPosition [560]
1.7 0.0 setShortReadMarkerOffset [599]
1.201 0.0 setShortReadMarkerOffset [635]
1.0 0.0 setShortReadMarkerOffset [669]
0.5 0.0 min_short [769]
0.4 0.0 min [788]
0.1 0.0 setShortReadMarkerPosition [968]
9.8 317.399 threadSequenceThroughGraph [7]
[58] 1.23 9.8 317.399 lockTwoNodes [58]
182.4 0.0 omp_test_lock [91]
124.499 0.0 omp_set_lock [44]
5.2 0.0 [libgomp.so.1.0.0] [94]
4.8 0.0 getNodeID [49]
0.4 0.0 [Import thunk omp_test_lock] [813]
0.1 0.0 [Import thunk omp_set_lock] [687]
0.0 249.4 removeLowCoverageNodesAndDenounceDubiousReads [66]
0.0 46.1 clipTipsHard [144]
0.0 18.7 main [14]
0.0 8.4 correctGraph [15]
[59] 1.21 0.0 322.6 concatenateGraph [59]
0.0 319.5 [Loop@0x40e270 at line 198 in concatenateGraph] [60]
0.0 3.1 renumberNodes [516]
0.0 319.5 concatenateGraph [59]
[60] 1.2 0.0 319.5 [Loop@0x40e270 at line 198 in concatenateGraph] [60]
0.0 164.642 [Loop@0x40e320 at line 217 in concatenateGraph] [100]
0.0 154.358 [Loop@0x40e294 at line 205 in concatenateGraph] [103]
0.2 0.0 simpleArcCount [459]
0.2 0.0 getTwinNode [228]
0.1 0.0 nodeCount [580]
1.3 299.222 remapBackOfNodeOntoNeighbour [55]
1.3 8.1 [Loop@0x416850 at line 894 in remapBackOfNodeOntoNeighbour] [374]
[61] 1.16 2.6 307.322 remapBackOfNodeMarkersOntoNeighbour [61]
2.1 176.828 injectShortReads [41]
0.1 57.6 commonNodeReads [173]
13.6 8.298 [Loop@0x417498 at line 1143 in remapBackOfNodeMarkersOntoNeighbour] [275]
10.0 7.897 [Loop@0x4173f8 at line 1069 in remapBackOfNodeMarkersOntoNeighbour] [308]
0.6 6.8 extractFrontOfNodeReads [404]
1.0 6.1 extractBackOfNodeReads [406]
3.1 1.0 [Loop@0x4170f0 at line 1033 in remapBackOfNodeMarkersOntoNeighbour] [471]
1.1 1.599 [Loop@0x417200 at line 1098 in remapBackOfNodeMarkersOntoNeighbour] [536]
0.0 1.9 addPassageMarker [581]
0.1 0.9 getStartOffset [676]
0.0 0.9 setPreviousInSequence [690]
0.7 0.0 _int_free [227]
0.1 0.6 setStartOffset [733]
0.3 0.3 getPreviousInSequence [658]
0.3 0.3 getPassageMarkerFinish [616]
0.0 0.5 getPassageMarkerStart [752]
0.2 0.2 setNextInSequence [797]
0.2 0.2 setPassageMarkerFinish [645]
0.2 0.2 getPassageMarkerLength [810]
0.0 0.3 getPassageMarkerStatus [849]
0.1 0.2 passageMarkerDirection [853]
0.0 0.2 getPassageMarkerSequenceID [887]
0.0 0.2 getNextInNode [546]
0.1 0.0 setPassageMarkerStart [768]
0.1 0.0 incrementOriginalVirtualCoverage [322]
0.0 0.1 setPassageMarkerStatus [403]
0.0 0.1 getNode [360]
0.0 0.1 getFinishOffset [981]
0.0 308.6 main [14]
[62] 1.16 0.0 308.6 importRoadMapArray [62]
6.705 233.995 [Loop@0x42f1e8 at line 154 in importRoadMapArray] [76]
1.8 65.9 [Loop@0x42f110 at line 127 in importRoadMapArray] [157]
0.2 0.0 [Loop@0x42f1b0 at line 148 in importRoadMapArray] [866]
0.0 160.042 [Loop@0x40e320 at line 217 in concatenateGraph] [100]
0.0 145.958 [Loop@0x40e294 at line 205 in concatenateGraph] [103]
[63] 1.15 0.0 306.0 concatenateStringOfNodes [63]
0.0 293.7 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
0.0 6.1 reallocateNodeDescriptor [424]
0.0 3.0 [Loop@0x40e1e4 at line 180 in concatenateStringOfNodes] [518]
0.0 2.7 [Loop@0x40de14 at line 94 in concatenateStringOfNodes] [534]
0.0 0.5 [Loop@0x40e17c at line 170 in concatenateStringOfNodes] [778]
0.0 293.7 concatenateStringOfNodes [63]
[64] 1.1 0.0 293.7 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
0.1 171.942 concatenateReadStarts [77]
0.7 114.558 injectShortReads [41]
0.1 3.4 directlyAppendDescriptors [494]
1.9 0.0 _int_free [227]
0.4 0.0 getMarker [624]
0.2 0.0 mergeNodeReads [754]
0.2 0.0 free [497]
0.1 0.0 getDestination [248]
0.1 0.0 getUniqueness [760]
273.407 0.0 mallocOrExit3 [67]
13.406 0.0 allocatePointer [109]
[65] 1.08 286.813 0.0 malloc [65]
0.0 281.0 main [14]
[66] 1.05 0.0 281.0 removeLowCoverageNodesAndDenounceDubiousReads [66]
0.0 249.4 concatenateGraph [59]
0.3 31.2 [Loop@0x414ada at line 1184 in removeLowCoverageNodesAndDenounceDubiousReads] [233]
0.0 0.1 [Loop@0x414bff at line 1260 in removeLowCoverageNodesAndDenounceDubiousReads] [942]
0.199 243.005 injectShortReads [41]
0.5 14.5 [Loop@0x41cd0e at line 1568 in importReadSet] [183]
0.2 5.9 [Loop@0x403d68 at line 2862 in createNodeReadStartArrays] [422]
0.0 5.2 commonNodeReads [173]
0.0 2.1 extractFrontOfNodeReads [404]
0.0 1.202 spreadReadIDs [304]
0.0 1.2 extractBackOfNodeReads [406]
0.0 0.2 newRecycleBin [900]
0.0 0.1 createReadsLocks [1033]
[67] 1.03 0.899 273.407 mallocOrExit3 [67]
273.407 0.0 malloc [65]
17.6 254.2 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
[68] 1.02 17.6 254.2 lockNode [68]
183.801 0.0 getNodeID [49]
69.7 0.0 omp_set_lock [44]
0.7 0.0 [libgomp.so.1.0.0] [94]
48.2 222.294 comparePaths [50]
[69] 1.02 48.2 222.294 [Loop@0x4196cb at line 2210 in comparePaths] [69]
55.699 51.8 getNodeTime [112]
1.6 80.297 getNodeTime [137]
9.9 0.2 getNodePrevious [363]
0.0 9.4 isPreviousToNode [372]
0.0 6.799 isPreviousToNode [411]
1.5 0.6 getNodeTime [561]
1.1 0.699 getNodePrevious [594]
1.2 0.3 getNodeTime [619]
0.0 0.6 [Loop@0x419a70 at line 112 in comparePaths] [742]
0.2 0.4 [Loop@0x419a30 at line 112 in comparePaths] [756]
199.895 0.0 [Loop@0x42f1e8 at line 154 in importRoadMapArray] [76]
34.9 0.0 [Loop@0x41cd0e at line 1568 in importReadSet] [183]
28.0 0.0 [Loop@0x42f110 at line 127 in importRoadMapArray] [157]
5.0 0.0 [Loop@0x40a990 at line 2309 in readPreGraphFile] [213]
[70] 1.01 267.795 0.0 __isoc99_sscanf [70]
30.325 222.675 computePartialReadToNodeMappingShort [72]
[71] 0.95 30.325 222.675 [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort] [71]
5.397 185.281 unLockRead [86]
17.898 12.2 lockRead [237]
0.8 0.0 getShortReadMarkerID [465]
0.7 0.0 getShortReadMarkerPosition [260]
0.4 0.0 getShortReadMarkerAtIndex [243]
0.0 253.0 [Loop@0x42729b at line 441 in computeReadToNodeMappings.omp_fn.1] [73]
[72] 0.95 0.0 253.0 computePartialReadToNodeMappingShort [72]
30.325 222.675 [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort] [71]
0.0 253.0 computeReadToNodeMappings.omp_fn.1 [74]
[73] 0.95 0.0 253.0 [Loop@0x42729b at line 441 in computeReadToNodeMappings.omp_fn.1] [73]
0.0 253.0 computePartialReadToNodeMappingShort [72]
0.0 232.5 clone [1]
0.0 20.5 computeReadToNodeMappings [274]
[74] 0.95 0.0 253.0 computeReadToNodeMappings.omp_fn.1 [74]
0.0 253.0 [Loop@0x42729b at line 441 in computeReadToNodeMappings.omp_fn.1] [73]
13.1 229.7 connectPreNodeToTheNext [29]
[75] 0.91 13.1 229.7 lockTwoNodes [75]
213.0 0.0 omp_set_lock [44]
16.4 0.0 [libgomp.so.1.0.0] [94]
0.3 0.0 [Import thunk omp_set_lock] [687]
6.705 233.995 importRoadMapArray [62]
[76] 0.9 6.705 233.995 [Loop@0x42f1e8 at line 154 in importRoadMapArray] [76]
199.895 0.0 __isoc99_sscanf [70]
33.8 0.0 fgets [85]
0.2 0.0 [Import thunk __isoc99_sscanf] [759]
0.1 0.0 [Import thunk fgets] [767]
0.1 171.942 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
0.0 31.7 pushNeighbours [142]
0.2 28.9 concatenateNodesAndVaccinate [169]
[77] 0.87 0.3 232.542 concatenateReadStarts [77]
1.0 166.042 injectShortReads [41]
23.8 22.2 [Loop@0x40dd60 at line 68 in concatenateReadStarts] [194]
5.9 10.2 [Loop@0x40dce0 at line 54 in concatenateReadStarts] [326]
2.2 0.0 _int_free [227]
0.6 0.0 getNodeReads [688]
0.5 0.0 getNodeReadCount [707]
0.1 0.0 getTwinNode [228]
0.0 202.8 clone [1]
0.0 21.2 orderInsertionMarkers [279]
[78] 0.84 0.0 224.0 orderInsertionMarkers.omp_fn.0 [78]
0.9 223.1 [Loop@0x4320d0 at line 154 in orderInsertionMarkers.omp_fn.0] [79]
0.9 223.1 orderInsertionMarkers.omp_fn.0 [78]
[79] 0.84 0.9 223.1 [Loop@0x4320d0 at line 154 in orderInsertionMarkers.omp_fn.0] [79]
84.4 138.5 qsort_r [43]
0.1 0.0 qsort [964]
0.0 0.1 msort_with_tmp [1025]
25.1 192.3 threadSequenceThroughGraph [7]
[80] 0.82 25.1 192.3 lockNode [80]
122.4 0.0 omp_set_lock [44]
69.6 0.0 getNodeID [49]
0.2 0.0 [libgomp.so.1.0.0] [94]
0.1 0.0 [Import thunk omp_set_lock] [687]
0.2 216.39 tourBus [24]
0.1 0.0 tourBus_local [937]
[81] 0.81 0.3 216.39 dfh_extractmin [81]
0.0 216.39 dfh_extractminel [82]
0.0 216.39 dfh_extractmin [81]
[82] 0.81 0.0 216.39 dfh_extractminel [82]
0.4 126.593 dfh_consolidate [108]
0.9 88.397 [Loop@0x41b000 at line 293 in dfh_extractminel] [126]
0.0 0.1 dfh_removerootlist [1010]
0.0 207.0 importPreGraph [16]
[83] 0.78 0.0 207.0 referenceGraphKmers [83]
0.0 140.9 sortKmerOccurenceTable [105]
0.0 39.7 [Loop@0x42c240 at line 536 in referenceGraphKmers] [207]
0.0 26.4 [Loop@0x42c130 at line 502 in referenceGraphKmers] [249]
5.2 197.404 createPreNodes [51]
[84] 0.76 5.2 197.404 [Loop@0x432850 at line 390 in createPreNodes] [84]
0.8 90.803 [Loop@0x432bfd at line 430 in createPreNodes] [119]
1.6 89.8 [Loop@0x4329dc at line 461 in createPreNodes] [120]
0.4 11.2 [Loop@0x432907 at line 427 in createPreNodes] [350]
2.8 0.0 pushNucleotide [185]
38.1 0.0 [Loop@0x41cc29 at line 1545 in importReadSet] [216]
37.6 0.0 [Loop@0x42f110 at line 127 in importRoadMapArray] [157]
36.3 0.0 [Loop@0x41ce48 at line 1599 in importReadSet] [204]
34.8 0.0 [Loop@0x41cce8 at line 1564 in importReadSet] [121]
33.8 0.0 [Loop@0x42f1e8 at line 154 in importRoadMapArray] [76]
11.2 0.0 [Loop@0x432907 at line 427 in createPreNodes] [350]
5.9 0.0 [Loop@0x432bfd at line 430 in createPreNodes] [119]
1.6 0.0 [Loop@0x40a990 at line 2309 in readPreGraphFile] [213]
1.2 0.0 [Loop@0x42c240 at line 536 in referenceGraphKmers] [207]
1.0 0.0 [Loop@0x42c130 at line 502 in referenceGraphKmers] [249]
[85] 0.76 201.501 0.0 fgets [85]
5.397 185.281 [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort] [71]
[86] 0.72 5.397 185.281 unLockRead [86]
182.381 0.0 omp_unset_lock [48]
2.6 0.0 [libgomp.so.1.0.0] [94]
0.3 0.0 [Import thunk omp_unset_lock] [447]
0.0 189.6 [Loop@0x429de4 at line 1593 in computeNodeToNodeMappings.omp_fn.3] [88]
[87] 0.71 0.0 189.6 projectFromNode [87]
13.7 175.8 [Loop@0x429963 at line 1429 in projectFromNode] [90]
0.1 0.0 getUniqueness [760]
0.0 189.6 computeNodeToNodeMappings.omp_fn.3 [89]
[88] 0.71 0.0 189.6 [Loop@0x429de4 at line 1593 in computeNodeToNodeMappings.omp_fn.3] [88]
0.0 189.6 projectFromNode [87]
0.0 176.1 clone [1]
0.0 13.5 computeNodeToNodeMappings [338]
[89] 0.71 0.0 189.6 computeNodeToNodeMappings.omp_fn.3 [89]
0.0 189.6 [Loop@0x429de4 at line 1593 in computeNodeToNodeMappings.omp_fn.3] [88]
13.7 175.8 projectFromNode [87]
[90] 0.71 13.7 175.8 [Loop@0x429963 at line 1429 in projectFromNode] [90]
48.4 126.6 projectFromShortRead [93]
0.6 0.0 getShortReadMarkerID [465]
0.2 0.0 getShortReadMarkerAtIndex [243]
182.4 0.0 lockTwoNodes [58]
[91] 0.68 182.4 0.0 omp_test_lock [91]
13.5 166.0 connectPreNodeToTheNext [29]
[92] 0.67 13.5 166.0 unLockTwoNodes [92]
148.6 0.0 omp_unset_lock [48]
16.6 0.0 [libgomp.so.1.0.0] [94]
0.8 0.0 [Import thunk omp_unset_lock] [447]
48.4 126.6 [Loop@0x429963 at line 1429 in projectFromNode] [90]
[93] 0.66 48.4 126.6 projectFromShortRead [93]
0.2 69.598 [Loop@0x429a08 at line 1442 in projectFromShortRead] [156]
0.4 55.302 [Loop@0x429af0 at line 1464 in projectFromShortRead] [180]
0.4 0.0 getInsertLength [721]
0.4 0.0 getShortReadMarkerID [465]
0.2 0.0 getShortReadMarkerPosition [260]
0.1 0.0 getShortReadMarkerOffset [997]
114.799 0.0 createArc [35]
16.6 0.0 unLockTwoNodes [92]
16.4 0.0 lockTwoNodes [75]
5.9 0.0 lockTwoNodes [281]
5.2 0.0 lockTwoNodes [58]
2.6 0.0 unLockRead [86]
2.6 0.0 unLockTwoNodes [383]
2.2 0.0 projectFromSingleRead [203]
1.9 0.0 unLockTwoNodes [181]
1.8 0.0 [Loop@0x429a08 at line 1442 in projectFromShortRead] [156]
0.8 0.0 allocateConnection [585]
0.7 0.0 lockNode [68]
0.4 0.0 lockRead [237]
0.3 0.0 computeReadToNodeMappings [274]
0.2 0.0 lockNode [80]
0.2 0.0 computeNodeToNodeMappings [338]
0.2 0.0 fillUpGraph [25]
0.2 0.0 computeReadToNodeCounts [379]
0.1 0.0 unLockNode [145]
0.1 0.0 allocateConnection [863]
0.1 0.0 connectPreNodes [99]
0.1 0.0 orderInsertionMarkers [279]
[94] 0.65 173.399 0.0 [libgomp.so.1.0.0] [94]
0.0 172.5 orderNodeReadStartArrays [96]
[95] 0.65 0.0 172.5 [Loop@0x40449b at line 2881 in orderNodeReadStartArrays] [95]
124.6 47.9 qsort_r [43]
0.0 172.5 fillUpGraph [25]
[96] 0.65 0.0 172.5 orderNodeReadStartArrays [96]
0.0 172.5 [Loop@0x40449b at line 2881 in orderNodeReadStartArrays] [95]
0.0 172.096 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
[97] 0.65 0.0 172.096 remapNodeOntoNeighbour [97]
0.2 153.696 remapNodeMarkersOntoNeighbour [104]
0.0 12.8 remapNodeArcsOntoNeighbour [342]
0.0 4.1 remapNodeTimesOntoNeighbour [475]
1.1 0.1 remapNodeFibHeapReferencesOntoNode [437]
0.1 0.0 getTwinNode [228]
0.0 170.1 main [14]
[98] 0.64 0.0 170.1 importReadSet [98]
0.2 90.4 [Loop@0x41cce8 at line 1564 in importReadSet] [121]
0.9 39.9 [Loop@0x41ce48 at line 1599 in importReadSet] [204]
0.2 38.1 [Loop@0x41cc29 at line 1545 in importReadSet] [216]
0.0 0.3 computeSecondInPair [843]
0.0 0.1 callocOrExit3 [221]
0.0 168.0 newPreGraph_pg [37]
[99] 0.63 0.0 168.0 connectPreNodes [99]
0.0 167.2 connectPreNodes.omp_fn.2 [26]
0.7 0.0 [Loop@0x4338dc at line 846 in connectPreNodes] [731]
0.1 0.0 [libgomp.so.1.0.0] [94]
0.0 164.642 [Loop@0x40e270 at line 198 in concatenateGraph] [60]
[100] 0.62 0.0 164.642 [Loop@0x40e320 at line 217 in concatenateGraph] [100]
0.0 160.042 concatenateStringOfNodes [63]
2.1 0.0 getTwinNode [228]
1.5 0.0 getDestination [248]
0.9 0.0 simpleArcCount [459]
0.1 0.0 getArc [351]
0.0 157.1 [Loop@0x40b8d0 at line 619 in main] [102]
[101] 0.59 0.0 157.1 exploitShortReadPairs [101]
0.0 82.9 [Loop@0x426660 at line 1229 in exploitShortReadPairs] [135]
0.0 74.2 buildScaffold [141]
0.0 157.1 main [14]
[102] 0.59 0.0 157.1 [Loop@0x40b8d0 at line 619 in main] [102]
0.0 157.1 exploitShortReadPairs [101]
0.0 154.358 [Loop@0x40e270 at line 198 in concatenateGraph] [60]
[103] 0.58 0.0 154.358 [Loop@0x40e294 at line 205 in concatenateGraph] [103]
0.0 145.958 concatenateStringOfNodes [63]
3.0 0.0 getDestination [248]
2.7 0.0 simpleArcCount [459]
2.6 0.0 getTwinNode [228]
0.1 0.0 getArc [351]
0.2 153.696 remapNodeOntoNeighbour [97]
[104] 0.58 0.2 153.696 remapNodeMarkersOntoNeighbour [104]
0.9 118.798 injectShortReads [41]
14.899 1.6 [Loop@0x416690 at line 773 in remapNodeMarkersOntoNeighbour] [321]
13.399 1.7 [Loop@0x4165f8 at line 808 in remapNodeMarkersOntoNeighbour] [332]
0.0 0.8 [Loop@0x416264 at line 718 in remapNodeMarkersOntoNeighbour] [712]
0.6 0.0 _int_free [227]
0.3 0.0 getNodeReads [688]
0.2 0.0 getNodeReadCount [707]
0.2 0.0 [Loop@0x4164e8 at line 773 in remapNodeMarkersOntoNeighbour] [915]
0.1 0.0 [Loop@0x416590 at line 808 in remapNodeMarkersOntoNeighbour] [943]
0.0 0.1 getPassageMarkerStart [752]
0.1 0.0 mergeNodeReads [754]
0.0 140.9 referenceGraphKmers [83]
[105] 0.53 0.0 140.9 sortKmerOccurenceTable [105]
118.505 19.495 qsort_r [43]
0.2 1.5 [Loop@0x435df8 at line 63 in sortKmerOccurenceTable] [597]
0.2 1.0 [Loop@0x435f4b at line 157 in sortKmerOccurenceTable] [643]
28.6 109.8 qsort_r [43]
0.0 0.1 msort_with_tmp [1025]
[106] 0.52 28.6 109.9 compareInsertionMarkers [106]
12.4 54.3 getInsertionMarkerPosition [160]
15.9 27.3 getInsertionMarkerPosition [201]
55.7 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
29.899 0.0 [Loop@0x419ddd at line 590 in compareSequences] [132]
24.6 0.0 threadSequenceThroughGraph [7]
11.2 0.0 [Loop@0x42d820 at line 848 in threadSequenceThroughGraph] [218]
9.0 0.0 [Loop@0x42de10 at line 683 in ghostThreadSequenceThroughGraph] [217]
0.3 0.0 [Loop@0x419340 at line 636 in mapSlowOntoFast] [708]
[107] 0.49 130.699 0.0 getNucleotide [107]
0.4 126.593 dfh_extractminel [82]
0.0 0.1 dfh_extractminel [1021]
[108] 0.48 0.4 126.693 dfh_consolidate [108]
16.999 104.895 [Loop@0x41ad00 at line 321 in dfh_consolidate] [110]
2.5 1.9 [Loop@0x41aeff at line 311 in dfh_consolidate] [464]
0.4 0.0 [Loop@0x41acc0 at line 328 in dfh_consolidate] [801]
54.2 0.0 allocateSmallNodeList [167]
51.7 0.0 allocateSmallNodeList [182]
2.9 12.606 createArc [35]
0.0 0.6 allocateFibHeapEl [761]
0.2 0.0 allocateConnectionStack [864]
0.0 0.2 allocateNode [885]
0.1 0.0 allocateConnectionStack [940]
0.1 0.0 createAnalogousArc [245]
0.1 0.0 allocateNodeList [1023]
0.1 0.0 allocateNodeList [1028]
0.1 0.0 allocateConnection [585]
0.1 0.0 allocateDFibHeapNode [1034]
[109] 0.46 109.6 13.406 allocatePointer [109]
13.406 0.0 malloc [65]
16.999 104.895 dfh_consolidate [108]
[110] 0.46 16.999 104.895 [Loop@0x41ad00 at line 321 in dfh_consolidate] [110]
1.1 95.495 [Loop@0x41ad60 at line 414 in dfh_consolidate] [113]
2.0 6.299 dfh_removerootlist [386]
108.5 0.0 connectPreNodeToTheNext [29]
0.2 0.0 [Loop@0x43227f at line 891 in connectPreNodes.omp_fn.2] [307]
0.1 0.0 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
[111] 0.41 108.8 0.0 getPreNodeLength_pg [111]
55.699 51.8 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[112] 0.4 55.699 51.8 getNodeTime [112]
51.8 0.0 getNodeID [49]
1.1 95.495 [Loop@0x41ad00 at line 321 in dfh_consolidate] [110]
[113] 0.36 1.1 95.495 [Loop@0x41ad60 at line 414 in dfh_consolidate] [113]
2.299 90.196 dfh_heaplink [115]
3.0 0.0 dfh_compare [521]
30.5 1.6 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
27.5 0.5 threadSequenceThroughGraph [7]
18.0 0.2 [Loop@0x42de10 at line 683 in ghostThreadSequenceThroughGraph] [217]
15.8 0.0 [Loop@0x42d820 at line 848 in threadSequenceThroughGraph] [218]
1.5 0.0 [Loop@0x42c4a0 at line 543 in referenceGraphKmers] [293]
0.4 0.0 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
[114] 0.36 93.7 2.3 reversePushNucleotide [114]
2.3 0.0 shiftRight [548]
2.299 90.196 [Loop@0x41ad60 at line 414 in dfh_consolidate] [113]
[115] 0.35 2.299 90.196 dfh_heaplink [115]
0.3 89.896 dfhe_insertbefore [123]
90.8 1.1 [Loop@0x427558 at line 343 in computeReadToNodeCounts.omp_fn.0] [118]
[116] 0.34 90.8 1.1 [Loop@0x4275b0 at line 358 in computeReadToNodeCounts.omp_fn.0] [116]
0.8 0.0 getShortReadMarkerID [465]
0.3 0.0 getShortReadMarkerAtIndex [243]
0.0 83.2 clone [1]
0.0 8.7 computeReadToNodeCounts [379]
[117] 0.34 0.0 91.9 computeReadToNodeCounts.omp_fn.0 [117]
0.0 91.9 [Loop@0x427558 at line 343 in computeReadToNodeCounts.omp_fn.0] [118]
0.0 91.9 computeReadToNodeCounts.omp_fn.0 [117]
[118] 0.34 0.0 91.9 [Loop@0x427558 at line 343 in computeReadToNodeCounts.omp_fn.0] [118]
90.8 1.1 [Loop@0x4275b0 at line 358 in computeReadToNodeCounts.omp_fn.0] [116]
0.8 90.803 [Loop@0x432850 at line 390 in createPreNodes] [84]
[119] 0.34 0.8 90.803 [Loop@0x432bfd at line 430 in createPreNodes] [119]
0.3 65.999 [Loop@0x432bfd at line 506 in createPreNodes] [161]
0.9 17.604 [Loop@0x432faa at line 602 in createPreNodes] [303]
5.9 0.0 fgets [85]
0.1 0.0 [Import thunk fgets] [767]
1.6 89.8 [Loop@0x432850 at line 390 in createPreNodes] [84]
[120] 0.34 1.6 89.8 [Loop@0x4329dc at line 461 in createPreNodes] [120]
1.2 88.6 [Loop@0x432a00 at line 461 in createPreNodes] [125]
0.2 90.4 importReadSet [98]
[121] 0.34 0.2 90.4 [Loop@0x41cce8 at line 1564 in importReadSet] [121]
1.9 53.5 [Loop@0x41cd0e at line 1568 in importReadSet] [183]
34.8 0.0 fgets [85]
0.2 0.0 [Import thunk fgets] [767]
0.0 90.5 correctGraph [15]
[122] 0.34 0.0 90.5 determineEligibleStartingPoints [122]
0.1 74.3 [Loop@0x41a326 at line 497 in determineEligibleStartingPoints] [140]
0.2 15.9 [Loop@0x41a20d at line 473 in determineEligibleStartingPoints] [325]
0.3 89.896 dfh_heaplink [115]
[123] 0.34 0.3 89.896 dfhe_insertbefore [123]
89.896 0.0 dfhe_insertafter [124]
89.896 0.0 dfhe_insertbefore [123]
[124] 0.34 89.896 0.0 dfhe_insertafter [124]
1.2 88.6 [Loop@0x4329dc at line 461 in createPreNodes] [120]
[125] 0.34 1.2 88.6 [Loop@0x432a00 at line 461 in createPreNodes] [125]
0.8 87.8 [Loop@0x432a08 at line 461 in createPreNodes] [128]
0.9 88.397 dfh_extractminel [82]
[126] 0.34 0.9 88.397 [Loop@0x41b000 at line 293 in dfh_extractminel] [126]
86.497 1.9 dfh_insertrootlist [129]
0.0 60.3 main [14]
0.0 28.8 clipTips_pg [200]
[127] 0.33 0.0 89.1 concatenatePreGraph_pg [127]
0.2 66.8 [Loop@0x434140 at line 142 in concatenatePreGraph_pg] [159]
0.0 22.1 renumberPreNodes_pg [273]
0.8 87.8 [Loop@0x432a00 at line 461 in createPreNodes] [125]
[128] 0.33 0.8 87.8 [Loop@0x432a08 at line 461 in createPreNodes] [128]
87.0 0.0 _IO_getc [53]
0.8 0.0 [Import thunk _IO_getc] [416]
86.497 1.9 [Loop@0x41b000 at line 293 in dfh_extractminel] [126]
[129] 0.33 86.497 1.9 dfh_insertrootlist [129]
1.9 0.0 dfhe_insertafter [576]
0.7 87.298 [Loop@0x419dab at line 589 in comparePaths] [131]
0.0 0.2 comparePaths [50]
[130] 0.33 0.7 87.498 compareSequences [130]
33.599 53.699 [Loop@0x419ddd at line 590 in compareSequences] [132]
0.2 0.0 [Loop@0x419cfa at line 584 in compareSequences] [879]
0.0 87.998 comparePaths [50]
[131] 0.33 0.0 87.998 [Loop@0x419dab at line 589 in comparePaths] [131]
0.7 87.298 compareSequences [130]
33.599 53.699 compareSequences [130]
[132] 0.33 33.599 53.699 [Loop@0x419ddd at line 590 in compareSequences] [132]
29.899 0.0 getNucleotide [107]
23.8 0.0 max [259]
0.0 82.9 [Loop@0x426669 at line 1178 in exploitShortReadPairs] [134]
[133] 0.31 0.0 82.9 expandLongNodes [133]
0.0 82.8 expandLongNode [136]
0.1 0.0 getUniqueness [760]
0.0 82.9 [Loop@0x426660 at line 1229 in exploitShortReadPairs] [135]
[134] 0.31 0.0 82.9 [Loop@0x426669 at line 1178 in exploitShortReadPairs] [134]
0.0 82.9 expandLongNodes [133]
0.0 82.9 exploitShortReadPairs [101]
[135] 0.31 0.0 82.9 [Loop@0x426660 at line 1229 in exploitShortReadPairs] [135]
0.0 82.9 [Loop@0x426669 at line 1178 in exploitShortReadPairs] [134]
0.0 82.8 expandLongNodes [133]
[136] 0.31 0.0 82.8 expandLongNode [136]
0.0 78.8 [Loop@0x4263b0 at line 1158 in expandLongNode] [138]
0.0 3.2 [Loop@0x4261eb at line 131 in expandLongNode] [513]
0.0 0.8 unmarkInterestingNodes [696]
1.6 80.297 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[137] 0.31 1.6 80.297 getNodeTime [137]
79.797 0.0 getNodeID [49]
0.5 0.0 nodeCount [580]
0.0 78.8 expandLongNode [136]
[138] 0.3 0.0 78.8 [Loop@0x4263b0 at line 1158 in expandLongNode] [138]
0.0 73.5 pushNeighbours [142]
0.0 5.2 correctGraphLocally [440]
0.0 0.1 findOppositeNode [999]
0.0 77.9 newPreGraph_pg [37]
[139] 0.29 0.0 77.9 setInsertionMarkers [139]
0.6 44.7 [Loop@0x4333ac at line 214 in setInsertionMarkers] [196]
0.0 21.3 orderInsertionMarkers [279]
0.4 10.4 [Loop@0x4332b7 at line 177 in setInsertionMarkers] [357]
0.5 0.0 [Loop@0x433373 at line 205 in setInsertionMarkers] [775]
0.1 74.3 determineEligibleStartingPoints [122]
[140] 0.28 0.1 74.3 [Loop@0x41a326 at line 497 in determineEligibleStartingPoints] [140]
0.1 61.4 fh_extractmin [149]
12.8 0.0 getNodeID [49]
0.0 74.2 exploitShortReadPairs [101]
[141] 0.28 0.0 74.2 buildScaffold [141]
0.0 24.9 removeUnreliableConnections [250]
0.0 22.1 computeReadToNodeMappings [274]
0.0 13.7 computeNodeToNodeMappings [338]
0.0 9.0 computeReadToNodeCounts [379]
0.0 1.8 estimateMissingInsertLengths [589]
0.0 1.4 [Loop@0x42a990 at line 1814 in buildScaffold] [626]
0.0 1.3 getSequenceLengths [533]
0.0 73.5 [Loop@0x4263b0 at line 1158 in expandLongNode] [138]
[142] 0.28 0.0 73.5 pushNeighbours [142]
0.0 31.7 concatenateReadStarts [77]
0.0 25.0 injectShortReads [41]
0.0 11.8 absorbExtension [344]
0.0 3.4 appendGap [502]
0.0 1.2 absorbExtensionInScaffold [651]
0.0 0.2 [Loop@0x425688 at line 928 in pushNeighbours] [895]
0.0 0.1 adjustShortReadsByLength [930]
0.0 0.1 destroyNode [276]
35.9 0.0 getInsertionMarkerPosition [160]
22.1 0.0 getInsertionMarkerPosition [201]
4.899 0.0 getInsertionMarkerPosition [367]
4.3 0.0 getInsertionMarkerPosition [390]
2.8 0.0 getInsertionMarkerPosition [463]
1.999 0.0 [Loop@0x432faa at line 602 in createPreNodes] [303]
0.8 0.0 getInsertionMarkerPosition [649]
0.6 0.0 [Loop@0x432bfd at line 506 in createPreNodes] [164]
0.1 0.0 getInsertionMarkerPosition [977]
[143] 0.28 73.498 0.0 getStart [143]
0.0 37.0 correctGraph [15]
0.0 36.4 main [14]
[144] 0.28 0.0 73.4 clipTipsHard [144]
0.0 46.1 concatenateGraph [59]
0.0 27.3 [Loop@0x415a93 at line 2454 in clipTipsHard] [247]
12.1 60.6 threadSequenceThroughGraph [7]
[145] 0.27 12.1 60.6 unLockNode [145]
54.8 0.0 omp_unset_lock [48]
3.4 0.0 getNodeID [49]
2.3 0.0 [Import thunk omp_unset_lock] [447]
0.1 0.0 [libgomp.so.1.0.0] [94]
0.1 70.799 concatenatePathNodes [147]
[146] 0.27 0.1 70.799 [Loop@0x418be0 at line 2070 in concatenatePathNodes] [146]
0.2 70.099 simplifyNode [153]
0.1 0.2 getNextInSequence [347]
0.0 0.2 getNode [360]
0.0 70.899 cleanUpRedundancy [40]
[147] 0.27 0.0 70.899 concatenatePathNodes [147]
0.1 70.799 [Loop@0x418be0 at line 2070 in concatenatePathNodes] [146]
66.2 0.0 threadSequenceThroughGraph [7]
1.1 0.0 [Loop@0x414ada at line 1184 in removeLowCoverageNodesAndDenounceDubiousReads] [233]
0.9 0.0 projectFromSingleRead [203]
0.7 0.0 projectFromReadPair [184]
0.7 0.0 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
0.7 0.0 [Loop@0x41530b at line 531 in extractSequence] [394]
0.2 0.0 [Loop@0x4138d2 at line 1419 in removeHighCoverageNodes] [705]
0.1 0.0 [Loop@0x414bff at line 1260 in removeLowCoverageNodesAndDenounceDubiousReads] [942]
0.1 0.0 isUniqueSolexa [993]
[148] 0.27 70.7 0.0 getNodeLength [148]
0.1 61.4 [Loop@0x41a326 at line 497 in determineEligibleStartingPoints] [140]
0.0 9.0 [Loop@0x41a980 at line 444 in updateNodeStatus] [285]
[149] 0.26 0.1 70.4 fh_extractmin [149]
0.5 69.7 fh_extractminel [154]
0.2 0.0 deallocateFibHeapEl [875]
7.7 54.6 [Loop@0x42f7ce at line 1149 in exportPreGraph_pg] [166]
0.7 7.3 [Loop@0x42f787 at line 1217 in exportPreGraph_pg] [151]
[150] 0.26 8.4 61.9 exportPreNode_pg [150]
5.3 53.9 velvetFprintf [17]
2.7 0.0 getNucleotideInDescriptor_pg [530]
0.0 70.3 exportPreGraph_pg [152]
[151] 0.26 0.0 70.3 [Loop@0x42f787 at line 1217 in exportPreGraph_pg] [151]
0.0 62.3 [Loop@0x42f7ce at line 1149 in exportPreGraph_pg] [166]
0.7 7.3 exportPreNode_pg [150]
0.0 70.3 main [14]
[152] 0.26 0.0 70.3 exportPreGraph_pg [152]
0.0 70.3 [Loop@0x42f787 at line 1217 in exportPreGraph_pg] [151]
0.2 70.099 [Loop@0x418be0 at line 2070 in concatenatePathNodes] [146]
[153] 0.26 0.2 70.099 simplifyNode [153]
0.0 69.999 [Loop@0x41816a at line 1975 in simplifyNode] [155]
0.1 0.0 getTwinNode [228]
0.5 69.7 fh_extractmin [149]
[154] 0.26 0.5 69.7 fh_extractminel [154]
0.4 45.5 fh_consolidate [195]
0.9 22.5 [Loop@0x40d280 at line 534 in fh_extractminel] [262]
0.2 0.2 fh_removerootlist [811]
0.0 69.999 simplifyNode [153]
[155] 0.26 0.0 69.999 [Loop@0x41816a at line 1975 in simplifyNode] [155]
0.0 60.599 concatenateNodesAndVaccinate [169]
1.1 4.2 transferNodeData [376]
0.0 3.9 [Loop@0x418340 at line 112 in simplifyNode] [486]
0.2 0.0 getDestination [248]
0.2 69.598 projectFromShortRead [93]
[156] 0.26 0.2 69.598 [Loop@0x429a08 at line 1442 in projectFromShortRead] [156]
5.1 36.4 projectFromSingleRead [203]
1.0 24.298 createConnection [162]
1.8 0.0 [libgomp.so.1.0.0] [94]
1.0 0.0 omp_unset_lock [48]
1.8 65.9 importRoadMapArray [62]
[157] 0.25 1.8 65.9 [Loop@0x42f110 at line 127 in importRoadMapArray] [157]
37.6 0.0 fgets [85]
28.0 0.0 __isoc99_sscanf [70]
0.2 0.0 [Import thunk __isoc99_sscanf] [759]
0.1 0.0 [Import thunk fgets] [767]
67.6 0.0 getDestination_pg [42]
[158] 0.25 67.6 0.0 PREARC_FI2P [158]
0.2 66.8 concatenatePreGraph_pg [127]
[159] 0.25 0.2 66.8 [Loop@0x434140 at line 142 in concatenatePreGraph_pg] [159]
0.2 49.5 [Loop@0x434154 at line 146 in concatenatePreGraph_pg] [188]
0.0 16.0 [Loop@0x4341ba at line 165 in concatenatePreGraph_pg] [327]
0.8 0.0 getPreNodeInPreGraph_pg [508]
0.2 0.0 getPreArc_pg [559]
0.1 0.0 preNodeCount_pg [662]
12.4 54.3 compareInsertionMarkers [106]
[160] 0.25 12.4 54.3 getInsertionMarkerPosition [160]
35.9 0.0 getStart [143]
18.4 0.0 getFinish [230]
0.3 65.999 [Loop@0x432bfd at line 430 in createPreNodes] [119]
[161] 0.25 0.3 65.999 [Loop@0x432bfd at line 506 in createPreNodes] [161]
0.1 65.899 [Loop@0x432bfd at line 506 in createPreNodes] [163]
1.7 29.7 projectFromSingleRead [203]
1.0 24.298 [Loop@0x429a08 at line 1442 in projectFromShortRead] [156]
0.1 9.302 projectFromReadPair [184]
[162] 0.25 2.8 63.3 createConnection [162]
2.1 20.702 findOrCreateConnection [257]
0.3 20.9 lockTwoNodes [281]
8.6 0.0 readjustConnectionInTree [382]
0.4 8.098 unLockTwoNodes [383]
0.0 1.5 createTwinConnectionInTree [617]
0.5 0.0 getNodeInGraph [47]
0.2 0.0 getUniqueness [760]
0.1 65.899 [Loop@0x432bfd at line 506 in createPreNodes] [161]
[163] 0.25 0.1 65.899 [Loop@0x432bfd at line 506 in createPreNodes] [163]
1.0 64.899 [Loop@0x432bfd at line 506 in createPreNodes] [164]
1.0 64.899 [Loop@0x432bfd at line 506 in createPreNodes] [163]
[164] 0.25 1.0 64.899 [Loop@0x432bfd at line 506 in createPreNodes] [164]
14.6 15.098 [Loop@0x432de1 at line 554 in createPreNodes] [239]
0.2 23.303 addPreNodeToPreGraph_pg [223]
0.4 10.598 [Loop@0x432cb2 at line 119 in createPreNodes] [355]
0.6 0.0 getStart [143]
0.1 0.0 getPosition [584]
2.0 62.0 threadSequenceThroughGraph [7]
[165] 0.24 2.0 62.0 memorizeNode [165]
2.5 59.5 allocateSmallNodeList [167]
0.0 62.3 [Loop@0x42f787 at line 1217 in exportPreGraph_pg] [151]
[166] 0.23 0.0 62.3 [Loop@0x42f7ce at line 1149 in exportPreGraph_pg] [166]
7.7 54.6 exportPreNode_pg [150]
2.5 59.5 memorizeNode [165]
[167] 0.23 2.5 59.5 allocateSmallNodeList [167]
54.2 0.0 allocatePointer [109]
3.0 0.0 omp_get_thread_num [380]
1.3 0.0 getRecycleBinInArray [408]
1.0 0.0 [Import thunk omp_get_thread_num] [456]
8.0 53.5 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
[168] 0.23 8.0 53.5 isNodeMemorized [168]
53.5 0.0 [Loop@0x42db42 at line 226 in isNodeMemorized] [186]
0.0 60.599 [Loop@0x41816a at line 1975 in simplifyNode] [155]
[169] 0.23 0.0 60.599 concatenateNodesAndVaccinate [169]
0.2 28.9 concatenateReadStarts [77]
0.4 11.6 injectShortReads [41]
0.1 5.4 [Loop@0x418472 at line 1986 in concatenateNodesAndVaccinate] [433]
0.0 5.0 appendDescriptors [317]
0.0 4.499 destroyNode [276]
0.0 2.0 [Loop@0x41852a at line 2001 in concatenateNodesAndVaccinate] [568]
1.2 0.0 _int_free [227]
0.0 0.8 [Loop@0x418439 at line 1976 in concatenateNodesAndVaccinate] [709]
0.3 0.0 mergeNodeReads [754]
0.0 0.2 [Loop@0x4184e0 at line 1994 in concatenateNodesAndVaccinate] [909]
0.0 60.4 [Loop@0x413aaf at line 980 in exportLongNodeSequences] [172]
[170] 0.23 0.0 60.4 exportLongNodeSequence [170]
0.0 51.9 findLowCoverageRegions [187]
0.5 5.9 [Loop@0x413330 at line 927 in exportLongNodeSequence] [419]
0.0 2.0 expandNode [565]
0.0 0.1 velvetFprintf [17]
0.0 60.4 main [14]
[171] 0.23 0.0 60.4 exportLongNodeSequences [171]
0.0 60.4 [Loop@0x413aaf at line 980 in exportLongNodeSequences] [172]
0.0 60.4 exportLongNodeSequences [171]
[172] 0.23 0.0 60.4 [Loop@0x413aaf at line 980 in exportLongNodeSequences] [172]
0.0 60.4 exportLongNodeSequence [170]
0.1 57.6 remapBackOfNodeMarkersOntoNeighbour [61]
0.0 0.9 remapEmptyPathMarkersOntoMiddlePathSimple [299]
[173] 0.22 0.1 58.5 commonNodeReads [173]
45.2 1.3 [Loop@0x403bad at line 2959 in commonNodeReads] [193]
0.0 5.2 mallocOrExit3 [67]
3.5 0.0 [Loop@0x403ce8 at line 3006 in commonNodeReads] [495]
3.3 0.0 [Loop@0x403ca0 at line 2997 in commonNodeReads] [506]
56.4 0.0 keyInAccelerationTable [175]
1.4 0.0 keyInAccelerationTable [623]
[174] 0.22 57.8 0.0 getKmerKey [174]
1.4 56.4 findKmerInKmerOccurenceTable [2]
[175] 0.22 1.4 56.4 keyInAccelerationTable [175]
56.4 0.0 getKmerKey [174]
57.601 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[176] 0.22 57.601 0.0 setShortReadMarkerOffset [176]
30.9 0.0 threadSequenceThroughGraph [7]
25.7 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
[177] 0.21 56.6 0.0 getKmerOccurenceNodeID [177]
0.7 55.4 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
[178] 0.21 0.7 55.4 memorizeNode [178]
1.5 53.9 allocateSmallNodeList [182]
52.098 3.999 tourBusNode [31]
[179] 0.21 52.098 3.999 getArcBetweenNodes [179]
3.999 0.0 [Loop@0x4027d3 at line 337 in getArcBetweenNodes] [483]
0.4 55.302 projectFromShortRead [93]
[180] 0.21 0.4 55.302 [Loop@0x429af0 at line 1464 in projectFromShortRead] [180]
40.8 14.502 projectFromReadPair [184]
7.6 47.9 threadSequenceThroughGraph [7]
[181] 0.21 7.6 47.9 unLockTwoNodes [181]
41.7 0.0 omp_unset_lock [48]
2.7 0.0 getNodeID [49]
1.9 0.0 [libgomp.so.1.0.0] [94]
1.6 0.0 [Import thunk omp_unset_lock] [447]
1.5 53.9 memorizeNode [178]
[182] 0.21 1.5 53.9 allocateSmallNodeList [182]
51.7 0.0 allocatePointer [109]
1.0 0.0 omp_get_thread_num [380]
0.8 0.0 getRecycleBinInArray [408]
0.4 0.0 [Import thunk omp_get_thread_num] [456]
1.9 53.5 [Loop@0x41cce8 at line 1564 in importReadSet] [121]
[183] 0.21 1.9 53.5 [Loop@0x41cd0e at line 1568 in importReadSet] [183]
34.9 0.0 __isoc99_sscanf [70]
0.5 14.5 mallocOrExit3 [67]
3.4 0.0 [Loop@0x41cd15 at line 1580 in importReadSet] [498]
0.2 0.0 [Import thunk __isoc99_sscanf] [759]
40.8 14.502 [Loop@0x429af0 at line 1464 in projectFromShortRead] [180]
[184] 0.21 40.8 14.502 projectFromReadPair [184]
0.1 9.302 createConnection [162]
2.2 0.0 getNodeInGraph [47]
1.8 0.0 getNodeID [49]
0.7 0.0 getNodeLength [148]
0.2 0.0 omp_unset_lock [48]
0.2 0.0 getTwinNode [228]
19.1 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
13.2 0.0 threadSequenceThroughGraph [7]
8.0 0.0 [Loop@0x432de1 at line 554 in createPreNodes] [239]
4.7 0.0 [Loop@0x42d820 at line 848 in threadSequenceThroughGraph] [218]
4.2 0.0 [Loop@0x42de10 at line 683 in ghostThreadSequenceThroughGraph] [217]
2.8 0.0 [Loop@0x432850 at line 390 in createPreNodes] [84]
0.8 0.0 [Loop@0x42c4a0 at line 543 in referenceGraphKmers] [293]
0.6 0.0 newDescriptor_pg [232]
0.3 0.0 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
[185] 0.2 53.7 0.0 pushNucleotide [185]
53.5 0.0 isNodeMemorized [168]
[186] 0.2 53.5 0.0 [Loop@0x42db42 at line 226 in isNodeMemorized] [186]
0.0 51.9 exportLongNodeSequence [170]
[187] 0.19 0.0 51.9 findLowCoverageRegions [187]
0.0 19.001 sortCoords [300]
0.0 16.9 sortCoords [318]
0.0 7.5 getShortReadCoords [401]
0.0 5.0 getShortReadTwinCoords [444]
0.0 2.7 callocOrExit3 [221]
0.0 0.8 lowCoverageRegions [693]
0.2 49.5 [Loop@0x434140 at line 142 in concatenatePreGraph_pg] [159]
[188] 0.19 0.2 49.5 [Loop@0x434154 at line 146 in concatenatePreGraph_pg] [188]
0.2 32.4 concatenatePreNodes [220]
3.9 12.6 hasSinglePreArc_pg [208]
0.2 0.0 getOtherEnd_pg [592]
0.1 0.0 isLoop_pg [830]
0.1 0.0 getPreArc_pg [559]
0.0 49.5 activateArcLookupTable [190]
[189] 0.19 0.0 49.5 [Loop@0x404670 at line 1615 in activateArcLookupTable] [189]
49.3 0.0 [Loop@0x404686 at line 1620 in activateArcLookupTable] [191]
0.2 0.0 getNodeInGraph [924]
0.0 49.5 correctGraph [15]
[190] 0.19 0.0 49.5 activateArcLookupTable [190]
0.0 49.5 [Loop@0x404670 at line 1615 in activateArcLookupTable] [189]
49.3 0.0 [Loop@0x404670 at line 1615 in activateArcLookupTable] [189]
[191] 0.19 49.3 0.0 [Loop@0x404686 at line 1620 in activateArcLookupTable] [191]
47.9 0.0 qsort_r [43]
[192] 0.18 47.9 0.0 compareShortReadMarkers [192]
45.2 1.3 commonNodeReads [173]
[193] 0.17 45.2 1.3 [Loop@0x403bad at line 2959 in commonNodeReads] [193]
1.3 0.0 compareIDnums [628]
23.8 22.2 concatenateReadStarts [77]
[194] 0.17 23.8 22.2 [Loop@0x40dd60 at line 68 in concatenateReadStarts] [194]
11.6 0.0 getShortReadMarkerAtIndex [243]
5.9 0.0 getShortReadMarkerPosition [260]
4.7 0.0 setShortReadMarkerPosition [402]
0.4 45.5 fh_extractminel [154]
[195] 0.17 0.4 45.5 fh_consolidate [195]
9.6 29.4 [Loop@0x40cf90 at line 436 in fh_consolidate] [211]
2.3 3.5 [Loop@0x40d17f at line 408 in fh_consolidate] [427]
0.7 0.0 [Loop@0x40cf50 at line 443 in fh_consolidate] [723]
0.6 44.7 setInsertionMarkers [139]
[196] 0.17 0.6 44.7 [Loop@0x4333ac at line 214 in setInsertionMarkers] [196]
42.3 2.3 [Loop@0x4333d6 at line 222 in setInsertionMarkers] [197]
0.1 0.0 getAnnotationCount [681]
42.3 2.3 [Loop@0x4333ac at line 214 in setInsertionMarkers] [196]
[197] 0.17 42.3 2.3 [Loop@0x4333d6 at line 222 in setInsertionMarkers] [197]
1.7 0.0 incrementAnnotationCoordinates [596]
0.6 0.0 getAnnotSequenceID [328]
0.0 44.1 main [14]
[198] 0.17 0.0 44.1 convertSequences [198]
0.0 44.1 newTightStringArrayFromStringArray [199]
0.0 44.1 convertSequences [198]
[199] 0.17 0.0 44.1 newTightStringArrayFromStringArray [199]
0.4 40.3 [Loop@0x402370 at line 152 in newTightStringArrayFromStringArray] [205]
1.4 2.0 [Loop@0x402310 at line 144 in newTightStringArrayFromStringArray] [499]
0.0 44.1 main [14]
[200] 0.17 0.0 44.1 clipTips_pg [200]
0.0 28.8 concatenatePreGraph_pg [127]
0.0 15.3 [Loop@0x434278 at line 235 in clipTips_pg] [330]
15.9 27.3 compareInsertionMarkers [106]
[201] 0.16 15.9 27.3 getInsertionMarkerPosition [201]
22.1 0.0 getStart [143]
5.2 0.0 getFinish [230]
3.5 18.899 [Loop@0x419ae0 at line 2246 in comparePaths] [231]
1.5 13.999 [Loop@0x419bb0 at line 2264 in comparePaths] [256]
0.4 3.4 comparePaths [50]
[202] 0.16 5.4 36.297 addUncertainPassageMarker [202]
14.299 0.0 getTwinNode [228]
0.2 7.399 setMarker [354]
1.099 5.3 setNextInNode [395]
1.7 2.8 setTopOfTheNode [405]
1.0 0.0 PM_FI2P [671]
0.1 0.7 allocatePassageMarker [713]
0.1 0.7 allocatePassageMarker [720]
0.7 0.0 PM_FI2P [736]
0.2 0.0 getMarker [624]
5.1 36.4 [Loop@0x429a08 at line 1442 in projectFromShortRead] [156]
[203] 0.16 5.1 36.4 projectFromSingleRead [203]
1.7 29.7 createConnection [162]
2.2 0.0 [libgomp.so.1.0.0] [94]
1.0 0.0 omp_unset_lock [48]
0.9 0.0 getNodeLength [148]
0.8 0.0 getNodeInGraph [47]
0.1 0.0 getTwinNode [228]
0.9 39.9 importReadSet [98]
[204] 0.15 0.9 39.9 [Loop@0x41ce48 at line 1599 in importReadSet] [204]
36.3 0.0 fgets [85]
2.2 0.0 __strncpy_ssse3 [558]
1.3 0.0 [Loop@0x41ce71 at line 1612 in importReadSet] [631]
0.1 0.0 [Import thunk strncpy] [995]
0.4 40.3 newTightStringArrayFromStringArray [199]
[205] 0.15 0.4 40.3 [Loop@0x402370 at line 152 in newTightStringArrayFromStringArray] [205]
0.0 34.702 [Loop@0x402389 at line 124 in newTightStringArrayFromStringArray] [226]
0.0 5.598 fillTightStringWithString [206]
16.898 17.804 [Loop@0x402389 at line 124 in newTightStringArrayFromStringArray] [226]
0.0 5.598 [Loop@0x402370 at line 152 in newTightStringArrayFromStringArray] [205]
[206] 0.15 16.898 23.402 fillTightStringWithString [206]
4.299 13.504 writeNucleotide [309]
5.598 0.0 _int_free [227]
0.0 39.7 referenceGraphKmers [83]
[207] 0.15 0.0 39.7 [Loop@0x42c240 at line 536 in referenceGraphKmers] [207]
1.4 18.199 [Loop@0x42c4a0 at line 543 in referenceGraphKmers] [293]
1.4 17.501 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
1.2 0.0 fgets [85]
3.9 12.6 [Loop@0x434154 at line 146 in concatenatePreGraph_pg] [188]
1.8 10.1 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
3.1 7.9 [Loop@0x4341ba at line 165 in concatenatePreGraph_pg] [327]
[208] 0.15 8.8 30.6 hasSinglePreArc_pg [208]
26.5 4.1 getNextPreArc_pg [235]
0.9 38.4 threadSequenceThroughGraph [7]
[209] 0.15 0.9 38.4 isNodeMemorized [209]
38.4 0.0 [Loop@0x42d0be at line 226 in isNodeMemorized] [215]
1.5 37.8 exportGraph [18]
[210] 0.15 1.5 37.8 exportNode [210]
0.9 19.1 velvetFprintf [17]
1.4 14.8 [Loop@0x4076f4 at line 548 in exportNode] [324]
0.4 1.2 [Loop@0x4077b7 at line 548 in exportNode] [601]
9.6 29.4 fh_consolidate [195]
[211] 0.15 9.6 29.4 [Loop@0x40cf90 at line 436 in fh_consolidate] [211]
0.9 21.7 [Loop@0x40cff0 at line 436 in fh_consolidate] [263]
1.4 5.4 fh_removerootlist [409]
0.0 39.0 importPreGraph [16]
[212] 0.15 0.0 39.0 readPreGraphFile [212]
0.3 38.5 [Loop@0x40a990 at line 2309 in readPreGraphFile] [213]
0.0 0.2 allocateNodeSpace [929]
0.3 38.5 readPreGraphFile [212]
[213] 0.15 0.3 38.5 [Loop@0x40a990 at line 2309 in readPreGraphFile] [213]
1.0 27.8 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
5.0 0.0 __isoc99_sscanf [70]
0.2 2.3 callocOrExit3 [221]
1.6 0.0 fgets [85]
0.0 0.6 addEmptyNodeToGraph [762]
38.7 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
[214] 0.15 38.7 0.0 incrementReadStartCount [214]
38.4 0.0 isNodeMemorized [209]
[215] 0.14 38.4 0.0 [Loop@0x42d0be at line 226 in isNodeMemorized] [215]
0.2 38.1 importReadSet [98]
[216] 0.14 0.2 38.1 [Loop@0x41cc29 at line 1545 in importReadSet] [216]
38.1 0.0 fgets [85]
6.8 31.4 ghostThreadSequenceThroughGraph [11]
[217] 0.14 6.8 31.4 [Loop@0x42de10 at line 683 in ghostThreadSequenceThroughGraph] [217]
18.0 0.2 reversePushNucleotide [114]
9.0 0.0 getNucleotide [107]
4.2 0.0 pushNucleotide [185]
6.0 31.7 threadSequenceThroughGraph [7]
[218] 0.14 6.0 31.7 [Loop@0x42d820 at line 848 in threadSequenceThroughGraph] [218]
15.8 0.0 reversePushNucleotide [114]
11.2 0.0 getNucleotide [107]
4.7 0.0 pushNucleotide [185]
37.4 0.0 [Loop@0x431967 at line 83 in createPreArc_pg] [38]
[219] 0.14 37.4 0.0 getPreArc_pg [219]
0.2 32.4 [Loop@0x434154 at line 146 in concatenatePreGraph_pg] [188]
0.0 4.2 [Loop@0x4341ba at line 165 in concatenatePreGraph_pg] [327]
[220] 0.14 0.2 36.6 concatenatePreNodes [220]
0.1 14.1 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
0.0 10.7 [Loop@0x433f90 at line 123 in concatenatePreNodes] [358]
0.1 4.7 [Loop@0x433f15 at line 109 in concatenatePreNodes] [451]
0.0 2.9 appendDescriptors_pg [487]
0.0 2.5 [Loop@0x433e80 at line 83 in concatenatePreNodes] [543]
0.0 0.7 callocOrExit3 [221]
0.0 0.3 setPreNodeDescriptor_pg [823]
0.0 0.2 [Loop@0x4340b8 at line 94 in concatenatePreNodes] [918]
0.2 0.0 [Loop@0x433f65 at line 103 in concatenatePreNodes] [919]
0.0 0.1 getDestination_pg [484]
0.0 10.8 mergeDescriptors [343]
0.2 7.9 newDescriptor_pg [232]
0.0 4.0 reallocateNodeDescriptor [424]
0.0 2.7 findLowCoverageRegions [187]
0.2 2.3 [Loop@0x40a990 at line 2309 in readPreGraphFile] [213]
0.0 2.4 mergeDescriptors [468]
0.0 2.4 addBufferToDescriptor [501]
0.0 1.8 newTightString [586]
0.0 0.7 concatenatePreNodes [220]
0.0 0.3 allocArrayArrayAllocate [289]
0.0 0.2 allocateNodeSpace [929]
0.0 0.1 importReadSet [98]
0.0 0.1 activateReadStarts [989]
0.0 0.1 correctGraph [15]
[221] 0.14 0.4 35.8 callocOrExit3 [221]
35.7 0.0 __libc_calloc [225]
0.1 0.0 [Import thunk calloc] [1030]
36.1 0.0 getArcBetweenNodes [52]
[222] 0.14 36.1 0.0 [Loop@0x40559d at line 357 in getArcBetweenNodes] [222]
0.2 23.303 [Loop@0x432bfd at line 506 in createPreNodes] [164]
0.0 12.405 [Loop@0x432faa at line 602 in createPreNodes] [303]
[223] 0.13 0.2 35.708 addPreNodeToPreGraph_pg [223]
0.0 35.708 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [224]
0.0 35.708 addPreNodeToPreGraph_pg [223]
[224] 0.13 0.0 35.708 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [224]
0.0 23.409 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [261]
2.1 10.199 newDescriptor_pg [232]
35.7 0.0 callocOrExit3 [221]
[225] 0.13 35.7 0.0 __libc_calloc [225]
0.0 34.702 [Loop@0x402370 at line 152 in newTightStringArrayFromStringArray] [205]
[226] 0.13 0.0 34.702 [Loop@0x402389 at line 124 in newTightStringArrayFromStringArray] [226]
16.898 17.804 fillTightStringWithString [206]
7.5 0.0 injectShortReads [41]
7.2 0.0 destroyNode [276]
5.598 0.0 fillTightStringWithString [206]
2.2 0.0 concatenateReadStarts [77]
1.9 0.0 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
1.9 0.0 destroyPreNode_pg [356]
1.6 0.0 [Loop@0x436210 at line 242 in destroyAllocArrayArray] [605]
1.4 0.0 destroyRecycleBinChunks [614]
1.2 0.0 concatenateNodesAndVaccinate [169]
0.9 0.0 extractFrontOfNodeReads [404]
0.7 0.0 remapBackOfNodeMarkersOntoNeighbour [61]
0.6 0.0 remapNodeMarkersOntoNeighbour [104]
0.6 0.0 appendDescriptors [317]
0.5 0.0 [Loop@0x42f690 at line 374 in destroyPreGraph_pg] [642]
0.3 0.0 setPreNodeDescriptor_pg [823]
0.1 0.0 spreadReadIDs [304]
0.1 0.0 extractBackOfNodeReads [406]
[227] 0.13 34.298 0.0 _int_free [227]
14.299 0.0 addUncertainPassageMarker [202]
10.8 0.0 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
2.6 0.0 [Loop@0x40e294 at line 205 in concatenateGraph] [103]
2.1 0.0 [Loop@0x40e320 at line 217 in concatenateGraph] [100]
1.2 0.0 [Loop@0x4153e7 at line 2435 in getTipLength] [523]
0.9 0.0 [Loop@0x40de14 at line 94 in concatenateStringOfNodes] [534]
0.6 0.0 [Loop@0x42be4c at line 407 in isLocalTwinDeadEnd] [698]
0.4 0.0 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
0.2 0.0 remapBackOfNodeOntoNeighbour [55]
0.2 0.0 [Loop@0x40e270 at line 198 in concatenateGraph] [60]
0.2 0.0 projectFromReadPair [184]
0.1 0.0 markInterestingNodes [512]
0.1 0.0 simplifyNode [153]
0.1 0.0 concatenateReadStarts [77]
0.1 0.0 projectFromSingleRead [203]
0.1 0.0 remapNodeArcsOntoNeighbour [342]
0.1 0.0 remapNodeOntoNeighbour [97]
0.1 0.0 [Loop@0x413093 at line 857 in getShortReadTwinCoords] [445]
[228] 0.13 34.2 0.0 getTwinNode [228]
34.199 0.0 tourBusNode [31]
[229] 0.13 34.199 0.0 nextTodoTicket [229]
18.4 0.0 getInsertionMarkerPosition [160]
5.2 0.0 getInsertionMarkerPosition [201]
4.4 0.0 getInsertionMarkerPosition [367]
2.9 0.0 getInsertionMarkerPosition [390]
1.7 0.0 [Loop@0x432faa at line 602 in createPreNodes] [303]
1.1 0.0 getInsertionMarkerPosition [463]
0.4 0.0 getInsertionMarkerPosition [649]
[230] 0.13 34.1 0.0 getFinish [230]
1.399 32.699 comparePaths [50]
[231] 0.13 1.399 32.699 [Loop@0x419ae0 at line 2246 in comparePaths] [231]
3.5 18.899 addUncertainPassageMarker [202]
0.0 5.1 connectPassageMarkers [378]
1.0 2.7 setPassageMarkerStatus [403]
0.6 0.5 getNode [360]
0.1 0.3 getNodePrevious [789]
0.7 19.699 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [271]
2.1 10.199 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [224]
0.0 1.299 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [261]
[232] 0.13 2.8 31.197 newDescriptor_pg [232]
0.2 7.9 callocOrExit3 [221]
3.0 5.0 [Loop@0x42fd7d at line 1015 in newDescriptor_pg] [391]
7.799 0.0 _IO_getc [53]
4.698 0.0 writeNucleotideInDescriptor_pg [384]
1.1 0.0 writeNucleotideInDescriptor_pg [664]
0.6 0.0 pushNucleotide [185]
0.3 0.0 __ctype_b_loc [448]
0.1 0.2 [Loop@0x42ff74 at line 1025 in newDescriptor_pg] [856]
0.2 0.0 copyKmers [609]
0.1 0.0 [Import thunk _IO_getc] [416]
0.3 31.2 removeLowCoverageNodesAndDenounceDubiousReads [66]
[233] 0.12 0.3 31.2 [Loop@0x414ada at line 1184 in removeLowCoverageNodesAndDenounceDubiousReads] [233]
0.0 30.0 removeNodeAndDenounceDubiousReads [238]
1.1 0.0 getNodeLength [148]
0.1 0.0 getNodeInGraph [47]
10.398 20.7 injectShortReads [41]
[234] 0.12 10.398 20.7 [Loop@0x403668 at line 3540 in injectShortReads] [234]
13.1 0.0 setShortReadMarkerPosition [340]
7.6 0.0 setShortReadMarkerOffset [397]
26.5 4.1 hasSinglePreArc_pg [208]
[235] 0.11 26.5 4.1 getNextPreArc_pg [235]
4.1 0.0 PREARC_FI2P [473]
0.0 30.497 tourBusArc [33]
[236] 0.11 0.0 30.497 destroyPaths [236]
0.3 16.297 [Loop@0x415a00 at line 1851 in destroyPaths] [320]
0.2 13.699 [Loop@0x415a10 at line 1854 in destroyPaths] [337]
17.898 12.2 [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort] [71]
[237] 0.11 17.898 12.2 lockRead [237]
11.5 0.0 omp_set_lock [44]
0.4 0.0 [libgomp.so.1.0.0] [94]
0.3 0.0 [Import thunk omp_set_lock] [687]
0.0 30.0 [Loop@0x414ada at line 1184 in removeLowCoverageNodesAndDenounceDubiousReads] [233]
[238] 0.11 0.0 30.0 removeNodeAndDenounceDubiousReads [238]
15.4 0.9 [Loop@0x414f6d at line 1193 in removeNodeAndDenounceDubiousReads] [323]
0.0 11.7 destroyNode [276]
1.7 0.2 [Loop@0x414fe5 at line 1204 in removeNodeAndDenounceDubiousReads] [573]
0.1 0.0 getNodeReadCount [707]
14.6 15.098 [Loop@0x432bfd at line 506 in createPreNodes] [164]
[239] 0.11 14.6 15.098 [Loop@0x432de1 at line 554 in createPreNodes] [239]
8.0 0.0 pushNucleotide [185]
5.798 0.0 getAnnotationLength [428]
0.9 0.0 getPosition [584]
0.4 0.0 getNextAnnotation [682]
29.4 0.0 threadSequenceThroughGraph [7]
[240] 0.11 29.4 0.0 incrementVirtualCoverage [240]
1.0 27.8 [Loop@0x40a990 at line 2309 in readPreGraphFile] [213]
[241] 0.11 1.0 27.8 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
26.0 0.0 _IO_getc [53]
0.5 0.0 writeNucleotideInDescriptor [777]
0.3 0.0 [Import thunk _IO_getc] [416]
0.2 0.0 writeNucleotideInDescriptor [871]
0.2 0.0 writeNucleotideInDescriptor [877]
0.2 0.0 writeNucleotideInDescriptor [880]
0.2 0.0 writeNucleotideInDescriptor [907]
0.1 0.0 writeNucleotideInDescriptor [974]
0.1 0.0 writeNucleotideInDescriptor [1029]
28.799 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[242] 0.11 28.799 0.0 setShortReadMarkerPosition [242]
11.6 0.0 [Loop@0x40dd60 at line 68 in concatenateReadStarts] [194]
4.0 0.0 [Loop@0x417498 at line 1143 in remapBackOfNodeMarkersOntoNeighbour] [275]
3.999 0.0 [Loop@0x4173f8 at line 1069 in remapBackOfNodeMarkersOntoNeighbour] [308]
3.0 0.0 [Loop@0x40dce0 at line 54 in concatenateReadStarts] [326]
2.2 0.0 [Loop@0x410b08 at line 1816 in usedReads] [413]
0.7 0.0 [Loop@0x4165f8 at line 808 in remapNodeMarkersOntoNeighbour] [332]
0.5 0.0 [Loop@0x417200 at line 1098 in remapBackOfNodeMarkersOntoNeighbour] [536]
0.4 0.0 [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort] [71]
0.4 0.0 [Loop@0x4170f0 at line 1033 in remapBackOfNodeMarkersOntoNeighbour] [471]
0.3 0.0 [Loop@0x4275b0 at line 358 in computeReadToNodeCounts.omp_fn.0] [116]
0.2 0.0 [Loop@0x416690 at line 773 in remapNodeMarkersOntoNeighbour] [321]
0.2 0.0 [Loop@0x429963 at line 1429 in projectFromNode] [90]
0.2 0.0 [Loop@0x410b70 at line 1824 in usedReads] [542]
0.1 0.0 [Loop@0x423cd0 at line 741 in adjustShortReadsByLength] [931]
0.1 0.0 [Loop@0x412b20 at line 444 in printShortCounts] [316]
0.1 0.0 [Loop@0x412fad at line 843 in getShortReadCoords] [400]
0.1 0.0 [Loop@0x413093 at line 857 in getShortReadTwinCoords] [445]
[243] 0.11 28.099 0.0 getShortReadMarkerAtIndex [243]
2.3 10.797 [Loop@0x415a00 at line 1851 in destroyPaths] [320]
1.4 9.399 [Loop@0x415a10 at line 1854 in destroyPaths] [337]
0.4 1.3 [Loop@0x418c40 at line 1860 in destroyPaths] [570]
0.1 1.4 destroyPaths [479]
0.0 0.599 [Loop@0x405100 at line 487 in destroyNode] [738]
[244] 0.1 4.2 23.496 destroyPassageMarker [244]
4.899 4.8 extractPassageMarker [368]
3.4 0.0 PM_FI2P [504]
0.1 3.1 deallocatePassageMarker [510]
2.299 0.0 PM_FI2P [553]
2.0 0.0 PM_FI2P [449]
1.599 0.0 PM_FI2P [608]
1.099 0.0 PM_FI2P [666]
0.2 0.0 deallocatePassageMarker [876]
4.3 12.5 [Loop@0x415c3e at line 680 in remapNodeArcsOntoTarget] [286]
3.8 1.6 [Loop@0x418472 at line 1986 in concatenateNodesAndVaccinate] [433]
1.5 3.5 [Loop@0x416c20 at line 859 in remapBackOfNodeArcsOntoNeighbour] [439]
0.1 0.1 [Loop@0x40e17c at line 170 in concatenateStringOfNodes] [778]
0.0 0.1 [Loop@0x41790d at line 1581 in remapEmptyPathArcsOntoMiddlePathSimple] [936]
[245] 0.1 9.7 17.8 createAnalogousArc [245]
11.9 5.6 getArcBetweenNodes [314]
0.1 0.0 allocatePointer [109]
0.1 0.0 allocateArc [878]
0.1 0.0 getMultiplicity [1015]
0.8 26.5 [Loop@0x415a93 at line 2454 in clipTipsHard] [247]
[246] 0.1 0.8 26.5 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
10.8 0.0 getTwinNode [228]
10.0 0.0 getArc [351]
0.0 3.1 getTipLength [515]
0.1 1.8 destroyNode [276]
0.5 0.0 getNodeInGraph [47]
0.2 0.0 nodeCount [580]
0.0 27.3 clipTipsHard [144]
[247] 0.1 0.0 27.3 [Loop@0x415a93 at line 2454 in clipTipsHard] [247]
0.8 26.5 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
8.999 0.0 initializeTodoLists [267]
6.1 0.0 [Loop@0x41a990 at line 445 in updateNodeStatus] [352]
3.0 0.0 [Loop@0x40e294 at line 205 in concatenateGraph] [103]
1.5 0.0 [Loop@0x40e320 at line 217 in concatenateGraph] [100]
1.5 0.0 [Loop@0x4153e7 at line 2435 in getTipLength] [523]
1.4 0.0 [Loop@0x40de14 at line 94 in concatenateStringOfNodes] [534]
1.3 0.0 transferNodeData [376]
0.9 0.0 [Loop@0x42be0b at line 396 in isLocalDeadEnd] [583]
0.8 0.0 [Loop@0x4160ce at line 1200 in remapNodeInwardReferencesOntoNode] [556]
0.7 0.0 [Loop@0x40e1e4 at line 180 in concatenateStringOfNodes] [518]
0.3 0.0 [Loop@0x40e17c at line 170 in concatenateStringOfNodes] [778]
0.2 0.0 [Loop@0x416b53 at line 1200 in remapNodeInwardReferencesOntoNode] [549]
0.2 0.0 [Loop@0x41816a at line 1975 in simplifyNode] [155]
0.2 0.0 [Loop@0x42be4c at line 407 in isLocalTwinDeadEnd] [698]
0.1 0.0 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
[248] 0.1 27.199 0.0 getDestination [248]
0.0 26.4 referenceGraphKmers [83]
[249] 0.1 0.0 26.4 [Loop@0x42c130 at line 502 in referenceGraphKmers] [249]
0.1 25.3 [Loop@0x42c13c at line 502 in referenceGraphKmers] [251]
1.0 0.0 fgets [85]
0.0 24.9 buildScaffold [141]
0.2 1.2 [Loop@0x42a9b5 at line 1701 in buildScaffold] [625]
[250] 0.1 0.2 26.1 removeUnreliableConnections [250]
0.0 24.9 countShortReads [255]
0.1 1.1 testConnection [646]
0.1 25.3 [Loop@0x42c130 at line 502 in referenceGraphKmers] [249]
[251] 0.1 0.1 25.3 [Loop@0x42c13c at line 502 in referenceGraphKmers] [251]
24.7 0.0 _IO_getc [53]
0.6 0.0 [Import thunk _IO_getc] [416]
0.0 12.7 remapNodeArcsOntoNeighbour [342]
0.0 12.5 remapBackOfNodeArcsOntoNeighbour [313]
[252] 0.09 0.0 25.2 remapNodeArcsOntoTarget [252]
0.0 20.7 [Loop@0x415c3e at line 680 in remapNodeArcsOntoTarget] [286]
0.0 4.5 concatenateTodoLists [461]
24.5 0.4 [Loop@0x4270fb at line 1670 in countShortReads] [254]
[253] 0.09 24.5 0.4 [Loop@0x42715e at line 1678 in countShortReads] [253]
0.4 0.0 getShortReadMarkerID [465]
0.0 24.9 countShortReads [255]
[254] 0.09 0.0 24.9 [Loop@0x4270fb at line 1670 in countShortReads] [254]
24.5 0.4 [Loop@0x42715e at line 1678 in countShortReads] [253]
0.0 24.9 removeUnreliableConnections [250]
[255] 0.09 0.0 24.9 countShortReads [255]
0.0 24.9 [Loop@0x4270fb at line 1670 in countShortReads] [254]
0.8 23.698 comparePaths [50]
[256] 0.09 0.8 23.698 [Loop@0x419bb0 at line 2264 in comparePaths] [256]
1.5 13.999 addUncertainPassageMarker [202]
0.0 4.0 connectPassageMarkers [378]
0.9 1.9 setPassageMarkerStatus [403]
0.5 0.6 getNode [360]
0.1 0.2 getNodePrevious [834]
2.1 20.702 createConnection [162]
0.3 1.2 createTwinConnectionInTree [617]
[257] 0.09 2.4 21.902 findOrCreateConnection [257]
1.7 17.7 splayConnection [297]
0.502 1.3 allocateConnection [585]
0.4 0.0 getNodeID [49]
0.1 0.1 allocateConnection [863]
0.1 0.0 nodeCount [580]
0.2 23.799 comparePaths [50]
[258] 0.09 0.2 23.799 extractSequence [258]
0.2 14.799 [Loop@0x415368 at line 541 in extractSequence] [333]
0.3 7.6 [Loop@0x41530b at line 531 in extractSequence] [394]
0.1 0.4 getNextInSequence [347]
0.1 0.3 setTightStringLength [791]
23.8 0.0 [Loop@0x419ddd at line 590 in compareSequences] [132]
[259] 0.09 23.8 0.0 max [259]
6.4 0.0 [Loop@0x40dce0 at line 54 in concatenateReadStarts] [326]
5.9 0.0 [Loop@0x40dd60 at line 68 in concatenateReadStarts] [194]
4.298 0.0 [Loop@0x417498 at line 1143 in remapBackOfNodeMarkersOntoNeighbour] [275]
3.898 0.0 [Loop@0x4173f8 at line 1069 in remapBackOfNodeMarkersOntoNeighbour] [308]
0.7 0.0 [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort] [71]
0.699 0.0 [Loop@0x417200 at line 1098 in remapBackOfNodeMarkersOntoNeighbour] [536]
0.6 0.0 [Loop@0x416690 at line 773 in remapNodeMarkersOntoNeighbour] [321]
0.6 0.0 [Loop@0x4165f8 at line 808 in remapNodeMarkersOntoNeighbour] [332]
0.3 0.0 [Loop@0x4170f0 at line 1033 in remapBackOfNodeMarkersOntoNeighbour] [471]
0.2 0.0 projectFromShortRead [93]
[260] 0.09 23.595 0.0 getShortReadMarkerPosition [260]
0.0 23.409 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [224]
[261] 0.09 0.0 23.409 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [261]
1.711 20.399 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [271]
0.0 1.299 newDescriptor_pg [232]
0.9 22.5 fh_extractminel [154]
[262] 0.09 0.9 22.5 [Loop@0x40d280 at line 534 in fh_extractminel] [262]
18.5 4.0 fh_insertrootlist [265]
0.9 21.7 [Loop@0x40cf90 at line 436 in fh_consolidate] [211]
[263] 0.08 0.9 21.7 [Loop@0x40cff0 at line 436 in fh_consolidate] [263]
0.5 20.9 fh_heaplink [277]
0.3 0.0 fh_compare [828]
22.6 0.0 threadSequenceThroughGraph [7]
[264] 0.08 22.6 0.0 getKmerOccurencePosition [264]
18.5 4.0 [Loop@0x40d280 at line 534 in fh_extractminel] [262]
[265] 0.08 18.5 4.0 fh_insertrootlist [265]
4.0 0.0 fhe_insertafter [480]
0.0 22.4 correctGraph [15]
[266] 0.08 0.0 22.4 [Loop@0x41a3a6 at line 2565 in correctGraph] [266]
0.0 21.399 [Loop@0x41a3eb at line 2359 in correctGraph] [278]
0.301 0.7 initializeTodoLists [267]
0.2 21.199 [Loop@0x41a3eb at line 2359 in correctGraph] [278]
0.301 0.7 [Loop@0x41a3a6 at line 2565 in correctGraph] [266]
[267] 0.08 0.501 21.899 initializeTodoLists [267]
11.3 0.0 getNodeID [49]
8.999 0.0 getDestination [248]
0.899 0.0 getNextArc [522]
0.5 0.0 getArc [351]
0.2 0.0 getNodeInGraph [47]
0.0 22.3 newPreGraph_pg [37]
[268] 0.08 0.0 22.3 [Loop@0x4337dd at line 341 in newPreGraph_pg] [268]
7.4 14.9 convertInsertionMarkers [269]
7.4 14.9 [Loop@0x4337dd at line 341 in newPreGraph_pg] [268]
[269] 0.08 7.4 14.9 convertInsertionMarkers [269]
13.9 0.0 getAnnotSequenceID [328]
0.8 0.0 getStartID [600]
0.2 0.0 getFinishID [490]
2.4 19.8 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
[270] 0.08 2.4 19.8 unLockNode [270]
18.6 0.0 omp_unset_lock [48]
1.2 0.0 getNodeID [49]
1.711 20.399 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [261]
[271] 0.08 1.711 20.399 [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg] [271]
0.7 19.699 newDescriptor_pg [232]
1.0 21.1 renumberPreNodes_pg [273]
[272] 0.08 1.0 21.1 [Loop@0x4301b8 at line 923 in renumberPreNodes_pg] [272]
0.0 21.1 [Loop@0x43022b at line 942 in renumberPreNodes_pg] [282]
0.0 22.1 concatenatePreGraph_pg [127]
[273] 0.08 0.0 22.1 renumberPreNodes_pg [273]
1.0 21.1 [Loop@0x4301b8 at line 923 in renumberPreNodes_pg] [272]
0.0 22.1 buildScaffold [141]
[274] 0.08 0.0 22.1 computeReadToNodeMappings [274]
0.0 20.5 computeReadToNodeMappings.omp_fn.1 [74]
0.0 1.1 allocateReadToNodeTables [655]
0.3 0.0 [libgomp.so.1.0.0] [94]
0.0 0.1 [Loop@0x4279c0 at line 473 in computeReadToNodeMappings] [985]
0.0 0.1 createReadsLocks [1033]
13.6 8.298 remapBackOfNodeMarkersOntoNeighbour [61]
[275] 0.08 13.6 8.298 [Loop@0x417498 at line 1143 in remapBackOfNodeMarkersOntoNeighbour] [275]
4.298 0.0 getShortReadMarkerPosition [260]
4.0 0.0 getShortReadMarkerAtIndex [243]
0.0 11.7 removeNodeAndDenounceDubiousReads [238]
0.0 4.499 concatenateNodesAndVaccinate [169]
0.1 2.2 [Loop@0x40e1e4 at line 180 in concatenateStringOfNodes] [518]
0.1 1.8 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
0.0 0.6 [Loop@0x4138d2 at line 1419 in removeHighCoverageNodes] [705]
0.0 0.3 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.0 0.1 [Loop@0x4051c0 at line 3792 in destroyGraph] [934]
0.0 0.1 pushNeighbours [142]
[276] 0.08 0.2 21.299 destroyNode [276]
0.0 7.5 [Loop@0x4050b0 at line 477 in destroyNode] [399]
7.2 0.0 _int_free [227]
0.1 4.5 [Loop@0x405080 at line 466 in destroyNode] [460]
1.3 0.0 free [497]
0.0 0.699 [Loop@0x405100 at line 487 in destroyNode] [738]
0.5 20.9 [Loop@0x40cff0 at line 436 in fh_consolidate] [263]
[277] 0.08 0.5 20.9 fh_heaplink [277]
0.4 20.5 fhe_insertbefore [284]
0.0 21.399 [Loop@0x41a3a6 at line 2565 in correctGraph] [266]
[278] 0.08 0.0 21.399 [Loop@0x41a3eb at line 2359 in correctGraph] [278]
0.2 21.199 initializeTodoLists [267]
0.0 21.3 setInsertionMarkers [139]
[279] 0.08 0.0 21.3 orderInsertionMarkers [279]
0.0 21.2 orderInsertionMarkers.omp_fn.0 [78]
0.1 0.0 [libgomp.so.1.0.0] [94]
0.7 20.5 threadSequenceThroughGraph [7]
[280] 0.08 0.7 20.5 unMemorizeNodes [280]
1.1 19.4 [Loop@0x42d69c at line 188 in unMemorizeNodes] [287]
0.3 20.9 createConnection [162]
[281] 0.08 0.3 20.9 lockTwoNodes [281]
14.9 0.0 omp_set_lock [44]
5.9 0.0 [libgomp.so.1.0.0] [94]
0.1 0.0 [Import thunk omp_set_lock] [687]
0.0 21.1 [Loop@0x4301b8 at line 923 in renumberPreNodes_pg] [272]
[282] 0.08 0.0 21.1 [Loop@0x43022b at line 942 in renumberPreNodes_pg] [282]
0.8 10.3 [Loop@0x43023c at line 900 in renumberPreNodes_pg] [353]
0.4 9.5 [Loop@0x43034c at line 900 in renumberPreNodes_pg] [366]
0.1 0.0 getPreArc_pg [957]
0.0 21.0 [Loop@0x41a4bf at line 2568 in correctGraph] [22]
[283] 0.08 0.0 21.0 updateNodeStatus [283]
0.0 20.8 [Loop@0x41a980 at line 444 in updateNodeStatus] [285]
0.0 0.2 newFibHeap [898]
0.4 20.5 fh_heaplink [277]
[284] 0.08 0.4 20.5 fhe_insertbefore [284]
20.5 0.0 fhe_insertafter [288]
0.0 20.8 updateNodeStatus [283]
[285] 0.08 0.0 20.8 [Loop@0x41a980 at line 444 in updateNodeStatus] [285]
0.0 11.3 [Loop@0x41a990 at line 445 in updateNodeStatus] [352]
0.0 9.0 fh_extractmin [149]
0.5 0.0 getArc [351]
0.0 20.7 remapNodeArcsOntoTarget [252]
[286] 0.08 0.0 20.7 [Loop@0x415c3e at line 680 in remapNodeArcsOntoTarget] [286]
4.3 12.5 createAnalogousArc [245]
2.7 1.2 destroyArc [319]
1.1 19.4 unMemorizeNodes [280]
[287] 0.08 1.1 19.4 [Loop@0x42d69c at line 188 in unMemorizeNodes] [287]
4.2 15.2 deallocateSmallNodeList [294]
20.5 0.0 fhe_insertbefore [284]
[288] 0.08 20.5 0.0 fhe_insertafter [288]
19.3 0.4 allocatePreArc_pg [291]
0.3 0.1 allocatePreArc_pg [805]
[289] 0.08 19.6 0.5 allocArrayArrayAllocate [289]
0.0 0.3 callocOrExit3 [221]
0.1 0.0 [Import thunk omp_get_thread_num] [456]
0.1 0.0 omp_get_thread_num [380]
0.4 19.6 ghostThreadSequenceThroughGraph [11]
[290] 0.08 0.4 19.6 unMemorizeNodes [290]
1.5 18.1 [Loop@0x42dc11 at line 188 in unMemorizeNodes] [292]
0.0 19.7 createPreArc_pg [36]
[291] 0.07 0.0 19.7 allocatePreArc_pg [291]
19.3 0.4 allocArrayArrayAllocate [289]
1.5 18.1 unMemorizeNodes [290]
[292] 0.07 1.5 18.1 [Loop@0x42dc11 at line 188 in unMemorizeNodes] [292]
2.1 16.0 deallocateSmallNodeList [306]
1.4 18.199 [Loop@0x42c240 at line 536 in referenceGraphKmers] [207]
[293] 0.07 1.4 18.199 [Loop@0x42c4a0 at line 543 in referenceGraphKmers] [293]
15.7 0.0 _IO_getc [53]
1.5 0.0 reversePushNucleotide [114]
0.8 0.0 pushNucleotide [185]
0.199 0.0 [Import thunk _IO_getc] [416]
4.2 15.2 [Loop@0x42d69c at line 188 in unMemorizeNodes] [287]
[294] 0.07 4.2 15.2 deallocateSmallNodeList [294]
10.1 0.0 deallocatePointer [301]
1.8 0.0 omp_get_thread_num [380]
1.8 0.0 getRecycleBinInArray [408]
1.5 0.0 [Import thunk omp_get_thread_num] [456]
0.0 19.4 newPreGraph_pg [37]
[295] 0.07 0.0 19.4 countPreNodes [295]
1.8 17.6 [Loop@0x433508 at line 276 in countPreNodes] [296]
1.8 17.6 countPreNodes [295]
[296] 0.07 1.8 17.6 [Loop@0x433508 at line 276 in countPreNodes] [296]
0.6 11.4 [Loop@0x433570 at line 287 in countPreNodes] [345]
0.3 4.7 [Loop@0x43367f at line 119 in countPreNodes] [446]
0.3 0.0 getAnnotationCount [681]
0.3 0.0 sequenceCount_pg [794]
1.7 17.7 findOrCreateConnection [257]
[297] 0.07 1.7 17.7 splayConnection [297]
10.6 7.1 [Loop@0x4286e4 at line 882 in splayConnection] [312]
0.0 19.316 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
[298] 0.07 0.0 19.316 remapEmptyPathOntoMiddlePath [298]
0.0 19.216 remapEmptyPathMarkersOntoMiddlePathSimple [299]
0.0 0.1 remapEmptyPathArcsOntoMiddlePathSimple [935]
0.0 19.216 remapEmptyPathOntoMiddlePath [298]
[299] 0.07 0.0 19.216 remapEmptyPathMarkersOntoMiddlePathSimple [299]
0.0 18.316 [Loop@0x417bc6 at line 1622 in remapEmptyPathMarkersOntoMiddlePathSimple] [305]
0.0 0.9 commonNodeReads [173]
0.0 19.001 findLowCoverageRegions [187]
[300] 0.07 0.0 19.001 sortCoords [300]
11.9 7.1 qsort_r [43]
10.1 0.0 deallocateSmallNodeList [294]
8.4 0.0 deallocateSmallNodeList [306]
0.3 0.0 deallocateConnectionStack [815]
0.1 0.0 deallocateArc [903]
0.1 0.0 [Loop@0x4050b0 at line 477 in destroyNode] [399]
[301] 0.07 19.0 0.0 deallocatePointer [301]
1.4 17.501 [Loop@0x42c240 at line 536 in referenceGraphKmers] [207]
[302] 0.07 1.4 17.501 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
9.3 0.0 _IO_getc [53]
0.8 5.802 recordKmerOccurence [414]
0.7 0.0 getNodeLength [148]
0.4 0.0 reversePushNucleotide [114]
0.3 0.0 pushNucleotide [185]
0.1 0.0 getNodeInGraph [47]
0.1 0.0 compareKmers [4]
0.9 17.604 [Loop@0x432bfd at line 430 in createPreNodes] [119]
[303] 0.07 0.9 17.604 [Loop@0x432faa at line 602 in createPreNodes] [303]
0.0 12.405 addPreNodeToPreGraph_pg [223]
1.999 0.0 getStart [143]
1.7 0.0 getFinish [230]
0.6 0.2 convertMarker [719]
0.7 0.0 getInsertionMarkerPosition [726]
0.0 18.316 [Loop@0x417bc6 at line 1622 in remapEmptyPathMarkersOntoMiddlePathSimple] [305]
[304] 0.07 0.0 18.316 spreadReadIDs [304]
10.712 5.001 [Loop@0x4038e6 at line 3339 in spreadReadIDs] [329]
0.0 1.202 mallocOrExit3 [67]
0.3 0.7 [Loop@0x403978 at line 3743 in spreadReadIDs] [668]
0.0 0.3 [Loop@0x403a78 at line 3779 in spreadReadIDs] [836]
0.1 0.0 _int_free [227]
0.0 18.316 remapEmptyPathMarkersOntoMiddlePathSimple [299]
[305] 0.07 0.0 18.316 [Loop@0x417bc6 at line 1622 in remapEmptyPathMarkersOntoMiddlePathSimple] [305]
0.0 18.316 spreadReadIDs [304]
2.1 16.0 [Loop@0x42dc11 at line 188 in unMemorizeNodes] [292]
[306] 0.07 2.1 16.0 deallocateSmallNodeList [306]
8.4 0.0 deallocatePointer [301]
3.0 0.0 getRecycleBinInArray [408]
3.0 0.0 omp_get_thread_num [380]
1.6 0.0 [Import thunk omp_get_thread_num] [456]
0.4 17.7 [Loop@0x432270 at line 699 in connectPreNodes.omp_fn.2] [28]
[307] 0.07 0.4 17.7 [Loop@0x43227f at line 891 in connectPreNodes.omp_fn.2] [307]
0.6 16.3 connectPreNodeToTheNext [29]
0.2 0.4 chooseNextInternalPreNode [739]
0.2 0.0 getPreNodeLength_pg [111]
10.0 7.897 remapBackOfNodeMarkersOntoNeighbour [61]
[308] 0.07 10.0 7.897 [Loop@0x4173f8 at line 1069 in remapBackOfNodeMarkersOntoNeighbour] [308]
3.999 0.0 getShortReadMarkerAtIndex [243]
3.898 0.0 getShortReadMarkerPosition [260]
4.299 13.504 fillTightStringWithString [206]
[309] 0.07 4.299 13.504 writeNucleotide [309]
13.504 0.0 writeNucleotideNumber [339]
0.0 17.7 main [14]
[310] 0.07 0.0 17.7 displayGeneralStatistics [310]
0.0 17.7 [Loop@0x4128ec at line 432 in displayGeneralStatistics] [311]
0.0 17.7 displayGeneralStatistics [310]
[311] 0.07 0.0 17.7 [Loop@0x4128ec at line 432 in displayGeneralStatistics] [311]
0.0 17.3 printShortCounts [315]
0.0 0.4 velvetFprintf [17]
10.6 7.1 splayConnection [297]
[312] 0.07 10.6 7.1 [Loop@0x4286e4 at line 882 in splayConnection] [312]
5.0 0.0 getNodeID [49]
1.2 0.0 connectionSingleRotateWithLeft [650]
0.9 0.0 connectionSingleRotateWithRight [685]
0.0 17.7 remapBackOfNodeOntoNeighbour [55]
[313] 0.07 0.0 17.7 remapBackOfNodeArcsOntoNeighbour [313]
0.0 12.5 remapNodeArcsOntoTarget [252]
0.1 5.1 [Loop@0x416c20 at line 859 in remapBackOfNodeArcsOntoNeighbour] [439]
11.9 5.6 createAnalogousArc [245]
[314] 0.07 11.9 5.6 getArcBetweenNodes [314]
5.6 0.0 [Loop@0x4052ef at line 337 in getArcBetweenNodes] [431]
0.0 17.3 [Loop@0x4128ec at line 432 in displayGeneralStatistics] [311]
[315] 0.06 0.0 17.3 printShortCounts [315]
17.1 0.2 [Loop@0x412b20 at line 444 in printShortCounts] [316]
17.1 0.2 printShortCounts [315]
[316] 0.06 17.1 0.2 [Loop@0x412b20 at line 444 in printShortCounts] [316]
0.1 0.0 getShortReadMarkerAtIndex [243]
0.1 0.0 getShortReadMarkerID [465]
0.0 12.0 absorbExtension [344]
0.0 5.0 concatenateNodesAndVaccinate [169]
[317] 0.06 0.0 17.0 appendDescriptors [317]
0.3 11.9 mergeDescriptors [343]
0.8 3.4 mergeDescriptors [468]
0.6 0.0 _int_free [227]
0.0 16.9 findLowCoverageRegions [187]
[318] 0.06 0.0 16.9 sortCoords [318]
9.9 7.0 qsort_r [43]
6.7 0.7 [Loop@0x4050b0 at line 477 in destroyNode] [399]
4.4 0.1 [Loop@0x405080 at line 466 in destroyNode] [460]
2.7 1.2 [Loop@0x415c3e at line 680 in remapNodeArcsOntoTarget] [286]
0.5 0.3 [Loop@0x418439 at line 1976 in concatenateNodesAndVaccinate] [709]
[319] 0.06 14.3 2.3 destroyArc [319]
1.2 0.0 [Loop@0x404f40 at line 438 in destroyArc] [641]
0.9 0.0 [Loop@0x404f80 at line 453 in destroyArc] [686]
0.1 0.1 deallocateArc [903]
0.3 16.297 destroyPaths [236]
[320] 0.06 0.3 16.297 [Loop@0x415a00 at line 1851 in destroyPaths] [320]
2.3 10.797 destroyPassageMarker [244]
0.6 1.2 getNextInSequence [347]
0.7 0.7 allocArrayFree [423]
14.899 1.6 remapNodeMarkersOntoNeighbour [104]
[321] 0.06 14.899 1.6 [Loop@0x416690 at line 773 in remapNodeMarkersOntoNeighbour] [321]
0.8 0.0 setShortReadMarkerPosition [402]
0.6 0.0 getShortReadMarkerPosition [260]
0.2 0.0 getShortReadMarkerAtIndex [243]
16.3 0.0 threadSequenceThroughGraph [7]
0.1 0.0 remapBackOfNodeMarkersOntoNeighbour [61]
[322] 0.06 16.4 0.0 incrementOriginalVirtualCoverage [322]
15.4 0.9 removeNodeAndDenounceDubiousReads [238]
[323] 0.06 15.4 0.9 [Loop@0x414f6d at line 1193 in removeNodeAndDenounceDubiousReads] [323]
0.9 0.0 getShortReadMarkerID [465]
1.4 14.8 exportNode [210]
[324] 0.06 1.4 14.8 [Loop@0x4076f4 at line 548 in exportNode] [324]
1.2 11.6 velvetFprintf [17]
2.0 0.0 getNucleotideInDescriptor [571]
0.2 15.9 determineEligibleStartingPoints [122]
[325] 0.06 0.2 15.9 [Loop@0x41a20d at line 473 in determineEligibleStartingPoints] [325]
0.1 7.5 [Loop@0x41a240 at line 479 in determineEligibleStartingPoints] [398]
0.2 5.4 [Loop@0x41a2b7 at line 489 in determineEligibleStartingPoints] [430]
0.1 2.2 fh_insertkey [527]
0.2 0.0 getArc [351]
0.2 0.0 getNodeInGraph [47]
5.9 10.2 concatenateReadStarts [77]
[326] 0.06 5.9 10.2 [Loop@0x40dce0 at line 54 in concatenateReadStarts] [326]
6.4 0.0 getShortReadMarkerPosition [260]
3.0 0.0 getShortReadMarkerAtIndex [243]
0.8 0.0 setShortReadMarkerPosition [402]
0.0 16.0 [Loop@0x434140 at line 142 in concatenatePreGraph_pg] [159]
[327] 0.06 0.0 16.0 [Loop@0x4341ba at line 165 in concatenatePreGraph_pg] [327]
3.1 7.9 hasSinglePreArc_pg [208]
0.0 4.2 concatenatePreNodes [220]
0.2 0.6 getOtherEnd_pg [592]
13.9 0.0 convertInsertionMarkers [269]
1.3 0.0 [Loop@0x4332db at line 185 in setInsertionMarkers] [362]
0.6 0.0 [Loop@0x4333d6 at line 222 in setInsertionMarkers] [197]
[328] 0.06 15.8 0.0 getAnnotSequenceID [328]
10.712 5.001 spreadReadIDs [304]
[329] 0.06 10.712 5.001 [Loop@0x4038e6 at line 3339 in spreadReadIDs] [329]
4.201 0.0 setShortReadMarkerOffset [467]
0.6 0.0 setShortReadMarkerOffset [749]
0.2 0.0 setShortReadMarkerPosition [888]
0.0 15.3 clipTips_pg [200]
[330] 0.06 0.0 15.3 [Loop@0x434278 at line 235 in clipTips_pg] [330]
1.1 14.2 [Loop@0x43428c at line 242 in clipTips_pg] [331]
1.1 14.2 [Loop@0x434278 at line 235 in clipTips_pg] [330]
[331] 0.06 1.1 14.2 [Loop@0x43428c at line 242 in clipTips_pg] [331]
1.3 9.4 isEligibleTip [359]
2.4 0.0 getPreNodeInPreGraph_pg [508]
0.0 0.7 destroyPreNode_pg [356]
0.4 0.0 preNodeCount_pg [662]
13.399 1.7 remapNodeMarkersOntoNeighbour [104]
[332] 0.06 13.399 1.7 [Loop@0x4165f8 at line 808 in remapNodeMarkersOntoNeighbour] [332]
0.7 0.0 getShortReadMarkerAtIndex [243]
0.6 0.0 getShortReadMarkerPosition [260]
0.4 0.0 setShortReadMarkerPosition [402]
0.2 14.799 extractSequence [258]
[333] 0.06 0.2 14.799 [Loop@0x415368 at line 541 in extractSequence] [333]
0.0 11.799 appendNodeSequence [349]
0.6 0.9 getNode [360]
0.2 0.7 isTerminal [392]
0.2 0.4 getNextInSequence [347]
12.299 0.0 createArc [35]
2.1 0.0 recordKmerOccurence [414]
[334] 0.05 14.399 0.0 GOMP_critical_start [334]
0.1 14.1 concatenatePreNodes [220]
[335] 0.05 0.1 14.1 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
1.8 10.1 hasSinglePreArc_pg [208]
0.2 0.6 getOtherEnd_pg [592]
0.6 0.0 getPreArc_pg [559]
0.0 0.5 getDestination_pg [484]
0.1 0.1 isLoop_pg [830]
0.1 0.0 getPreNodeLength_pg [111]
14.1 0.0 qsort_r [43]
[336] 0.05 14.1 0.0 compareCoords [336]
0.2 13.699 destroyPaths [236]
[337] 0.05 0.2 13.699 [Loop@0x415a10 at line 1854 in destroyPaths] [337]
1.4 9.399 destroyPassageMarker [244]
0.8 1.1 getNextInSequence [347]
0.4 0.6 allocArrayFree [423]
0.0 13.7 buildScaffold [141]
[338] 0.05 0.0 13.7 computeNodeToNodeMappings [338]
0.0 13.5 computeNodeToNodeMappings.omp_fn.3 [89]
0.2 0.0 [libgomp.so.1.0.0] [94]
13.504 0.0 writeNucleotide [309]
[339] 0.05 13.504 0.0 writeNucleotideNumber [339]
13.1 0.0 [Loop@0x403668 at line 3540 in injectShortReads] [234]
[340] 0.05 13.1 0.0 setShortReadMarkerPosition [340]
12.803 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[341] 0.05 12.803 0.0 setShortReadMarkerOffset [341]
0.0 12.8 remapNodeOntoNeighbour [97]
[342] 0.05 0.0 12.8 remapNodeArcsOntoNeighbour [342]
0.0 12.7 remapNodeArcsOntoTarget [252]
0.1 0.0 getTwinNode [228]
0.3 11.9 appendDescriptors [317]
[343] 0.05 0.3 11.9 mergeDescriptors [343]
0.0 10.8 callocOrExit3 [221]
0.8 0.0 [Loop@0x406123 at line 762 in mergeDescriptors] [718]
0.3 0.0 [Loop@0x4060ac at line 744 in mergeDescriptors] [852]
0.0 11.8 pushNeighbours [142]
0.0 0.2 [Loop@0x425688 at line 928 in pushNeighbours] [895]
[344] 0.05 0.0 12.0 absorbExtension [344]
0.0 12.0 appendDescriptors [317]
0.6 11.4 [Loop@0x433508 at line 276 in countPreNodes] [296]
[345] 0.05 0.6 11.4 [Loop@0x433570 at line 287 in countPreNodes] [345]
0.1 8.0 [Loop@0x4335be at line 119 in countPreNodes] [388]
0.8 0.9 [Loop@0x433611 at line 309 in countPreNodes] [598]
0.0 1.2 getInsertionMarkerPosition [649]
0.3 0.0 getPosition [584]
0.0 0.1 getInsertionMarkerPosition [977]
6.8 0.0 [Loop@0x41a240 at line 479 in determineEligibleStartingPoints] [398]
5.0 0.0 [Loop@0x41a2b7 at line 489 in determineEligibleStartingPoints] [430]
0.1 0.0 tourBusArc [33]
[346] 0.04 11.9 0.0 getMultiplicity [346]
1.8 0.3 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.8 1.1 [Loop@0x415a10 at line 1854 in destroyPaths] [337]
0.6 1.2 [Loop@0x415a00 at line 1851 in destroyPaths] [320]
0.5 0.9 [Loop@0x41530b at line 531 in extractSequence] [394]
0.5 0.7 [Loop@0x418ad8 at line 1896 in markerLeadsToNode] [492]
0.2 0.4 [Loop@0x415368 at line 541 in extractSequence] [333]
0.4 0.2 [Loop@0x415278 at line 2188 in pathContainsReference] [410]
0.3 0.2 [Loop@0x4189db at line 1881 in mapDistancesOntoPaths] [575]
0.1 0.4 extractSequence [258]
0.4 0.0 [Loop@0x418ab0 at line 1896 in markerLeadsToNode] [660]
0.1 0.2 [Loop@0x418be0 at line 2070 in concatenatePathNodes] [146]
0.0 0.2 [Loop@0x41898d at line 1872 in mapDistancesOntoPaths] [689]
0.0 0.1 pathContainsReference [407]
0.1 0.0 destroyPaths [479]
0.1 0.0 [Loop@0x418c40 at line 1860 in destroyPaths] [570]
0.0 0.1 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
[347] 0.04 5.9 6.0 getNextInSequence [347]
6.0 0.0 PM_FI2P [425]
0.1 11.699 appendNodeSequence [349]
[348] 0.04 0.1 11.699 [Loop@0x405f5e at line 548 in appendNodeSequence] [348]
10.599 0.0 getNucleotideInDescriptor [361]
0.6 0.5 writeNucleotideAtPosition [632]
0.0 11.799 [Loop@0x415368 at line 541 in extractSequence] [333]
[349] 0.04 0.0 11.799 appendNodeSequence [349]
0.1 11.699 [Loop@0x405f5e at line 548 in appendNodeSequence] [348]
0.4 11.2 [Loop@0x432850 at line 390 in createPreNodes] [84]
[350] 0.04 0.4 11.2 [Loop@0x432907 at line 427 in createPreNodes] [350]
11.2 0.0 fgets [85]
10.0 0.0 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
0.5 0.0 initializeTodoLists [267]
0.5 0.0 [Loop@0x41a980 at line 444 in updateNodeStatus] [285]
0.2 0.0 [Loop@0x41a20d at line 473 in determineEligibleStartingPoints] [325]
0.1 0.0 [Loop@0x40e320 at line 217 in concatenateGraph] [100]
0.1 0.0 [Loop@0x40e294 at line 205 in concatenateGraph] [103]
[351] 0.04 11.4 0.0 getArc [351]
0.0 11.3 [Loop@0x41a980 at line 444 in updateNodeStatus] [285]
[352] 0.04 0.0 11.3 [Loop@0x41a990 at line 445 in updateNodeStatus] [352]
6.1 0.0 getDestination [248]
3.9 0.0 getNodeStatus [365]
0.5 0.0 getNextArc [522]
0.0 0.5 fh_insertkey [527]
0.3 0.0 setNodeStatus [819]
0.8 10.3 [Loop@0x43022b at line 942 in renumberPreNodes_pg] [282]
[353] 0.04 0.8 10.3 [Loop@0x43023c at line 900 in renumberPreNodes_pg] [353]
9.0 0.6 updatePreArcData_pg [369]
0.1 0.6 getNextPreArc_pg [734]
0.2 7.399 addUncertainPassageMarker [202]
2.0 0.9 extractPassageMarker [368]
0.1 0.5 addPassageMarker [581]
[354] 0.04 2.3 8.799 setMarker [354]
1.199 5.3 getTwinMarker [417]
0.9 1.4 setTopOfTheNode [405]
0.4 10.598 [Loop@0x432bfd at line 506 in createPreNodes] [164]
[355] 0.04 0.4 10.598 [Loop@0x432cb2 at line 119 in createPreNodes] [355]
0.499 9.299 getInsertionMarkerPosition [367]
0.2 0.6 convertMarker [700]
0.1 10.1 [Loop@0x433f90 at line 123 in concatenatePreNodes] [358]
0.0 0.7 [Loop@0x43428c at line 242 in clipTips_pg] [331]
[356] 0.04 0.1 10.8 destroyPreNode_pg [356]
0.0 4.6 [Loop@0x4306a6 at line 310 in destroyPreNode_pg] [458]
0.0 3.8 [Loop@0x430640 at line 310 in destroyPreNode_pg] [488]
1.9 0.0 _int_free [227]
0.4 0.0 free [497]
0.1 0.0 [Import thunk free] [965]
0.4 10.4 setInsertionMarkers [139]
[357] 0.04 0.4 10.4 [Loop@0x4332b7 at line 177 in setInsertionMarkers] [357]
9.0 1.3 [Loop@0x4332db at line 185 in setInsertionMarkers] [362]
0.1 0.0 getAnnotationCount [681]
0.0 10.7 concatenatePreNodes [220]
[358] 0.04 0.0 10.7 [Loop@0x433f90 at line 123 in concatenatePreNodes] [358]
0.1 10.1 destroyPreNode_pg [356]
0.2 0.2 getDestination_pg [484]
0.1 0.0 getPreArc_pg [559]
1.3 9.4 [Loop@0x43428c at line 242 in clipTips_pg] [331]
[359] 0.04 1.3 9.4 isEligibleTip [359]
0.0 8.2 [Loop@0x433bd2 at line 195 in isEligibleTip] [387]
0.7 0.0 getPreArc_pg [559]
0.0 0.5 simplePreArcCount_pg [385]
0.9 1.5 [Loop@0x418ad8 at line 1896 in markerLeadsToNode] [492]
0.9 0.8 [Loop@0x41530b at line 531 in extractSequence] [394]
0.6 0.9 [Loop@0x415368 at line 541 in extractSequence] [333]
0.6 0.5 [Loop@0x419ae0 at line 2246 in comparePaths] [231]
0.5 0.6 [Loop@0x419bb0 at line 2264 in comparePaths] [256]
0.2 0.7 [Loop@0x415278 at line 2188 in pathContainsReference] [410]
0.3 0.4 [Loop@0x418ab0 at line 1896 in markerLeadsToNode] [660]
0.1 0.3 [Loop@0x4189db at line 1881 in mapDistancesOntoPaths] [575]
0.0 0.3 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.1 0.1 transferNodeData [376]
0.0 0.2 [Loop@0x418be0 at line 2070 in concatenatePathNodes] [146]
0.0 0.1 remapBackOfNodeMarkersOntoNeighbour [61]
[360] 0.04 4.2 6.4 getNode [360]
6.4 0.0 PM_FI2P [418]
10.599 0.0 [Loop@0x405f5e at line 548 in appendNodeSequence] [348]
[361] 0.04 10.599 0.0 getNucleotideInDescriptor [361]
9.0 1.3 [Loop@0x4332b7 at line 177 in setInsertionMarkers] [357]
[362] 0.04 9.0 1.3 [Loop@0x4332db at line 185 in setInsertionMarkers] [362]
1.3 0.0 getAnnotSequenceID [328]
9.9 0.2 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[363] 0.04 9.9 0.2 getNodePrevious [363]
0.1 0.0 getNodeID [49]
0.1 0.0 nodeCount [580]
7.396 0.0 createArc [35]
2.299 0.0 recordKmerOccurence [414]
0.4 0.0 allocateConnection [585]
[364] 0.04 10.095 0.0 GOMP_critical_end [364]
3.9 0.0 [Loop@0x41a990 at line 445 in updateNodeStatus] [352]
2.9 0.0 nextStartingPoint [434]
1.4 0.0 tourBusArc [33]
1.0 0.0 [Loop@0x42be0b at line 396 in isLocalDeadEnd] [583]
0.8 0.0 [Loop@0x42bdb5 at line 396 in clipTipsVeryHardLocally] [478]
[365] 0.04 10.0 0.0 getNodeStatus [365]
0.4 9.5 [Loop@0x43022b at line 942 in renumberPreNodes_pg] [282]
[366] 0.04 0.4 9.5 [Loop@0x43034c at line 900 in renumberPreNodes_pg] [366]
8.3 0.8 updatePreArcData_pg [377]
0.1 0.3 getNextPreArc_pg [792]
0.499 9.299 [Loop@0x432cb2 at line 119 in createPreNodes] [355]
[367] 0.04 0.499 9.299 getInsertionMarkerPosition [367]
4.899 0.0 getStart [143]
4.4 0.0 getFinish [230]
4.899 4.8 destroyPassageMarker [244]
[368] 0.04 4.899 4.8 extractPassageMarker [368]
2.0 0.9 setMarker [354]
1.5 0.0 PM_FI2P [611]
0.1 0.3 setTopOfTheNode [405]
9.0 0.6 [Loop@0x43023c at line 900 in renumberPreNodes_pg] [353]
[369] 0.04 9.0 0.6 updatePreArcData_pg [369]
0.6 0.0 PREARC_FI2P [755]
0.0 9.6 main [14]
[370] 0.04 0.0 9.6 logFinalStats [370]
0.0 9.5 usedReads [371]
0.0 0.1 n50 [1014]
0.0 9.5 logFinalStats [370]
[371] 0.04 0.0 9.5 usedReads [371]
0.0 9.2 [Loop@0x410a59 at line 1797 in usedReads] [375]
0.1 0.2 [Loop@0x410bad at line 1797 in usedReads] [857]
0.0 9.4 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[372] 0.04 0.0 9.4 isPreviousToNode [372]
4.5 4.9 [Loop@0x41983a at line 143 in isPreviousToNode] [373]
4.5 4.9 isPreviousToNode [372]
[373] 0.04 4.5 4.9 [Loop@0x41983a at line 143 in isPreviousToNode] [373]
0.1 4.6 getNodeTime [455]
0.2 0.0 getNodePrevious [912]
0.0 9.4 remapBackOfNodeOntoNeighbour [55]
[374] 0.04 0.0 9.4 [Loop@0x416850 at line 894 in remapBackOfNodeOntoNeighbour] [374]
1.3 8.1 remapBackOfNodeMarkersOntoNeighbour [61]
0.0 9.2 usedReads [371]
[375] 0.03 0.0 9.2 [Loop@0x410a59 at line 1797 in usedReads] [375]
4.4 2.3 [Loop@0x410b08 at line 1816 in usedReads] [413]
2.2 0.3 [Loop@0x410b70 at line 1824 in usedReads] [542]
1.1 4.2 [Loop@0x41816a at line 1975 in simplifyNode] [155]
0.2 3.7 [Loop@0x418340 at line 112 in simplifyNode] [486]
[376] 0.03 1.3 7.9 transferNodeData [376]
0.6 1.3 remapNodeFibHeapReferencesOntoNode [437]
0.0 1.6 concatenateTodoLists [606]
1.3 0.0 getDestination [248]
0.0 1.2 getNodePrevious [640]
1.1 0.0 setNodePrevious [663]
0.3 0.0 getNodeTime [835]
0.1 0.1 getNode [360]
0.1 0.0 getNodeTime [953]
0.1 0.0 getNodePrevious [1000]
0.1 0.0 getNextArc [522]
8.3 0.8 [Loop@0x43034c at line 900 in renumberPreNodes_pg] [366]
[377] 0.03 8.3 0.8 updatePreArcData_pg [377]
0.8 0.0 PREARC_FI2P [716]
0.0 5.1 [Loop@0x419ae0 at line 2246 in comparePaths] [231]
0.0 4.0 [Loop@0x419bb0 at line 2264 in comparePaths] [256]
[378] 0.03 0.0 9.1 connectPassageMarkers [378]
1.6 6.5 setPreviousInSequence [389]
0.2 0.8 setNextInSequence [670]
0.0 9.0 buildScaffold [141]
[379] 0.03 0.0 9.0 computeReadToNodeCounts [379]
0.0 8.7 computeReadToNodeCounts.omp_fn.0 [117]
0.2 0.0 [libgomp.so.1.0.0] [94]
0.0 0.1 [Loop@0x4276f0 at line 373 in computeReadToNodeCounts] [986]
3.0 0.0 allocateSmallNodeList [167]
3.0 0.0 deallocateSmallNodeList [306]
1.8 0.0 deallocateSmallNodeList [294]
1.0 0.0 allocateSmallNodeList [182]
0.1 0.0 allocArrayArrayAllocate [289]
[380] 0.03 8.9 0.0 omp_get_thread_num [380]
4.6 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
3.2 0.0 threadSequenceThroughGraph [7]
0.9 0.0 [Loop@0x41bce8 at line 1729 in getSequenceLengths] [532]
[381] 0.03 8.7 0.0 getLength [381]
8.6 0.0 createConnection [162]
[382] 0.03 8.6 0.0 readjustConnectionInTree [382]
0.4 8.098 createConnection [162]
[383] 0.03 0.4 8.098 unLockTwoNodes [383]
5.498 0.0 omp_unset_lock [48]
2.6 0.0 [libgomp.so.1.0.0] [94]
4.698 0.0 newDescriptor_pg [232]
3.8 0.0 [Loop@0x42fd7d at line 1015 in newDescriptor_pg] [391]
[384] 0.03 8.498 0.0 writeNucleotideInDescriptor_pg [384]
0.5 7.4 [Loop@0x433bd2 at line 195 in isEligibleTip] [387]
0.0 0.5 isEligibleTip [359]
[385] 0.03 0.5 7.9 simplePreArcCount_pg [385]
0.2 7.7 [Loop@0x4300ff at line 83 in simplePreArcCount_pg] [393]
2.0 6.299 [Loop@0x41ad00 at line 321 in dfh_consolidate] [110]
[386] 0.03 2.0 6.299 dfh_removerootlist [386]
6.299 0.0 dfhe_remove [420]
0.0 8.2 isEligibleTip [359]
[387] 0.03 0.0 8.2 [Loop@0x433bd2 at line 195 in isEligibleTip] [387]
0.5 7.4 simplePreArcCount_pg [385]
0.2 0.1 getDestination_pg [484]
0.1 8.0 [Loop@0x433570 at line 287 in countPreNodes] [345]
[388] 0.03 0.1 8.0 [Loop@0x4335be at line 119 in countPreNodes] [388]
0.8 7.2 getInsertionMarkerPosition [390]
1.6 6.5 connectPassageMarkers [378]
[389] 0.03 1.6 6.5 setPreviousInSequence [389]
4.2 0.0 PM_FI2P [469]
1.5 0.0 PM_FI2P [612]
0.8 0.0 PM_FI2P [714]
0.8 7.2 [Loop@0x4335be at line 119 in countPreNodes] [388]
[390] 0.03 0.8 7.2 getInsertionMarkerPosition [390]
4.3 0.0 getStart [143]
2.9 0.0 getFinish [230]
3.0 5.0 newDescriptor_pg [232]
[391] 0.03 3.0 5.0 [Loop@0x42fd7d at line 1015 in newDescriptor_pg] [391]
3.8 0.0 writeNucleotideInDescriptor_pg [384]
0.5 0.7 popNucleotide [652]
1.5 2.3 [Loop@0x41530b at line 531 in extractSequence] [394]
0.8 1.8 [Loop@0x415278 at line 2188 in pathContainsReference] [410]
0.2 0.7 [Loop@0x415368 at line 541 in extractSequence] [333]
0.2 0.0 [Loop@0x41898d at line 1872 in mapDistancesOntoPaths] [689]
0.1 0.0 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.0 0.1 pathContainsReference [407]
0.0 0.1 [Loop@0x4189db at line 1881 in mapDistancesOntoPaths] [575]
0.0 0.1 [Loop@0x4184e0 at line 1994 in concatenateNodesAndVaccinate] [909]
[392] 0.03 2.8 5.1 isTerminal [392]
5.1 0.0 PM_FI2P [441]
0.2 7.7 simplePreArcCount_pg [385]
[393] 0.03 0.2 7.7 [Loop@0x4300ff at line 83 in simplePreArcCount_pg] [393]
6.9 0.8 getNextPreArc_pg [396]
0.3 7.6 extractSequence [258]
[394] 0.03 0.3 7.6 [Loop@0x41530b at line 531 in extractSequence] [394]
1.5 2.3 isTerminal [392]
0.9 0.8 getNode [360]
0.5 0.9 getNextInSequence [347]
0.7 0.0 getNodeLength [148]
1.099 5.3 addUncertainPassageMarker [202]
0.4 0.3 insertPassageMarker [729]
0.2 0.5 addPassageMarker [581]
[395] 0.03 1.699 6.1 setNextInNode [395]
2.9 0.0 PM_FI2P [449]
0.2 2.2 getTwinMarker [545]
0.4 0.0 PM_FI2P [798]
0.3 0.0 PM_FI2P [855]
0.1 0.0 PM_FI2P [955]
6.9 0.8 [Loop@0x4300ff at line 83 in simplePreArcCount_pg] [393]
[396] 0.03 6.9 0.8 getNextPreArc_pg [396]
0.8 0.0 PREARC_FI2P [697]
7.6 0.0 [Loop@0x403668 at line 3540 in injectShortReads] [234]
[397] 0.03 7.6 0.0 setShortReadMarkerOffset [397]
0.1 7.5 [Loop@0x41a20d at line 473 in determineEligibleStartingPoints] [325]
[398] 0.03 0.1 7.5 [Loop@0x41a240 at line 479 in determineEligibleStartingPoints] [398]
6.8 0.0 getMultiplicity [346]
0.7 0.0 getNextArc [522]
0.0 7.5 destroyNode [276]
[399] 0.03 0.0 7.5 [Loop@0x4050b0 at line 477 in destroyNode] [399]
6.7 0.7 destroyArc [319]
0.1 0.0 deallocatePointer [301]
7.4 0.1 getShortReadCoords [401]
[400] 0.03 7.4 0.1 [Loop@0x412fad at line 843 in getShortReadCoords] [400]
0.1 0.0 getShortReadMarkerAtIndex [243]
0.0 7.5 findLowCoverageRegions [187]
[401] 0.03 0.0 7.5 getShortReadCoords [401]
7.4 0.1 [Loop@0x412fad at line 843 in getShortReadCoords] [400]
4.7 0.0 [Loop@0x40dd60 at line 68 in concatenateReadStarts] [194]
0.8 0.0 [Loop@0x416690 at line 773 in remapNodeMarkersOntoNeighbour] [321]
0.8 0.0 [Loop@0x40dce0 at line 54 in concatenateReadStarts] [326]
0.4 0.0 [Loop@0x417200 at line 1098 in remapBackOfNodeMarkersOntoNeighbour] [536]
0.4 0.0 [Loop@0x4165f8 at line 808 in remapNodeMarkersOntoNeighbour] [332]
0.3 0.0 [Loop@0x4170f0 at line 1033 in remapBackOfNodeMarkersOntoNeighbour] [471]
[402] 0.03 7.4 0.0 setShortReadMarkerPosition [402]
1.0 2.7 [Loop@0x419ae0 at line 2246 in comparePaths] [231]
0.9 1.9 [Loop@0x419bb0 at line 2264 in comparePaths] [256]
0.3 0.5 comparePaths [50]
0.0 0.1 remapBackOfNodeMarkersOntoNeighbour [61]
[403] 0.03 2.2 5.2 setPassageMarkerStatus [403]
3.4 0.0 PM_FI2P [500]
1.8 0.0 PM_FI2P [593]
0.6 6.8 remapBackOfNodeMarkersOntoNeighbour [61]
[404] 0.03 0.6 6.8 extractFrontOfNodeReads [404]
2.1 0.0 [Loop@0x4041be at line 3019 in extractFrontOfNodeReads] [562]
0.0 2.1 mallocOrExit3 [67]
1.5 0.2 [Loop@0x404255 at line 3082 in extractFrontOfNodeReads] [595]
0.9 0.0 _int_free [227]
1.7 2.8 addUncertainPassageMarker [202]
0.9 1.4 setMarker [354]
0.1 0.3 extractPassageMarker [368]
0.0 0.2 addPassageMarker [581]
[405] 0.03 2.7 4.7 setTopOfTheNode [405]
4.7 0.0 PM_FI2P [452]
1.0 6.1 remapBackOfNodeMarkersOntoNeighbour [61]
[406] 0.03 1.0 6.1 extractBackOfNodeReads [406]
2.8 0.0 [Loop@0x403eb1 at line 3155 in extractBackOfNodeReads] [529]
1.2 0.8 [Loop@0x403f54 at line 3213 in extractBackOfNodeReads] [566]
0.0 1.2 mallocOrExit3 [67]
0.1 0.0 _int_free [227]
0.0 7.0 comparePaths [50]
[407] 0.03 0.0 7.0 pathContainsReference [407]
0.3 6.5 [Loop@0x415278 at line 2188 in pathContainsReference] [410]
0.0 0.1 getNextInSequence [347]
0.0 0.1 isTerminal [392]
3.0 0.0 deallocateSmallNodeList [306]
1.8 0.0 deallocateSmallNodeList [294]
1.3 0.0 allocateSmallNodeList [167]
0.8 0.0 allocateSmallNodeList [182]
[408] 0.03 6.9 0.0 getRecycleBinInArray [408]
1.4 5.4 [Loop@0x40cf90 at line 436 in fh_consolidate] [211]
[409] 0.03 1.4 5.4 fh_removerootlist [409]
5.4 0.0 fhe_remove [435]
0.3 6.5 pathContainsReference [407]
[410] 0.03 0.3 6.5 [Loop@0x415278 at line 2188 in pathContainsReference] [410]
0.8 1.8 isTerminal [392]
0.0 1.8 [Loop@0x415290 at line 2190 in pathContainsReference] [590]
0.2 0.7 getNode [360]
0.4 0.2 getNextInSequence [347]
0.6 0.0 getMarker [624]
0.0 6.799 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[411] 0.03 0.0 6.799 isPreviousToNode [411]
3.2 3.599 [Loop@0x41990e at line 102 in isPreviousToNode] [412]
3.2 3.599 isPreviousToNode [411]
[412] 0.03 3.2 3.599 [Loop@0x41990e at line 102 in isPreviousToNode] [412]
0.1 3.399 getNodeTime [496]
0.1 0.0 getNodePrevious [1012]
4.4 2.3 [Loop@0x410a59 at line 1797 in usedReads] [375]
[413] 0.03 4.4 2.3 [Loop@0x410b08 at line 1816 in usedReads] [413]
2.2 0.0 getShortReadMarkerAtIndex [243]
0.1 0.0 getShortReadMarkerID [465]
0.8 5.802 [Loop@0x42c2d8 at line 571 in referenceGraphKmers] [302]
[414] 0.02 0.8 5.802 recordKmerOccurence [414]
2.299 0.0 GOMP_critical_end [364]
2.1 0.0 GOMP_critical_start [334]
1.302 0.0 copyKmers [609]
0.1 0.0 [Import thunk GOMP_critical_start] [1026]
3.8 2.8 createPreNodes [51]
[415] 0.02 3.8 2.8 [Loop@0x432ee1 at line 565 in createPreNodes] [415]
2.8 0.0 _IO_getc [53]
4.6 0.0 createPreNodes [51]
0.8 0.0 [Loop@0x432a08 at line 461 in createPreNodes] [128]
0.6 0.0 [Loop@0x42c13c at line 502 in referenceGraphKmers] [251]
0.3 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
0.199 0.0 [Loop@0x42c4a0 at line 543 in referenceGraphKmers] [293]
0.1 0.0 newDescriptor_pg [232]
[416] 0.02 6.599 0.0 [Import thunk _IO_getc] [416]
1.199 5.3 setMarker [354]
[417] 0.02 1.199 5.3 getTwinMarker [417]
5.3 0.0 PM_FI2P [438]
6.4 0.0 getNode [360]
[418] 0.02 6.4 0.0 PM_FI2P [418]
0.5 5.9 exportLongNodeSequence [170]
[419] 0.02 0.5 5.9 [Loop@0x413330 at line 927 in exportLongNodeSequence] [419]
0.1 5.6 velvetFprintf [17]
0.2 0.0 getNucleotideChar [902]
6.299 0.0 dfh_removerootlist [386]
[420] 0.02 6.299 0.0 dfhe_remove [420]
0.0 6.201 fillUpGraph [25]
[421] 0.02 0.0 6.201 createNodeReadStartArrays [421]
0.101 6.1 [Loop@0x403d68 at line 2862 in createNodeReadStartArrays] [422]
0.101 6.1 createNodeReadStartArrays [421]
[422] 0.02 0.101 6.1 [Loop@0x403d68 at line 2862 in createNodeReadStartArrays] [422]
0.2 5.9 mallocOrExit3 [67]
1.9 1.2 deallocatePassageMarker [510]
0.7 0.7 [Loop@0x415a00 at line 1851 in destroyPaths] [320]
0.4 0.6 [Loop@0x415a10 at line 1854 in destroyPaths] [337]
0.1 0.3 destroyPaths [479]
0.1 0.1 [Loop@0x418c40 at line 1860 in destroyPaths] [570]
0.0 0.1 [Loop@0x405100 at line 487 in destroyNode] [738]
[423] 0.02 3.2 3.0 allocArrayFree [423]
3.0 0.0 allocArrayGetElement [519]
0.0 6.1 concatenateStringOfNodes [63]
[424] 0.02 0.0 6.1 reallocateNodeDescriptor [424]
0.0 4.0 callocOrExit3 [221]
0.0 1.6 reallocOrExit4 [564]
0.0 0.5 [Loop@0x408280 at line 708 in reallocateNodeDescriptor] [782]
6.0 0.0 getNextInSequence [347]
[425] 0.02 6.0 0.0 PM_FI2P [425]
0.2 3.1 destroyPreArc_pg [457]
0.5 2.1 destroyPreArc_pg [489]
[426] 0.02 0.7 5.2 removePreArcFromList_pg [426]
0.1 3.4 [Loop@0x43055a at line 453 in removePreArcFromList_pg] [493]
0.8 0.9 getNextPreArc_pg [577]
2.3 3.5 fh_consolidate [195]
[427] 0.02 2.3 3.5 [Loop@0x40d17f at line 408 in fh_consolidate] [427]
1.0 2.3 fh_insertrootlist [507]
0.2 0.0 fh_compare [906]
5.798 0.0 [Loop@0x432de1 at line 554 in createPreNodes] [239]
[428] 0.02 5.798 0.0 getAnnotationLength [428]
5.7 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[429] 0.02 5.7 0.0 setShortReadMarkerPosition [429]
0.2 5.4 [Loop@0x41a20d at line 473 in determineEligibleStartingPoints] [325]
[430] 0.02 0.2 5.4 [Loop@0x41a2b7 at line 489 in determineEligibleStartingPoints] [430]
5.0 0.0 getMultiplicity [346]
0.4 0.0 getNextArc [522]
5.6 0.0 getArcBetweenNodes [314]
[431] 0.02 5.6 0.0 [Loop@0x4052ef at line 337 in getArcBetweenNodes] [431]
1.1 3.3 concatenateTodoLists [461]
1.1 0.0 concatenateTodoLists [606]
[432] 0.02 2.2 3.3 concatenateCommonTodoLists [432]
3.0 0.0 [Loop@0x4157d4 at line 175 in concatenateCommonTodoLists] [520]
0.3 0.0 [Loop@0x41584e at line 191 in concatenateCommonTodoLists] [827]
0.1 5.4 concatenateNodesAndVaccinate [169]
[433] 0.02 0.1 5.4 [Loop@0x418472 at line 1986 in concatenateNodesAndVaccinate] [433]
3.8 1.6 createAnalogousArc [245]
0.1 5.3 [Loop@0x41a4bf at line 2568 in correctGraph] [22]
[434] 0.02 0.1 5.3 nextStartingPoint [434]
2.9 0.0 getNodeStatus [365]
2.4 0.0 getNodeInGraph [47]
5.4 0.0 fh_removerootlist [409]
[435] 0.02 5.4 0.0 fhe_remove [435]
0.3 5.1 remapBackOfNodeOntoNeighbour [55]
[436] 0.02 0.3 5.1 remapBackOfNodeTimesOntoNeighbour [436]
0.0 2.3 remapNodeInwardReferencesOntoNode [550]
2.3 0.0 getNodeTime [551]
0.1 0.2 setNodePrevious [848]
0.2 0.0 getNodeTime [908]
1.0 1.3 remapBackOfNodeOntoNeighbour [55]
0.6 1.3 transferNodeData [376]
1.1 0.1 remapNodeOntoNeighbour [97]
[437] 0.02 2.7 2.7 remapNodeFibHeapReferencesOntoNode [437]
2.2 0.0 getNodeDHeapNode [557]
0.3 0.0 dfh_replacedata [846]
0.1 0.0 getNodeDHeapNode [958]
0.0 0.1 dfh_delete [1020]
5.3 0.0 getTwinMarker [417]
[438] 0.02 5.3 0.0 PM_FI2P [438]
0.1 5.1 remapBackOfNodeArcsOntoNeighbour [313]
[439] 0.02 0.1 5.1 [Loop@0x416c20 at line 859 in remapBackOfNodeArcsOntoNeighbour] [439]
1.5 3.5 createAnalogousArc [245]
0.1 0.0 getNextArc [522]
0.0 5.2 [Loop@0x4263b0 at line 1158 in expandLongNode] [138]
[440] 0.02 0.0 5.2 correctGraphLocally [440]
0.0 4.1 [Loop@0x42ba95 at line 423 in correctGraphLocally] [477]
0.7 0.3 [Loop@0x42bab8 at line 513 in correctGraphLocally] [677]
0.0 0.1 [Loop@0x42bb58 at line 459 in correctGraphLocally] [938]
5.1 0.0 isTerminal [392]
[441] 0.02 5.1 0.0 PM_FI2P [441]
4.7 0.3 createPreArc_pg [36]
[442] 0.02 4.7 0.3 addPreArcToPreNode_pg [442]
0.0 0.3 PREARC_I2P [817]
5.0 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[443] 0.02 5.0 0.0 setShortReadMarkerPosition [443]
0.0 5.0 findLowCoverageRegions [187]
[444] 0.02 0.0 5.0 getShortReadTwinCoords [444]
4.8 0.2 [Loop@0x413093 at line 857 in getShortReadTwinCoords] [445]
4.8 0.2 getShortReadTwinCoords [444]
[445] 0.02 4.8 0.2 [Loop@0x413093 at line 857 in getShortReadTwinCoords] [445]
0.1 0.0 getTwinNode [228]
0.1 0.0 getShortReadMarkerAtIndex [243]
0.3 4.7 [Loop@0x433508 at line 276 in countPreNodes] [296]
[446] 0.02 0.3 4.7 [Loop@0x43367f at line 119 in countPreNodes] [446]
0.5 3.9 getInsertionMarkerPosition [463]
0.3 0.0 getInsertionMarkerPosition [837]
2.3 0.0 unLockNode [145]
1.6 0.0 unLockTwoNodes [181]
0.8 0.0 unLockTwoNodes [92]
0.3 0.0 unLockRead [86]
[447] 0.02 5.0 0.0 [Import thunk omp_unset_lock] [447]
4.6 0.0 createPreNodes [51]
0.3 0.0 newDescriptor_pg [232]
[448] 0.02 4.9 0.0 __ctype_b_loc [448]
2.9 0.0 setNextInNode [395]
2.0 0.0 destroyPassageMarker [244]
[449] 0.02 4.9 0.0 PM_FI2P [449]
0.5 4.3 exportGraph [18]
[450] 0.02 0.5 4.3 sortNodeArcs [450]
3.3 0.0 [Loop@0x4078f0 at line 1824 in sortNodeArcs] [505]
0.7 0.3 arcMergeSort [667]
0.1 4.7 concatenatePreNodes [220]
[451] 0.02 0.1 4.7 [Loop@0x433f15 at line 109 in concatenatePreNodes] [451]
0.3 2.9 createAnalogousPreArc_pg [511]
0.6 0.7 getDestination_pg [484]
0.1 0.1 getNextPreArc_pg [577]
4.7 0.0 setTopOfTheNode [405]
[452] 0.02 4.7 0.0 PM_FI2P [452]
0.0 4.7 exportGraph [18]
[453] 0.02 0.0 4.7 [Loop@0x407cf1 at line 1716 in exportGraph] [453]
3.0 1.7 exportArc [454]
3.0 1.7 [Loop@0x407cf1 at line 1716 in exportGraph] [453]
[454] 0.02 3.0 1.7 exportArc [454]
0.0 1.7 velvetFprintf [17]
0.1 4.6 [Loop@0x41983a at line 143 in isPreviousToNode] [373]
[455] 0.02 0.1 4.6 getNodeTime [455]
4.6 0.0 getNodeID [49]
1.6 0.0 deallocateSmallNodeList [306]
1.5 0.0 deallocateSmallNodeList [294]
1.0 0.0 allocateSmallNodeList [167]
0.4 0.0 allocateSmallNodeList [182]
0.1 0.0 allocArrayArrayAllocate [289]
[456] 0.02 4.6 0.0 [Import thunk omp_get_thread_num] [456]
0.2 4.4 [Loop@0x4306a6 at line 310 in destroyPreNode_pg] [458]
[457] 0.02 0.2 4.4 destroyPreArc_pg [457]
0.2 3.1 removePreArcFromList_pg [426]
0.0 0.9 deallocatePreArc_pg [683]
0.2 0.0 PREARC_FI2P [874]
0.0 4.6 destroyPreNode_pg [356]
[458] 0.02 0.0 4.6 [Loop@0x4306a6 at line 310 in destroyPreNode_pg] [458]
0.2 4.4 destroyPreArc_pg [457]
2.7 0.0 [Loop@0x40e294 at line 205 in concatenateGraph] [103]
0.9 0.0 [Loop@0x40e320 at line 217 in concatenateGraph] [100]
0.4 0.0 [Loop@0x40de14 at line 94 in concatenateStringOfNodes] [534]
0.2 0.0 [Loop@0x40e270 at line 198 in concatenateGraph] [60]
0.2 0.0 getTipLength [515]
0.2 0.0 [Loop@0x4153e7 at line 2435 in getTipLength] [523]
[459] 0.02 4.6 0.0 simpleArcCount [459]
0.1 4.5 destroyNode [276]
[460] 0.02 0.1 4.5 [Loop@0x405080 at line 466 in destroyNode] [460]
4.4 0.1 destroyArc [319]
0.0 4.5 remapNodeArcsOntoTarget [252]
[461] 0.02 0.0 4.5 concatenateTodoLists [461]
1.1 3.3 concatenateCommonTodoLists [432]
0.1 0.0 concatenateTodoListIntoActive [741]
4.5 0.0 createPreArc_pg [36]
[462] 0.02 4.5 0.0 PREARC_FI2P [462]
0.5 3.9 [Loop@0x43367f at line 119 in countPreNodes] [446]
[463] 0.02 0.5 3.9 getInsertionMarkerPosition [463]
2.8 0.0 getStart [143]
1.1 0.0 getFinish [230]
2.5 1.9 dfh_consolidate [108]
[464] 0.02 2.5 1.9 [Loop@0x41aeff at line 311 in dfh_consolidate] [464]
0.3 1.2 dfh_insertrootlist [618]
0.4 0.0 dfh_compare [799]
0.9 0.0 [Loop@0x414f6d at line 1193 in removeNodeAndDenounceDubiousReads] [323]
0.8 0.0 [Loop@0x4275b0 at line 358 in computeReadToNodeCounts.omp_fn.0] [116]
0.8 0.0 [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort] [71]
0.6 0.0 [Loop@0x429963 at line 1429 in projectFromNode] [90]
0.4 0.0 [Loop@0x42715e at line 1678 in countShortReads] [253]
0.4 0.0 projectFromShortRead [93]
0.2 0.0 [Loop@0x414fe5 at line 1204 in removeNodeAndDenounceDubiousReads] [573]
0.1 0.0 [Loop@0x412b20 at line 444 in printShortCounts] [316]
0.1 0.0 [Loop@0x410b70 at line 1824 in usedReads] [542]
0.1 0.0 [Loop@0x410b08 at line 1816 in usedReads] [413]
[465] 0.02 4.4 0.0 getShortReadMarkerID [465]
2.2 0.0 [Loop@0x42df3f at line 1101 in fillUpGraph.omp_fn.3] [9]
2.1 0.0 [Loop@0x42ccd5 at line 1141 in fillUpGraph.omp_fn.4] [6]
[466] 0.02 4.3 0.0 isSecondInPair [466]
4.201 0.0 [Loop@0x4038e6 at line 3339 in spreadReadIDs] [329]
[467] 0.02 4.201 0.0 setShortReadMarkerOffset [467]
0.8 3.4 appendDescriptors [317]
[468] 0.02 0.8 3.4 mergeDescriptors [468]
0.0 2.4 callocOrExit3 [221]
0.7 0.0 [Loop@0x406201 at line 744 in mergeDescriptors] [724]
0.3 0.0 [Loop@0x40626a at line 762 in mergeDescriptors] [822]
4.2 0.0 setPreviousInSequence [389]
[469] 0.02 4.2 0.0 PM_FI2P [469]
4.1 0.0 _IO_vfprintf [19]
0.1 0.0 qsort_r [43]
[470] 0.02 4.2 0.0 [Import thunk free] [470]
3.1 1.0 remapBackOfNodeMarkersOntoNeighbour [61]
[471] 0.02 3.1 1.0 [Loop@0x4170f0 at line 1033 in remapBackOfNodeMarkersOntoNeighbour] [471]
0.4 0.0 getShortReadMarkerAtIndex [243]
0.3 0.0 setShortReadMarkerPosition [402]
0.3 0.0 getShortReadMarkerPosition [260]
4.1 0.0 getPreArcBetweenPreNodes_pg [39]
[472] 0.02 4.1 0.0 getNextPreArc_pg [472]
4.1 0.0 getNextPreArc_pg [235]
[473] 0.02 4.1 0.0 PREARC_FI2P [473]
0.6 3.5 remapNodeTimesOntoNeighbour [475]
[474] 0.02 0.6 3.5 remapNodeTimesOntoTargetNode [474]
0.0 2.2 remapNodeInwardReferencesOntoNode [555]
0.8 0.0 getNodeTime [715]
0.4 0.0 getNodePrevious [790]
0.0 0.1 isPreviousToNode [975]
0.0 4.1 remapNodeOntoNeighbour [97]
[475] 0.02 0.0 4.1 remapNodeTimesOntoNeighbour [475]
0.6 3.5 remapNodeTimesOntoTargetNode [474]
0.0 4.1 [Loop@0x42ba95 at line 423 in correctGraphLocally] [477]
[476] 0.02 0.0 4.1 clipTipsVeryHardLocally [476]
0.3 3.8 [Loop@0x42bdb5 at line 396 in clipTipsVeryHardLocally] [478]
0.0 4.1 correctGraphLocally [440]
[477] 0.02 0.0 4.1 [Loop@0x42ba95 at line 423 in correctGraphLocally] [477]
0.0 4.1 clipTipsVeryHardLocally [476]
0.3 3.8 clipTipsVeryHardLocally [476]
[478] 0.02 0.3 3.8 [Loop@0x42bdb5 at line 396 in clipTipsVeryHardLocally] [478]
0.0 1.9 isLocalDeadEnd [582]
0.3 0.8 isLocalTwinDeadEnd [657]
0.8 0.0 getNodeStatus [365]
0.1 2.0 cleanUpRedundancy [40]
0.0 2.0 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
[479] 0.02 0.1 4.0 destroyPaths [479]
0.0 2.0 [Loop@0x418c40 at line 1860 in destroyPaths] [570]
0.1 1.4 destroyPassageMarker [244]
0.1 0.3 allocArrayFree [423]
0.1 0.0 getNextInSequence [347]
4.0 0.0 fh_insertrootlist [265]
[480] 0.02 4.0 0.0 fhe_insertafter [480]
0.1 3.9 exportGraph [18]
[481] 0.02 0.1 3.9 [Loop@0x407c80 at line 1987 in exportGraph] [481]
1.0 2.9 exportArc [485]
4.0 0.0 qsort_r [43]
[482] 0.02 4.0 0.0 compareKmerOccurences [482]
3.999 0.0 getArcBetweenNodes [179]
[483] 0.02 3.999 0.0 [Loop@0x4027d3 at line 337 in getArcBetweenNodes] [483]
0.3 1.0 [Loop@0x433e80 at line 83 in concatenatePreNodes] [543]
0.6 0.7 [Loop@0x433f15 at line 109 in concatenatePreNodes] [451]
0.0 0.5 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
0.2 0.2 [Loop@0x433f90 at line 123 in concatenatePreNodes] [358]
0.2 0.1 [Loop@0x433bd2 at line 195 in isEligibleTip] [387]
0.0 0.1 concatenatePreNodes [220]
[484] 0.01 1.3 2.6 getDestination_pg [484]
2.6 0.0 PREARC_FI2P [537]
1.0 2.9 [Loop@0x407c80 at line 1987 in exportGraph] [481]
[485] 0.01 1.0 2.9 exportArc [485]
0.1 2.8 velvetFprintf [17]
0.0 3.9 [Loop@0x41816a at line 1975 in simplifyNode] [155]
[486] 0.01 0.0 3.9 [Loop@0x418340 at line 112 in simplifyNode] [486]
0.2 3.7 transferNodeData [376]
0.0 2.9 concatenatePreNodes [220]
0.2 0.7 [Loop@0x433e80 at line 83 in concatenatePreNodes] [543]
0.0 0.1 [Loop@0x4340b8 at line 94 in concatenatePreNodes] [918]
[487] 0.01 0.2 3.7 appendDescriptors_pg [487]
0.8 2.3 appendPositiveDescriptor_pg [517]
0.2 0.4 appendNegativeDescriptor_pg [748]
0.0 3.8 destroyPreNode_pg [356]
[488] 0.01 0.0 3.8 [Loop@0x430640 at line 310 in destroyPreNode_pg] [488]
0.3 3.5 destroyPreArc_pg [489]
0.3 3.5 [Loop@0x430640 at line 310 in destroyPreNode_pg] [488]
[489] 0.01 0.3 3.5 destroyPreArc_pg [489]
0.5 2.1 removePreArcFromList_pg [426]
0.0 0.6 deallocatePreArc_pg [746]
0.3 0.0 PREARC_FI2P [832]
3.4 0.0 [Loop@0x432390 at line 705 in connectAnnotation] [34]
0.2 0.0 convertInsertionMarkers [269]
[490] 0.01 3.6 0.0 getFinishID [490]
0.0 3.6 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
[491] 0.01 0.0 3.6 markerLeadsToNode [491]
0.0 3.6 [Loop@0x418ad8 at line 1896 in markerLeadsToNode] [492]
0.0 3.6 markerLeadsToNode [491]
[492] 0.01 0.0 3.6 [Loop@0x418ad8 at line 1896 in markerLeadsToNode] [492]
0.9 1.5 getNode [360]
0.5 0.7 getNextInSequence [347]
0.1 3.4 removePreArcFromList_pg [426]
[493] 0.01 0.1 3.4 [Loop@0x43055a at line 453 in removePreArcFromList_pg] [493]
2.0 0.7 getNextPreArc_pg [531]
0.2 0.5 getNextPreArc_pg [732]
0.1 3.4 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
[494] 0.01 0.1 3.4 directlyAppendDescriptors [494]
0.0 1.9 [Loop@0x407f3b at line 548 in directlyAppendDescriptors] [579]
0.0 1.4 [Loop@0x408074 at line 548 in directlyAppendDescriptors] [622]
0.1 0.0 getNodeLength [1002]
3.5 0.0 commonNodeReads [173]
[495] 0.01 3.5 0.0 [Loop@0x403ce8 at line 3006 in commonNodeReads] [495]
0.1 3.399 [Loop@0x41990e at line 102 in isPreviousToNode] [412]
[496] 0.01 0.1 3.399 getNodeTime [496]
3.399 0.0 getNodeID [49]
1.3 0.0 destroyNode [276]
0.8 0.0 injectShortReads [41]
0.7 0.0 [Loop@0x42f690 at line 374 in destroyPreGraph_pg] [642]
0.4 0.0 destroyPreNode_pg [356]
0.2 0.0 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
[497] 0.01 3.4 0.0 free [497]
3.4 0.0 [Loop@0x41cd0e at line 1568 in importReadSet] [183]
[498] 0.01 3.4 0.0 [Loop@0x41cd15 at line 1580 in importReadSet] [498]
1.4 2.0 newTightStringArrayFromStringArray [199]
[499] 0.01 1.4 2.0 [Loop@0x402310 at line 144 in newTightStringArrayFromStringArray] [499]
2.0 0.0 __strlen_sse42 [569]
3.4 0.0 setPassageMarkerStatus [403]
[500] 0.01 3.4 0.0 PM_FI2P [500]
0.0 2.6 appendGap [502]
0.1 0.7 [Loop@0x408554 at line 548 in appendGap] [699]
[501] 0.01 0.1 3.3 addBufferToDescriptor [501]
0.0 2.4 callocOrExit3 [221]
0.4 0.0 writeNucleotideInDescriptor [786]
0.3 0.0 getNucleotideInDescriptor [851]
0.0 0.2 reallocOrExit4 [564]
0.0 3.4 pushNeighbours [142]
[502] 0.01 0.0 3.4 appendGap [502]
0.0 2.6 addBufferToDescriptor [501]
0.0 0.8 [Loop@0x408554 at line 548 in appendGap] [699]
3.4 0.0 createPreNodes [51]
[503] 0.01 3.4 0.0 [Import thunk __ctype_b_loc] [503]
3.4 0.0 destroyPassageMarker [244]
[504] 0.01 3.4 0.0 PM_FI2P [504]
3.3 0.0 sortNodeArcs [450]
[505] 0.01 3.3 0.0 [Loop@0x4078f0 at line 1824 in sortNodeArcs] [505]
3.3 0.0 commonNodeReads [173]
[506] 0.01 3.3 0.0 [Loop@0x403ca0 at line 2997 in commonNodeReads] [506]
1.0 2.3 [Loop@0x40d17f at line 408 in fh_consolidate] [427]
[507] 0.01 1.0 2.3 fh_insertrootlist [507]
2.3 0.0 fhe_insertafter [552]
2.4 0.0 [Loop@0x43428c at line 242 in clipTips_pg] [331]
0.8 0.0 [Loop@0x434140 at line 142 in concatenatePreGraph_pg] [159]
[508] 0.01 3.2 0.0 getPreNodeInPreGraph_pg [508]
0.2 3.0 exportGraph [18]
[509] 0.01 0.2 3.0 sortNodeArcs [509]
1.9 0.0 [Loop@0x407a30 at line 1824 in sortNodeArcs] [574]
0.4 0.7 arcMergeSort [659]
0.1 3.1 destroyPassageMarker [244]
[510] 0.01 0.1 3.1 deallocatePassageMarker [510]
1.9 1.2 allocArrayFree [423]
0.3 2.9 [Loop@0x433f15 at line 109 in concatenatePreNodes] [451]
[511] 0.01 0.3 2.9 createAnalogousPreArc_pg [511]
1.7 0.1 addPreArcToPreNode_pg [591]
0.0 0.4 allocatePreArc_pg [805]
0.3 0.0 PREARC_FI2P [826]
0.0 0.3 [Loop@0x431bd1 at line 488 in createAnalogousPreArc_pg] [859]
0.1 0.0 PREARC_FI2P [960]
0.0 3.2 [Loop@0x4261eb at line 131 in expandLongNode] [513]
[512] 0.01 0.0 3.2 markInterestingNodes [512]
0.2 2.4 integrateDerivativeDistances [514]
0.1 0.1 resetMiniConnection [913]
0.1 0.0 getConnectionDestination [665]
0.1 0.0 getTwinNode [228]
0.1 0.0 getNodeID [49]
0.1 0.0 readjustMiniConnection [1031]
0.0 3.2 expandLongNode [136]
[513] 0.01 0.0 3.2 [Loop@0x4261eb at line 131 in expandLongNode] [513]
0.0 3.2 markInterestingNodes [512]
0.2 2.4 markInterestingNodes [512]
0.0 0.6 [Loop@0x4247ed at line 374 in absorbExtensionInScaffold] [678]
[514] 0.01 0.2 3.0 integrateDerivativeDistances [514]
0.4 2.5 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
0.1 0.0 getConnection [932]
0.0 3.1 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
[515] 0.01 0.0 3.1 getTipLength [515]
0.0 2.9 [Loop@0x4153e7 at line 2435 in getTipLength] [523]
0.2 0.0 simpleArcCount [459]
0.0 3.1 concatenateGraph [59]
[516] 0.01 0.0 3.1 renumberNodes [516]
2.9 0.0 [Loop@0x404760 at line 1139 in renumberNodes] [524]
0.2 0.0 [Loop@0x404868 at line 1183 in renumberNodes] [893]
0.8 2.3 appendDescriptors_pg [487]
[517] 0.01 0.8 2.3 appendPositiveDescriptor_pg [517]
2.1 0.0 [Loop@0x42fb19 at line 1321 in appendPositiveDescriptor_pg] [563]
0.2 0.0 getPreNodeInPreGraph_pg [926]
0.0 3.0 concatenateStringOfNodes [63]
[518] 0.01 0.0 3.0 [Loop@0x40e1e4 at line 180 in concatenateStringOfNodes] [518]
0.1 2.2 destroyNode [276]
0.7 0.0 getDestination [248]
3.0 0.0 allocArrayFree [423]
[519] 0.01 3.0 0.0 allocArrayGetElement [519]
3.0 0.0 concatenateCommonTodoLists [432]
[520] 0.01 3.0 0.0 [Loop@0x4157d4 at line 175 in concatenateCommonTodoLists] [520]
3.0 0.0 [Loop@0x41ad60 at line 414 in dfh_consolidate] [113]
[521] 0.01 3.0 0.0 dfh_compare [521]
0.899 0.0 initializeTodoLists [267]
0.7 0.0 [Loop@0x41a240 at line 479 in determineEligibleStartingPoints] [398]
0.5 0.0 [Loop@0x41a990 at line 445 in updateNodeStatus] [352]
0.4 0.0 [Loop@0x41a2b7 at line 489 in determineEligibleStartingPoints] [430]
0.2 0.0 [Loop@0x4160ce at line 1200 in remapNodeInwardReferencesOntoNode] [556]
0.1 0.0 [Loop@0x416c20 at line 859 in remapBackOfNodeArcsOntoNeighbour] [439]
0.1 0.0 transferNodeData [376]
0.1 0.0 [Loop@0x416b53 at line 1200 in remapNodeInwardReferencesOntoNode] [549]
[522] 0.01 2.999 0.0 getNextArc [522]
0.0 2.9 getTipLength [515]
[523] 0.01 0.0 2.9 [Loop@0x4153e7 at line 2435 in getTipLength] [523]
1.5 0.0 getDestination [248]
1.2 0.0 getTwinNode [228]
0.2 0.0 simpleArcCount [459]
2.9 0.0 renumberNodes [516]
[524] 0.01 2.9 0.0 [Loop@0x404760 at line 1139 in renumberNodes] [524]
0.1 2.8 main [14]
[525] 0.01 0.1 2.8 destroyPreGraph_pg [525]
0.0 1.6 destroyAllocArrayArray [604]
0.0 1.2 [Loop@0x42f690 at line 374 in destroyPreGraph_pg] [642]
0.1 2.8 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
[526] 0.01 0.1 2.8 mapDistancesOntoPaths [526]
0.1 1.8 [Loop@0x4189db at line 1881 in mapDistancesOntoPaths] [575]
0.1 0.8 [Loop@0x41898d at line 1872 in mapDistancesOntoPaths] [689]
0.1 2.2 [Loop@0x41a20d at line 473 in determineEligibleStartingPoints] [325]
0.0 0.5 [Loop@0x41a990 at line 445 in updateNodeStatus] [352]
0.0 0.1 [Loop@0x41237e at line 1019 in n50] [1013]
[527] 0.01 0.1 2.8 fh_insertkey [527]
0.0 2.6 fhe_newelem [541]
0.2 0.0 fh_insertel [925]
0.4 2.5 integrateDerivativeDistances [514]
[528] 0.01 0.4 2.5 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
0.9 0.0 getConnectionDestination [665]
0.7 0.0 getNodeID [49]
0.4 0.0 getTwinNode [228]
0.0 0.2 resetMiniConnection [922]
0.2 0.0 getConnectionDistance [927]
0.1 0.0 readjustMiniConnection [987]
2.8 0.0 extractBackOfNodeReads [406]
[529] 0.01 2.8 0.0 [Loop@0x403eb1 at line 3155 in extractBackOfNodeReads] [529]
2.7 0.0 exportPreNode_pg [150]
[530] 0.01 2.7 0.0 getNucleotideInDescriptor_pg [530]
2.0 0.7 [Loop@0x43055a at line 453 in removePreArcFromList_pg] [493]
[531] 0.01 2.0 0.7 getNextPreArc_pg [531]
0.7 0.0 PREARC_FI2P [730]
1.6 1.1 getSequenceLengths [533]
[532] 0.01 1.6 1.1 [Loop@0x41bce8 at line 1729 in getSequenceLengths] [532]
0.9 0.0 getLength [381]
0.2 0.0 getTightStringInArray [722]
0.0 1.4 main [14]
0.0 1.3 buildScaffold [141]
[533] 0.01 0.0 2.7 getSequenceLengths [533]
1.6 1.1 [Loop@0x41bce8 at line 1729 in getSequenceLengths] [532]
0.0 2.7 concatenateStringOfNodes [63]
[534] 0.01 0.0 2.7 [Loop@0x40de14 at line 94 in concatenateStringOfNodes] [534]
1.4 0.0 getDestination [248]
0.9 0.0 getTwinNode [228]
0.4 0.0 simpleArcCount [459]
2.7 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[535] 0.01 2.7 0.0 setShortReadMarkerPosition [535]
1.1 1.599 remapBackOfNodeMarkersOntoNeighbour [61]
[536] 0.01 1.1 1.599 [Loop@0x417200 at line 1098 in remapBackOfNodeMarkersOntoNeighbour] [536]
0.699 0.0 getShortReadMarkerPosition [260]
0.5 0.0 getShortReadMarkerAtIndex [243]
0.4 0.0 setShortReadMarkerPosition [402]
2.6 0.0 getDestination_pg [484]
[537] 0.01 2.6 0.0 PREARC_FI2P [537]
2.6 0.0 main [14]
[538] 0.01 2.6 0.0 _IO_fclose [538]
0.0 1.4 fillUpGraph [25]
0.0 1.2 correctGraph [15]
[539] 0.01 0.0 2.6 resetNodeStatus [539]
2.6 0.0 [Loop@0x402980 at line 620 in resetNodeStatus] [540]
2.6 0.0 resetNodeStatus [539]
[540] 0.01 2.6 0.0 [Loop@0x402980 at line 620 in resetNodeStatus] [540]
0.0 2.6 fh_insertkey [527]
[541] 0.01 0.0 2.6 fhe_newelem [541]
2.0 0.0 fhe_initelem [567]
0.0 0.6 allocateFibHeapEl [761]
2.2 0.3 [Loop@0x410a59 at line 1797 in usedReads] [375]
[542] 0.01 2.2 0.3 [Loop@0x410b70 at line 1824 in usedReads] [542]
0.2 0.0 getShortReadMarkerAtIndex [243]
0.1 0.0 getShortReadMarkerID [465]
0.0 2.5 concatenatePreNodes [220]
[543] 0.01 0.0 2.5 [Loop@0x433e80 at line 83 in concatenatePreNodes] [543]
0.3 1.0 getDestination_pg [484]
0.2 0.7 appendDescriptors_pg [487]
0.3 0.0 getPreArc_pg [559]
2.4 0.0 addReadStart [56]
[544] 0.01 2.4 0.0 getNodeID [544]
0.2 2.2 setNextInNode [395]
[545] 0.01 0.2 2.2 getTwinMarker [545]
2.2 0.0 PM_FI2P [554]
0.5 1.3 [Loop@0x415290 at line 2190 in pathContainsReference] [590]
0.2 0.1 [Loop@0x41852a at line 2001 in concatenateNodesAndVaccinate] [568]
0.0 0.2 remapBackOfNodeMarkersOntoNeighbour [61]
0.1 0.0 [Loop@0x4184e0 at line 1994 in concatenateNodesAndVaccinate] [909]
[546] 0.01 0.8 1.6 getNextInNode [546]
1.6 0.0 PM_FI2P [607]
2.1 0.0 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.2 0.0 tourBusNode [31]
[547] 0.01 2.3 0.0 _IO_fflush [547]
2.3 0.0 reversePushNucleotide [114]
[548] 0.01 2.3 0.0 shiftRight [548]
1.5 0.8 remapNodeInwardReferencesOntoNode [550]
[549] 0.01 1.5 0.8 [Loop@0x416b53 at line 1200 in remapNodeInwardReferencesOntoNode] [549]
0.0 0.4 getNodePrevious [804]
0.2 0.0 getDestination [248]
0.1 0.0 setNodePrevious [941]
0.1 0.0 getNextArc [522]
0.0 2.3 remapBackOfNodeTimesOntoNeighbour [436]
[550] 0.01 0.0 2.3 remapNodeInwardReferencesOntoNode [550]
1.5 0.8 [Loop@0x416b53 at line 1200 in remapNodeInwardReferencesOntoNode] [549]
2.3 0.0 remapBackOfNodeTimesOntoNeighbour [436]
[551] 0.01 2.3 0.0 getNodeTime [551]
2.3 0.0 fh_insertrootlist [507]
[552] 0.01 2.3 0.0 fhe_insertafter [552]
2.299 0.0 destroyPassageMarker [244]
[553] 0.01 2.299 0.0 PM_FI2P [553]
2.2 0.0 getTwinMarker [545]
[554] 0.01 2.2 0.0 PM_FI2P [554]
0.0 2.2 remapNodeTimesOntoTargetNode [474]
[555] 0.01 0.0 2.2 remapNodeInwardReferencesOntoNode [555]
0.2 2.0 [Loop@0x4160ce at line 1200 in remapNodeInwardReferencesOntoNode] [556]
0.2 2.0 remapNodeInwardReferencesOntoNode [555]
[556] 0.01 0.2 2.0 [Loop@0x4160ce at line 1200 in remapNodeInwardReferencesOntoNode] [556]
0.8 0.0 getDestination [248]
0.4 0.1 setNodePrevious [773]
0.0 0.5 getNodePrevious [779]
0.2 0.0 getNextArc [522]
2.2 0.0 remapNodeFibHeapReferencesOntoNode [437]
[557] 0.01 2.2 0.0 getNodeDHeapNode [557]
2.2 0.0 [Loop@0x41ce48 at line 1599 in importReadSet] [204]
[558] 0.01 2.2 0.0 __strncpy_ssse3 [558]
0.7 0.0 isEligibleTip [359]
0.6 0.0 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
0.3 0.0 [Loop@0x433e80 at line 83 in concatenatePreNodes] [543]
0.2 0.0 [Loop@0x434140 at line 142 in concatenatePreGraph_pg] [159]
0.1 0.0 [Loop@0x433f90 at line 123 in concatenatePreNodes] [358]
0.1 0.0 [Loop@0x4340b8 at line 94 in concatenatePreNodes] [918]
0.1 0.0 [Loop@0x434154 at line 146 in concatenatePreGraph_pg] [188]
[559] 0.01 2.1 0.0 getPreArc_pg [559]
2.1 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[560] 0.01 2.1 0.0 setShortReadMarkerPosition [560]
1.5 0.6 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[561] 0.01 1.5 0.6 getNodeTime [561]
0.4 0.0 nodeCount [580]
0.2 0.0 getNodeID [49]
2.1 0.0 extractFrontOfNodeReads [404]
[562] 0.01 2.1 0.0 [Loop@0x4041be at line 3019 in extractFrontOfNodeReads] [562]
2.1 0.0 appendPositiveDescriptor_pg [517]
[563] 0.01 2.1 0.0 [Loop@0x42fb19 at line 1321 in appendPositiveDescriptor_pg] [563]
0.0 1.6 reallocateNodeDescriptor [424]
0.0 0.3 setTightStringLength [791]
0.0 0.2 addBufferToDescriptor [501]
[564] 0.01 0.0 2.1 reallocOrExit4 [564]
2.0 0.0 __libc_realloc [572]
0.1 0.0 [Import thunk realloc] [963]
0.0 2.0 exportLongNodeSequence [170]
[565] 0.01 0.0 2.0 expandNode [565]
0.0 1.8 newTightString [586]
0.0 0.2 [Loop@0x405ea6 at line 2681 in expandNode] [905]
1.2 0.8 extractBackOfNodeReads [406]
[566] 0.01 1.2 0.8 [Loop@0x403f54 at line 3213 in extractBackOfNodeReads] [566]
0.3 0.0 setShortReadMarkerPosition [845]
0.2 0.0 setShortReadMarkerOffset [914]
0.2 0.0 setShortReadMarkerPosition [917]
0.1 0.0 setShortReadMarkerOffset [978]
2.0 0.0 fhe_newelem [541]
[567] 0.01 2.0 0.0 fhe_initelem [567]
0.0 2.0 concatenateNodesAndVaccinate [169]
[568] 0.01 0.0 2.0 [Loop@0x41852a at line 2001 in concatenateNodesAndVaccinate] [568]
0.0 1.1 disconnectNextPassageMarker [656]
0.0 0.5 getPreviousInSequence [658]
0.2 0.1 getNextInNode [546]
0.0 0.1 isInitial [812]
2.0 0.0 [Loop@0x402310 at line 144 in newTightStringArrayFromStringArray] [499]
[569] 0.01 2.0 0.0 __strlen_sse42 [569]
0.0 2.0 destroyPaths [479]
[570] 0.01 0.0 2.0 [Loop@0x418c40 at line 1860 in destroyPaths] [570]
0.4 1.3 destroyPassageMarker [244]
0.1 0.1 allocArrayFree [423]
0.1 0.0 getNextInSequence [347]
2.0 0.0 [Loop@0x4076f4 at line 548 in exportNode] [324]
[571] 0.01 2.0 0.0 getNucleotideInDescriptor [571]
2.0 0.0 reallocOrExit4 [564]
[572] 0.01 2.0 0.0 __libc_realloc [572]
1.7 0.2 removeNodeAndDenounceDubiousReads [238]
[573] 0.01 1.7 0.2 [Loop@0x414fe5 at line 1204 in removeNodeAndDenounceDubiousReads] [573]
0.2 0.0 getShortReadMarkerID [465]
1.9 0.0 sortNodeArcs [509]
[574] 0.01 1.9 0.0 [Loop@0x407a30 at line 1824 in sortNodeArcs] [574]
0.1 1.8 mapDistancesOntoPaths [526]
[575] 0.01 0.1 1.8 [Loop@0x4189db at line 1881 in mapDistancesOntoPaths] [575]
0.3 0.4 setPassageMarkerFinish [645]
0.3 0.2 getNextInSequence [347]
0.1 0.3 getNode [360]
0.0 0.1 setPassageMarkerStart [768]
0.0 0.1 isTerminal [392]
1.9 0.0 dfh_insertrootlist [129]
[576] 0.01 1.9 0.0 dfhe_insertafter [576]
0.8 0.9 removePreArcFromList_pg [426]
0.1 0.1 [Loop@0x433f15 at line 109 in concatenatePreNodes] [451]
[577] 0.01 0.9 1.0 getNextPreArc_pg [577]
1.0 0.0 PREARC_FI2P [672]
0.0 1.9 [Loop@0x407f3b at line 548 in directlyAppendDescriptors] [579]
[578] 0.01 0.0 1.9 catDescriptors [578]
1.3 0.0 getNucleotideInDescriptor [634]
0.6 0.0 writeNucleotideInDescriptor [740]
0.0 1.9 directlyAppendDescriptors [494]
[579] 0.01 0.0 1.9 [Loop@0x407f3b at line 548 in directlyAppendDescriptors] [579]
0.0 1.9 catDescriptors [578]
0.5 0.0 getNodeTime [137]
0.4 0.0 getNodeTime [561]
0.3 0.0 getNodeTime [619]
0.2 0.0 [Loop@0x415aa4 at line 2456 in clipTipsHard] [246]
0.2 0.0 setNodePrevious [848]
0.1 0.0 [Loop@0x40e270 at line 198 in concatenateGraph] [60]
0.1 0.0 getNodePrevious [363]
0.1 0.0 findOrCreateConnection [257]
[580] 0.01 1.9 0.0 nodeCount [580]
0.0 1.9 remapBackOfNodeMarkersOntoNeighbour [61]
[581] 0.01 0.0 1.9 addPassageMarker [581]
0.2 0.5 setNextInNode [395]
0.1 0.5 setMarker [354]
0.0 0.2 setTopOfTheNode [405]
0.1 0.1 allocatePassageMarker [910]
0.1 0.0 PM_FI2P [952]
0.1 0.0 PM_FI2P [1016]
0.0 1.9 [Loop@0x42bdb5 at line 396 in clipTipsVeryHardLocally] [478]
[582] 0.01 0.0 1.9 isLocalDeadEnd [582]
0.0 1.9 [Loop@0x42be0b at line 396 in isLocalDeadEnd] [583]
0.0 1.9 isLocalDeadEnd [582]
[583] 0.01 0.0 1.9 [Loop@0x42be0b at line 396 in isLocalDeadEnd] [583]
1.0 0.0 getNodeStatus [365]
0.9 0.0 getDestination [248]
0.9 0.0 [Loop@0x432de1 at line 554 in createPreNodes] [239]
0.6 0.0 [Loop@0x433611 at line 309 in countPreNodes] [598]
0.3 0.0 [Loop@0x433570 at line 287 in countPreNodes] [345]
0.1 0.0 [Loop@0x432bfd at line 506 in createPreNodes] [164]
[584] 0.01 1.9 0.0 getPosition [584]
0.502 1.3 findOrCreateConnection [257]
[585] 0.01 0.502 1.3 allocateConnection [585]
0.8 0.0 [libgomp.so.1.0.0] [94]
0.4 0.0 GOMP_critical_end [364]
0.1 0.0 allocatePointer [109]
0.0 1.8 expandNode [565]
[586] 0.01 0.0 1.8 newTightString [586]
0.0 1.8 callocOrExit3 [221]
0.0 1.8 remapBackOfNodeOntoNeighbour [55]
[587] 0.01 0.0 1.8 remapBackOfNodeDescriptorOntoNeighbour [587]
0.1 1.7 splitNodeDescriptor [588]
0.1 1.7 remapBackOfNodeDescriptorOntoNeighbour [587]
[588] 0.01 0.1 1.7 splitNodeDescriptor [588]
0.2 1.4 [Loop@0x4096a1 at line 548 in splitNodeDescriptor] [602]
0.0 0.1 [Loop@0x4097c8 at line 548 in splitNodeDescriptor] [992]
0.0 1.8 buildScaffold [141]
[589] 0.01 0.0 1.8 estimateMissingInsertLengths [589]
0.0 1.0 [Loop@0x426b58 at line 631 in estimateMissingInsertLengths] [680]
0.0 0.8 [Loop@0x4269dc at line 566 in estimateMissingInsertLengths] [691]
0.0 1.8 [Loop@0x415278 at line 2188 in pathContainsReference] [410]
[590] 0.01 0.0 1.8 [Loop@0x415290 at line 2190 in pathContainsReference] [590]
0.5 1.3 getNextInNode [546]
1.7 0.1 createAnalogousPreArc_pg [511]
[591] 0.01 1.7 0.1 addPreArcToPreNode_pg [591]
0.0 0.1 PREARC_I2P [1018]
0.2 0.6 [Loop@0x4341ba at line 165 in concatenatePreGraph_pg] [327]
0.2 0.6 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
0.2 0.0 [Loop@0x434154 at line 146 in concatenatePreGraph_pg] [188]
[592] 0.01 0.6 1.2 getOtherEnd_pg [592]
1.2 0.0 PREARC_FI2P [648]
1.8 0.0 setPassageMarkerStatus [403]
[593] 0.01 1.8 0.0 PM_FI2P [593]
1.1 0.699 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[594] 0.01 1.1 0.699 getNodePrevious [594]
0.699 0.0 getNodeID [49]
1.5 0.2 extractFrontOfNodeReads [404]
[595] 0.01 1.5 0.2 [Loop@0x404255 at line 3082 in extractFrontOfNodeReads] [595]
0.1 0.0 setShortReadMarkerOffset [951]
0.1 0.0 setShortReadMarkerOffset [1032]
1.7 0.0 [Loop@0x4333d6 at line 222 in setInsertionMarkers] [197]
[596] 0.01 1.7 0.0 incrementAnnotationCoordinates [596]
0.2 1.5 sortKmerOccurenceTable [105]
[597] 0.01 0.2 1.5 [Loop@0x435df8 at line 63 in sortKmerOccurenceTable] [597]
0.0 1.4 keyInAccelerationTable [623]
0.1 0.0 [Loop@0x435e50 at line 185 in sortKmerOccurenceTable] [996]
0.8 0.9 [Loop@0x433570 at line 287 in countPreNodes] [345]
[598] 0.01 0.8 0.9 [Loop@0x433611 at line 309 in countPreNodes] [598]
0.6 0.0 getPosition [584]
0.3 0.0 getNextAnnotation [682]
1.7 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[599] 0.01 1.7 0.0 setShortReadMarkerOffset [599]
0.9 0.0 connectAnnotation [30]
0.8 0.0 convertInsertionMarkers [269]
[600] 0.01 1.7 0.0 getStartID [600]
0.4 1.2 exportNode [210]
[601] 0.01 0.4 1.2 [Loop@0x4077b7 at line 548 in exportNode] [601]
1.2 0.0 getNucleotideInDescriptor [644]
0.2 1.4 splitNodeDescriptor [588]
[602] 0.01 0.2 1.4 [Loop@0x4096a1 at line 548 in splitNodeDescriptor] [602]
0.8 0.0 getNucleotideInDescriptor [710]
0.6 0.0 writeNucleotideInDescriptor [747]
0.0 1.6 main [14]
[603] 0.01 0.0 1.6 destroyGraph [603]
0.0 1.5 destroyRecycleBin [615]
0.0 0.1 [Loop@0x4051c0 at line 3792 in destroyGraph] [934]
0.0 1.6 destroyPreGraph_pg [525]
[604] 0.01 0.0 1.6 destroyAllocArrayArray [604]
0.0 1.6 [Loop@0x436210 at line 242 in destroyAllocArrayArray] [605]
0.0 1.6 destroyAllocArrayArray [604]
[605] 0.01 0.0 1.6 [Loop@0x436210 at line 242 in destroyAllocArrayArray] [605]
1.6 0.0 _int_free [227]
0.0 1.6 transferNodeData [376]
[606] 0.01 0.0 1.6 concatenateTodoLists [606]
1.1 0.0 concatenateCommonTodoLists [432]
0.5 0.0 concatenateTodoListIntoActive [741]
1.6 0.0 getNextInNode [546]
[607] 0.01 1.6 0.0 PM_FI2P [607]
1.599 0.0 destroyPassageMarker [244]
[608] 0.01 1.599 0.0 PM_FI2P [608]
1.302 0.0 recordKmerOccurence [414]
0.2 0.0 newDescriptor_pg [232]
[609] 0.01 1.502 0.0 copyKmers [609]
0.4 0.5 deallocatePreArc_pg [683]
0.3 0.3 deallocatePreArc_pg [746]
[610] 0.01 0.7 0.8 allocArrayArrayFree [610]
0.8 0.0 allocArrayGetElement [702]
1.5 0.0 extractPassageMarker [368]
[611] 0.01 1.5 0.0 PM_FI2P [611]
1.5 0.0 setPreviousInSequence [389]
[612] 0.01 1.5 0.0 PM_FI2P [612]
0.0 1.5 destroyRecycleBin [615]
[613] 0.01 0.0 1.5 [Loop@0x41b8cb at line 96 in destroyRecycleBin] [613]
0.1 1.4 destroyRecycleBinChunks [614]
0.1 1.4 [Loop@0x41b8cb at line 96 in destroyRecycleBin] [613]
[614] 0.01 0.1 1.4 destroyRecycleBinChunks [614]
1.4 0.0 _int_free [227]
0.0 1.5 destroyGraph [603]
[615] 0.01 0.0 1.5 destroyRecycleBin [615]
0.0 1.5 [Loop@0x41b8cb at line 96 in destroyRecycleBin] [613]
0.3 0.6 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
0.3 0.3 remapBackOfNodeMarkersOntoNeighbour [61]
[616] 0.01 0.6 0.9 getPassageMarkerFinish [616]
0.6 0.0 PM_FI2P [757]
0.3 0.0 PM_FI2P [844]
0.0 1.5 createConnection [162]
[617] 0.01 0.0 1.5 createTwinConnectionInTree [617]
0.3 1.2 findOrCreateConnection [257]
0.3 1.2 [Loop@0x41aeff at line 311 in dfh_consolidate] [464]
[618] 0.01 0.3 1.2 dfh_insertrootlist [618]
1.2 0.0 dfhe_insertafter [647]
1.2 0.3 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[619] 0.01 1.2 0.3 getNodeTime [619]
0.3 0.0 nodeCount [580]
0.7 0.0 allocatePassageMarker [713]
0.7 0.0 allocatePassageMarker [720]
0.1 0.0 allocatePassageMarker [910]
[620] 0.01 1.5 0.0 allocArrayAllocate [620]
0.0 1.4 [Loop@0x408074 at line 548 in directlyAppendDescriptors] [622]
[621] 0.01 0.0 1.4 reverseCatDescriptors [621]
1.3 0.0 getNucleotideInDescriptor [630]
0.1 0.0 writeNucleotideInDescriptor [1017]
0.0 1.4 directlyAppendDescriptors [494]
[622] 0.01 0.0 1.4 [Loop@0x408074 at line 548 in directlyAppendDescriptors] [622]
0.0 1.4 reverseCatDescriptors [621]
0.0 1.4 [Loop@0x435df8 at line 63 in sortKmerOccurenceTable] [597]
[623] 0.01 0.0 1.4 keyInAccelerationTable [623]
1.4 0.0 getKmerKey [174]
0.6 0.0 [Loop@0x415278 at line 2188 in pathContainsReference] [410]
0.4 0.0 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
0.2 0.0 addUncertainPassageMarker [202]
0.1 0.0 [Loop@0x4276f0 at line 373 in computeReadToNodeCounts] [986]
0.1 0.0 computePartialReadToNodeMappingLong [984]
[624] 0.01 1.4 0.0 getMarker [624]
0.0 1.4 [Loop@0x42a990 at line 1814 in buildScaffold] [626]
[625] 0.01 0.0 1.4 [Loop@0x42a9b5 at line 1701 in buildScaffold] [625]
0.2 1.2 removeUnreliableConnections [250]
0.0 1.4 buildScaffold [141]
[626] 0.01 0.0 1.4 [Loop@0x42a990 at line 1814 in buildScaffold] [626]
0.0 1.4 [Loop@0x42a9b5 at line 1701 in buildScaffold] [625]
0.5 0.8 injectShortReads [41]
[627] 0.0 0.5 0.8 [Loop@0x403610 at line 3776 in injectShortReads] [627]
0.6 0.0 setShortReadMarkerPosition [745]
0.2 0.0 setShortReadMarkerOffset [870]
1.3 0.0 [Loop@0x403bad at line 2959 in commonNodeReads] [193]
[628] 0.0 1.3 0.0 compareIDnums [628]
0.4 0.9 tourBusArc [33]
[629] 0.0 0.4 0.9 dfh_replacekey [629]
0.1 0.8 dfh_replacekeydata [684]
1.3 0.0 reverseCatDescriptors [621]
[630] 0.0 1.3 0.0 getNucleotideInDescriptor [630]
1.3 0.0 [Loop@0x41ce48 at line 1599 in importReadSet] [204]
[631] 0.0 1.3 0.0 [Loop@0x41ce71 at line 1612 in importReadSet] [631]
0.6 0.5 [Loop@0x405f5e at line 548 in appendNodeSequence] [348]
0.1 0.1 [Loop@0x405ea6 at line 2681 in expandNode] [905]
[632] 0.0 0.7 0.6 writeNucleotideAtPosition [632]
0.6 0.0 writeNucleotideNumber [750]
1.3 0.0 velvetFprintf [17]
[633] 0.0 1.3 0.0 [Import thunk vfprintf] [633]
1.3 0.0 catDescriptors [578]
[634] 0.0 1.3 0.0 getNucleotideInDescriptor [634]
1.201 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[635] 0.0 1.201 0.0 setShortReadMarkerOffset [635]
0.0 1.2 clone [1]
[636] 0.0 0.0 1.2 computeNodeToNodeMappings.omp_fn.5 [636]
0.0 1.2 [Loop@0x428420 at line 1093 in computeNodeToNodeMappings.omp_fn.5] [637]
0.0 1.2 computeNodeToNodeMappings.omp_fn.5 [636]
[637] 0.0 0.0 1.2 [Loop@0x428420 at line 1093 in computeNodeToNodeMappings.omp_fn.5] [637]
0.0 1.2 splayToList [638]
0.0 1.2 [Loop@0x428420 at line 1093 in computeNodeToNodeMappings.omp_fn.5] [637]
[638] 0.0 0.0 1.2 splayToList [638]
0.0 1.2 [Loop@0x428450 at line 1096 in splayToList] [639]
0.0 1.2 splayToList [638]
[639] 0.0 0.0 1.2 [Loop@0x428450 at line 1096 in splayToList] [639]
0.6 0.5 [Loop@0x428475 at line 1043 in splayToList] [653]
0.0 0.1 pushConnectionStack [939]
0.0 1.2 transferNodeData [376]
[640] 0.0 0.0 1.2 getNodePrevious [640]
1.2 0.0 getNodeID [49]
1.2 0.0 destroyArc [319]
[641] 0.0 1.2 0.0 [Loop@0x404f40 at line 438 in destroyArc] [641]
0.0 1.2 destroyPreGraph_pg [525]
[642] 0.0 0.0 1.2 [Loop@0x42f690 at line 374 in destroyPreGraph_pg] [642]
0.7 0.0 free [497]
0.5 0.0 _int_free [227]
0.2 1.0 sortKmerOccurenceTable [105]
[643] 0.0 0.2 1.0 [Loop@0x435f4b at line 157 in sortKmerOccurenceTable] [643]
0.1 0.9 compareKmerOccurences [674]
1.2 0.0 [Loop@0x4077b7 at line 548 in exportNode] [601]
[644] 0.0 1.2 0.0 getNucleotideInDescriptor [644]
0.3 0.4 [Loop@0x4189db at line 1881 in mapDistancesOntoPaths] [575]
0.2 0.2 remapBackOfNodeMarkersOntoNeighbour [61]
0.0 0.1 [Loop@0x41898d at line 1872 in mapDistancesOntoPaths] [689]
[645] 0.0 0.5 0.7 setPassageMarkerFinish [645]
0.5 0.0 PM_FI2P [776]
0.2 0.0 PM_FI2P [881]
0.1 1.1 removeUnreliableConnections [250]
[646] 0.0 0.1 1.1 testConnection [646]
0.0 1.0 expectedNumberOfConnections [675]
0.1 0.0 getUniqueness [760]
1.2 0.0 dfh_insertrootlist [618]
[647] 0.0 1.2 0.0 dfhe_insertafter [647]
1.2 0.0 getOtherEnd_pg [592]
[648] 0.0 1.2 0.0 PREARC_FI2P [648]
0.0 1.2 [Loop@0x433570 at line 287 in countPreNodes] [345]
[649] 0.0 0.0 1.2 getInsertionMarkerPosition [649]
0.8 0.0 getStart [143]
0.4 0.0 getFinish [230]
1.2 0.0 [Loop@0x4286e4 at line 882 in splayConnection] [312]
[650] 0.0 1.2 0.0 connectionSingleRotateWithLeft [650]
0.0 1.2 pushNeighbours [142]
[651] 0.0 0.0 1.2 absorbExtensionInScaffold [651]
0.2 0.8 [Loop@0x4247ed at line 374 in absorbExtensionInScaffold] [678]
0.1 0.1 [Loop@0x424ad3 at line 131 in absorbExtensionInScaffold] [890]
0.5 0.7 [Loop@0x42fd7d at line 1015 in newDescriptor_pg] [391]
[652] 0.0 0.5 0.7 popNucleotide [652]
0.7 0.0 shiftRight [737]
0.6 0.5 [Loop@0x428450 at line 1096 in splayToList] [639]
[653] 0.0 0.6 0.5 [Loop@0x428475 at line 1043 in splayToList] [653]
0.0 0.3 popConnectionStack [814]
0.0 0.2 pushConnectionStack [865]
1.1 0.0 allocateReadToNodeTables [655]
[654] 0.0 1.1 0.0 [Loop@0x427878 at line 423 in allocateReadToNodeTables] [654]
0.0 1.1 computeReadToNodeMappings [274]
[655] 0.0 0.0 1.1 allocateReadToNodeTables [655]
1.1 0.0 [Loop@0x427878 at line 423 in allocateReadToNodeTables] [654]
0.0 1.1 [Loop@0x41852a at line 2001 in concatenateNodesAndVaccinate] [568]
[656] 0.0 0.0 1.1 disconnectNextPassageMarker [656]
0.0 0.4 setPreviousInSequence [793]
0.2 0.0 getNextInSequence [872]
0.0 0.2 concatenatePassageMarkers [873]
0.0 0.2 getNextInSequence [883]
0.1 0.0 setPreviousInSequence [1004]
0.3 0.8 [Loop@0x42bdb5 at line 396 in clipTipsVeryHardLocally] [478]
[657] 0.0 0.3 0.8 isLocalTwinDeadEnd [657]
0.0 0.8 [Loop@0x42be4c at line 407 in isLocalTwinDeadEnd] [698]
0.3 0.3 remapBackOfNodeMarkersOntoNeighbour [61]
0.0 0.5 [Loop@0x41852a at line 2001 in concatenateNodesAndVaccinate] [568]
[658] 0.0 0.3 0.8 getPreviousInSequence [658]
0.4 0.0 PM_FI2P [800]
0.2 0.0 PM_FI2P [894]
0.2 0.0 PM_FI2P [916]
0.4 0.7 sortNodeArcs [509]
[659] 0.0 0.4 0.7 arcMergeSort [659]
0.4 0.1 arcMergeSort [781]
0.2 0.0 mergeArcLists [869]
0.0 1.1 markerLeadsToNode [661]
[660] 0.0 0.0 1.1 [Loop@0x418ab0 at line 1896 in markerLeadsToNode] [660]
0.3 0.4 getNode [360]
0.4 0.0 getNextInSequence [347]
0.0 1.1 [Loop@0x418a48 at line 2093 in cleanUpRedundancy] [46]
[661] 0.0 0.0 1.1 markerLeadsToNode [661]
0.0 1.1 [Loop@0x418ab0 at line 1896 in markerLeadsToNode] [660]
0.4 0.0 [Loop@0x43428c at line 242 in clipTips_pg] [331]
0.3 0.0 chooseNextInternalPreNode [739]
0.3 0.0 chooseNextInternalPreNode [717]
0.1 0.0 [Loop@0x434140 at line 142 in concatenatePreGraph_pg] [159]
[662] 0.0 1.1 0.0 preNodeCount_pg [662]
1.1 0.0 transferNodeData [376]
[663] 0.0 1.1 0.0 setNodePrevious [663]
1.1 0.0 newDescriptor_pg [232]
[664] 0.0 1.1 0.0 writeNucleotideInDescriptor_pg [664]
0.9 0.0 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
0.1 0.0 markInterestingNodes [512]
0.1 0.0 [Loop@0x4247ed at line 374 in absorbExtensionInScaffold] [678]
[665] 0.0 1.1 0.0 getConnectionDestination [665]
1.099 0.0 destroyPassageMarker [244]
[666] 0.0 1.099 0.0 PM_FI2P [666]
0.7 0.3 sortNodeArcs [450]
[667] 0.0 0.7 0.3 arcMergeSort [667]
0.3 0.0 mergeArcLists [820]
0.3 0.7 spreadReadIDs [304]
[668] 0.0 0.3 0.7 [Loop@0x403978 at line 3743 in spreadReadIDs] [668]
0.4 0.0 setShortReadMarkerPosition [795]
0.3 0.0 setShortReadMarkerOffset [821]
1.0 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[669] 0.0 1.0 0.0 setShortReadMarkerOffset [669]
0.2 0.8 connectPassageMarkers [378]
[670] 0.0 0.2 0.8 setNextInSequence [670]
0.8 0.0 PM_FI2P [704]
1.0 0.0 addUncertainPassageMarker [202]
[671] 0.0 1.0 0.0 PM_FI2P [671]
1.0 0.0 getNextPreArc_pg [577]
[672] 0.0 1.0 0.0 PREARC_FI2P [672]
0.2 0.8 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
[673] 0.0 0.2 0.8 mapSlowOntoFast [673]
0.5 0.3 [Loop@0x419340 at line 636 in mapSlowOntoFast] [708]
0.1 0.9 [Loop@0x435f4b at line 157 in sortKmerOccurenceTable] [643]
[674] 0.0 0.1 0.9 compareKmerOccurences [674]
0.9 0.0 compareKmers [4]
0.0 1.0 testConnection [646]
[675] 0.0 0.0 1.0 expectedNumberOfConnections [675]
0.1 0.3 norm [802]
0.0 0.3 norm [854]
0.0 0.1 normInt [972]
0.0 0.1 normInt [1003]
0.0 0.1 norm [1008]
0.1 0.9 remapBackOfNodeMarkersOntoNeighbour [61]
[676] 0.0 0.1 0.9 getStartOffset [676]
0.8 0.0 PM_FI2P [703]
0.1 0.0 PM_FI2P [979]
0.7 0.3 correctGraphLocally [440]
[677] 0.0 0.7 0.3 [Loop@0x42bab8 at line 513 in correctGraphLocally] [677]
0.3 0.0 getNodeID [49]
0.2 0.8 absorbExtensionInScaffold [651]
[678] 0.0 0.2 0.8 [Loop@0x4247ed at line 374 in absorbExtensionInScaffold] [678]
0.0 0.6 integrateDerivativeDistances [514]
0.0 0.1 createNewConnection [990]
0.1 0.0 getConnectionDestination [665]
0.9 0.1 [Loop@0x426b58 at line 631 in estimateMissingInsertLengths] [680]
[679] 0.0 0.9 0.1 measureCoOccurences [679]
0.1 0.0 sequenceCount [831]
0.0 1.0 estimateMissingInsertLengths [589]
[680] 0.0 0.0 1.0 [Loop@0x426b58 at line 631 in estimateMissingInsertLengths] [680]
0.9 0.1 measureCoOccurences [679]
0.4 0.0 [Loop@0x4321b0 at line 867 in connectPreNodes.omp_fn.2] [27]
0.3 0.0 [Loop@0x433508 at line 276 in countPreNodes] [296]
0.1 0.0 [Loop@0x4333ac at line 214 in setInsertionMarkers] [196]
0.1 0.0 [Loop@0x4332b7 at line 177 in setInsertionMarkers] [357]
[681] 0.0 0.9 0.0 getAnnotationCount [681]
0.4 0.0 [Loop@0x432de1 at line 554 in createPreNodes] [239]
0.3 0.0 [Loop@0x433611 at line 309 in countPreNodes] [598]
0.2 0.0 [Loop@0x432270 at line 699 in connectPreNodes.omp_fn.2] [28]
[682] 0.0 0.9 0.0 getNextAnnotation [682]
0.0 0.9 destroyPreArc_pg [457]
[683] 0.0 0.0 0.9 deallocatePreArc_pg [683]
0.4 0.5 allocArrayArrayFree [610]
0.1 0.8 dfh_replacekey [629]
[684] 0.0 0.1 0.8 dfh_replacekeydata [684]
0.7 0.0 dfh_compare [725]
0.0 0.1 [Loop@0x41b327 at line 436 in dfh_replacekeydata] [948]
0.9 0.0 [Loop@0x4286e4 at line 882 in splayConnection] [312]
[685] 0.0 0.9 0.0 connectionSingleRotateWithRight [685]
0.9 0.0 destroyArc [319]
[686] 0.0 0.9 0.0 [Loop@0x404f80 at line 453 in destroyArc] [686]
0.3 0.0 lockTwoNodes [75]
0.3 0.0 lockRead [237]
0.1 0.0 lockTwoNodes [58]
0.1 0.0 lockNode [80]
0.1 0.0 lockTwoNodes [281]
[687] 0.0 0.9 0.0 [Import thunk omp_set_lock] [687]
0.6 0.0 concatenateReadStarts [77]
0.3 0.0 remapNodeMarkersOntoNeighbour [104]
[688] 0.0 0.9 0.0 getNodeReads [688]
0.1 0.8 mapDistancesOntoPaths [526]
[689] 0.0 0.1 0.8 [Loop@0x41898d at line 1872 in mapDistancesOntoPaths] [689]
0.0 0.3 setPassageMarkerStart [768]
0.2 0.0 isTerminal [392]
0.0 0.2 getNextInSequence [347]
0.0 0.1 setPassageMarkerFinish [645]
0.0 0.9 remapBackOfNodeMarkersOntoNeighbour [61]
[690] 0.0 0.0 0.9 setPreviousInSequence [690]
0.4 0.0 PM_FI2P [803]
0.3 0.0 PM_FI2P [847]
0.2 0.0 PM_FI2P [896]
0.0 0.8 estimateMissingInsertLengths [589]
[691] 0.0 0.0 0.8 [Loop@0x4269dc at line 566 in estimateMissingInsertLengths] [691]
0.5 0.3 countCoOccurences [692]
0.5 0.3 [Loop@0x4269dc at line 566 in estimateMissingInsertLengths] [691]
[692] 0.0 0.5 0.3 countCoOccurences [692]
0.3 0.0 getInsertLength [721]
0.0 0.8 findLowCoverageRegions [187]
[693] 0.0 0.0 0.8 lowCoverageRegions [693]
0.7 0.1 [Loop@0x413535 at line 748 in lowCoverageRegions] [694]
0.7 0.1 lowCoverageRegions [693]
[694] 0.0 0.7 0.1 [Loop@0x413535 at line 748 in lowCoverageRegions] [694]
0.1 0.0 newMask [933]
0.1 0.7 unmarkInterestingNodes [696]
[695] 0.0 0.1 0.7 [Loop@0x426498 at line 1105 in unmarkInterestingNodes] [695]
0.2 0.2 popNodeRecord [807]
0.3 0.0 setSingleNodeStatus [818]
0.0 0.8 expandLongNode [136]
[696] 0.0 0.0 0.8 unmarkInterestingNodes [696]
0.1 0.7 [Loop@0x426498 at line 1105 in unmarkInterestingNodes] [695]
0.8 0.0 getNextPreArc_pg [396]
[697] 0.0 0.8 0.0 PREARC_FI2P [697]
0.0 0.8 isLocalTwinDeadEnd [657]
[698] 0.0 0.0 0.8 [Loop@0x42be4c at line 407 in isLocalTwinDeadEnd] [698]
0.6 0.0 getTwinNode [228]
0.2 0.0 getDestination [248]
0.0 0.8 appendGap [502]
[699] 0.0 0.0 0.8 [Loop@0x408554 at line 548 in appendGap] [699]
0.1 0.7 addBufferToDescriptor [501]
0.2 0.6 [Loop@0x432cb2 at line 119 in createPreNodes] [355]
[700] 0.0 0.2 0.6 convertMarker [700]
0.5 0.0 setFinishID [744]
0.1 0.0 setStartID [928]
0.8 0.0 correctGraph [15]
[701] 0.0 0.8 0.0 [Loop@0x41a04d at line 2541 in correctGraph] [701]
0.8 0.0 allocArrayArrayFree [610]
[702] 0.0 0.8 0.0 allocArrayGetElement [702]
0.8 0.0 getStartOffset [676]
[703] 0.0 0.8 0.0 PM_FI2P [703]
0.8 0.0 setNextInSequence [670]
[704] 0.0 0.8 0.0 PM_FI2P [704]
0.0 0.8 removeHighCoverageNodes [706]
[705] 0.0 0.0 0.8 [Loop@0x4138d2 at line 1419 in removeHighCoverageNodes] [705]
0.0 0.6 destroyNode [276]
0.2 0.0 getNodeLength [148]
0.0 0.8 main [14]
[706] 0.0 0.0 0.8 removeHighCoverageNodes [706]
0.0 0.8 [Loop@0x4138d2 at line 1419 in removeHighCoverageNodes] [705]
0.5 0.0 concatenateReadStarts [77]
0.2 0.0 remapNodeMarkersOntoNeighbour [104]
0.1 0.0 removeNodeAndDenounceDubiousReads [238]
[707] 0.0 0.8 0.0 getNodeReadCount [707]
0.5 0.3 mapSlowOntoFast [673]
[708] 0.0 0.5 0.3 [Loop@0x419340 at line 636 in mapSlowOntoFast] [708]
0.3 0.0 getNucleotide [107]
0.0 0.8 concatenateNodesAndVaccinate [169]
[709] 0.0 0.0 0.8 [Loop@0x418439 at line 1976 in concatenateNodesAndVaccinate] [709]
0.5 0.3 destroyArc [319]
0.8 0.0 [Loop@0x4096a1 at line 548 in splitNodeDescriptor] [602]
[710] 0.0 0.8 0.0 getNucleotideInDescriptor [710]
0.7 0.1 tourBusNode [31]
[711] 0.0 0.7 0.1 getNodeTime [711]
0.1 0.0 getNodeID [49]
0.0 0.8 remapNodeMarkersOntoNeighbour [104]
[712] 0.0 0.0 0.8 [Loop@0x416264 at line 718 in remapNodeMarkersOntoNeighbour] [712]
0.0 0.7 transposePassageMarker [728]
0.0 0.1 isInitial [812]
0.1 0.7 addUncertainPassageMarker [202]
[713] 0.0 0.1 0.7 allocatePassageMarker [713]
0.7 0.0 allocArrayAllocate [620]
0.8 0.0 setPreviousInSequence [389]
[714] 0.0 0.8 0.0 PM_FI2P [714]
0.8 0.0 remapNodeTimesOntoTargetNode [474]
[715] 0.0 0.8 0.0 getNodeTime [715]
0.8 0.0 updatePreArcData_pg [377]
[716] 0.0 0.8 0.0 PREARC_FI2P [716]
0.5 0.3 [Loop@0x4321b0 at line 867 in connectPreNodes.omp_fn.2] [27]
[717] 0.0 0.5 0.3 chooseNextInternalPreNode [717]
0.3 0.0 preNodeCount_pg [662]
0.8 0.0 mergeDescriptors [343]
[718] 0.0 0.8 0.0 [Loop@0x406123 at line 762 in mergeDescriptors] [718]
0.6 0.2 [Loop@0x432faa at line 602 in createPreNodes] [303]
[719] 0.0 0.6 0.2 convertMarker [719]
0.1 0.0 setFinishID [744]
0.1 0.0 setStartID [928]
0.1 0.7 addUncertainPassageMarker [202]
[720] 0.0 0.1 0.7 allocatePassageMarker [720]
0.7 0.0 allocArrayAllocate [620]
0.4 0.0 projectFromShortRead [93]
0.3 0.0 countCoOccurences [692]
[721] 0.0 0.7 0.0 getInsertLength [721]
0.5 0.0 [Loop@0x42df3f at line 1101 in fillUpGraph.omp_fn.3] [9]
0.2 0.0 [Loop@0x41bce8 at line 1729 in getSequenceLengths] [532]
[722] 0.0 0.7 0.0 getTightStringInArray [722]
0.7 0.0 fh_consolidate [195]
[723] 0.0 0.7 0.0 [Loop@0x40cf50 at line 443 in fh_consolidate] [723]
0.7 0.0 mergeDescriptors [468]
[724] 0.0 0.7 0.0 [Loop@0x406201 at line 744 in mergeDescriptors] [724]
0.7 0.0 dfh_replacekeydata [684]
[725] 0.0 0.7 0.0 dfh_compare [725]
0.7 0.0 [Loop@0x432faa at line 602 in createPreNodes] [303]
[726] 0.0 0.7 0.0 getInsertionMarkerPosition [726]
0.5 0.0 threadSequenceThroughGraph [7]
0.2 0.0 [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph] [12]
[727] 0.0 0.7 0.0 getWordLength [727]
0.0 0.7 [Loop@0x416264 at line 718 in remapNodeMarkersOntoNeighbour] [712]
[728] 0.0 0.0 0.7 transposePassageMarker [728]
0.0 0.7 insertPassageMarker [729]
0.0 0.7 transposePassageMarker [728]
[729] 0.0 0.0 0.7 insertPassageMarker [729]
0.4 0.3 setNextInNode [395]
0.7 0.0 getNextPreArc_pg [531]
[730] 0.0 0.7 0.0 PREARC_FI2P [730]
0.7 0.0 connectPreNodes [99]
[731] 0.0 0.7 0.0 [Loop@0x4338dc at line 846 in connectPreNodes] [731]
0.2 0.5 [Loop@0x43055a at line 453 in removePreArcFromList_pg] [493]
[732] 0.0 0.2 0.5 getNextPreArc_pg [732]
0.5 0.0 PREARC_FI2P [774]
0.1 0.6 remapBackOfNodeMarkersOntoNeighbour [61]
[733] 0.0 0.1 0.6 setStartOffset [733]
0.5 0.0 PM_FI2P [780]
0.1 0.0 PM_FI2P [1001]
0.1 0.6 [Loop@0x43023c at line 900 in renumberPreNodes_pg] [353]
[734] 0.0 0.1 0.6 getNextPreArc_pg [734]
0.6 0.0 PREARC_FI2P [758]
0.3 0.0 norm [802]
0.3 0.0 norm [854]
0.1 0.0 norm [1008]
[735] 0.0 0.7 0.0 exp [735]
0.7 0.0 addUncertainPassageMarker [202]
[736] 0.0 0.7 0.0 PM_FI2P [736]
0.7 0.0 popNucleotide [652]
[737] 0.0 0.7 0.0 shiftRight [737]
0.0 0.699 destroyNode [276]
[738] 0.0 0.0 0.699 [Loop@0x405100 at line 487 in destroyNode] [738]
0.0 0.599 destroyPassageMarker [244]
0.0 0.1 allocArrayFree [423]
0.2 0.4 [Loop@0x43227f at line 891 in connectPreNodes.omp_fn.2] [307]
[739] 0.0 0.2 0.4 chooseNextInternalPreNode [739]
0.3 0.0 preNodeCount_pg [662]
0.1 0.0 sequenceCount_pg [794]
0.6 0.0 catDescriptors [578]
[740] 0.0 0.6 0.0 writeNucleotideInDescriptor [740]
0.5 0.0 concatenateTodoLists [606]
0.1 0.0 concatenateTodoLists [461]
[741] 0.0 0.6 0.0 concatenateTodoListIntoActive [741]
0.0 0.6 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[742] 0.0 0.0 0.6 [Loop@0x419a70 at line 112 in comparePaths] [742]
0.3 0.3 getNodePrevious [743]
0.3 0.3 [Loop@0x419a70 at line 112 in comparePaths] [742]
[743] 0.0 0.3 0.3 getNodePrevious [743]
0.3 0.0 getNodeID [49]
0.5 0.0 convertMarker [700]
0.1 0.0 convertMarker [719]
[744] 0.0 0.6 0.0 setFinishID [744]
0.6 0.0 [Loop@0x403610 at line 3776 in injectShortReads] [627]
[745] 0.0 0.6 0.0 setShortReadMarkerPosition [745]
0.0 0.6 destroyPreArc_pg [489]
[746] 0.0 0.0 0.6 deallocatePreArc_pg [746]
0.3 0.3 allocArrayArrayFree [610]
0.6 0.0 [Loop@0x4096a1 at line 548 in splitNodeDescriptor] [602]
[747] 0.0 0.6 0.0 writeNucleotideInDescriptor [747]
0.2 0.4 appendDescriptors_pg [487]
[748] 0.0 0.2 0.4 appendNegativeDescriptor_pg [748]
0.4 0.0 [Loop@0x42fc13 at line 1355 in appendNegativeDescriptor_pg] [787]
0.6 0.0 [Loop@0x4038e6 at line 3339 in spreadReadIDs] [329]
[749] 0.0 0.6 0.0 setShortReadMarkerOffset [749]
0.6 0.0 writeNucleotideAtPosition [632]
[750] 0.0 0.6 0.0 writeNucleotideNumber [750]
0.6 0.0 getPassageMarkerStart [752]
[751] 0.0 0.6 0.0 PM_FI2P [751]
0.0 0.5 remapBackOfNodeMarkersOntoNeighbour [61]
0.0 0.1 remapNodeMarkersOntoNeighbour [104]
[752] 0.0 0.0 0.6 getPassageMarkerStart [752]
0.6 0.0 PM_FI2P [751]
0.0 0.6 main [14]
[753] 0.0 0.0 0.6 createReadPairingArray [753]
0.4 0.0 [Loop@0x41c05c at line 1385 in createReadPairingArray] [796]
0.2 0.0 [Loop@0x41c020 at line 1380 in createReadPairingArray] [892]
0.3 0.0 concatenateNodesAndVaccinate [169]
0.2 0.0 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
0.1 0.0 remapNodeMarkersOntoNeighbour [104]
[754] 0.0 0.6 0.0 mergeNodeReads [754]
0.6 0.0 updatePreArcData_pg [369]
[755] 0.0 0.6 0.0 PREARC_FI2P [755]
0.2 0.4 [Loop@0x4196cb at line 2210 in comparePaths] [69]
[756] 0.0 0.2 0.4 [Loop@0x419a30 at line 112 in comparePaths] [756]
0.1 0.3 getNodePrevious [808]
0.6 0.0 getPassageMarkerFinish [616]
[757] 0.0 0.6 0.0 PM_FI2P [757]
0.6 0.0 getNextPreArc_pg [734]
[758] 0.0 0.6 0.0 PREARC_FI2P [758]
0.2 0.0 [Loop@0x42f110 at line 127 in importRoadMapArray] [157]
0.2 0.0 [Loop@0x41cd0e at line 1568 in importReadSet] [183]
0.2 0.0 [Loop@0x42f1e8 at line 154 in importRoadMapArray] [76]
[759] 0.0 0.6 0.0 [Import thunk __isoc99_sscanf] [759]
0.2 0.0 createConnection [162]
0.1 0.0 projectFromNode [87]
0.1 0.0 testConnection [646]
0.1 0.0 expandLongNodes [133]
0.1 0.0 [Loop@0x40ded8 at line 109 in concatenateStringOfNodes] [64]
[760] 0.0 0.6 0.0 getUniqueness [760]
0.0 0.6 fhe_newelem [541]
[761] 0.0 0.0 0.6 allocateFibHeapEl [761]
0.0 0.6 allocatePointer [109]
0.0 0.6 [Loop@0x40a990 at line 2309 in readPreGraphFile] [213]
[762] 0.0 0.0 0.6 addEmptyNodeToGraph [762]
0.4 0.2 emptyNode [763]
0.4 0.2 addEmptyNodeToGraph [762]
[763] 0.0 0.4 0.2 emptyNode [763]
0.0 0.2 allocateNode [885]
0.0 0.501 clone [1]
[764] 0.0 0.0 0.501 createNodeLocks.omp_fn.1 [764]
0.1 0.401 [Loop@0x432040 at line 63 in createNodeLocks.omp_fn.1] [766]
0.401 0.0 [Loop@0x432040 at line 63 in createNodeLocks.omp_fn.1] [766]
0.1 0.0 [Loop@0x42c6f0 at line 72 in createNodeLocks.omp_fn.2] [867]
[765] 0.0 0.501 0.0 omp_init_lock [765]
0.1 0.401 createNodeLocks.omp_fn.1 [764]
[766] 0.0 0.1 0.401 [Loop@0x432040 at line 63 in createNodeLocks.omp_fn.1] [766]
0.401 0.0 omp_init_lock [765]
0.2 0.0 [Loop@0x41cce8 at line 1564 in importReadSet] [121]
0.1 0.0 [Loop@0x42f1e8 at line 154 in importRoadMapArray] [76]
0.1 0.0 [Loop@0x42f110 at line 127 in importRoadMapArray] [157]
0.1 0.0 [Loop@0x432bfd at line 430 in createPreNodes] [119]
[767] 0.0 0.5 0.0 [Import thunk fgets] [767]
0.0 0.3 [Loop@0x41898d at line 1872 in mapDistancesOntoPaths] [689]
0.1 0.0 remapBackOfNodeMarkersOntoNeighbour [61]
0.0 0.1 [Loop@0x4189db at line 1881 in mapDistancesOntoPaths] [575]
[768] 0.0 0.1 0.4 setPassageMarkerStart [768]
0.4 0.0 PM_FI2P [806]
0.5 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[769] 0.0 0.5 0.0 min_short [769]
0.0 0.5 tourBusNode [31]
[770] 0.0 0.0 0.5 freeDoneTickets [770]
0.5 0.0 [Loop@0x41a910 at line 427 in freeDoneTickets] [771]
0.5 0.0 freeDoneTickets [770]
[771] 0.0 0.5 0.0 [Loop@0x41a910 at line 427 in freeDoneTickets] [771]
0.5 0.0 createPreArc_pg [36]
[772] 0.0 0.5 0.0 addPreArcToPreNode_pg [772]
0.4 0.1 [Loop@0x4160ce at line 1200 in remapNodeInwardReferencesOntoNode] [556]
[773] 0.0 0.4 0.1 setNodePrevious [773]
0.1 0.0 getNodeID [49]
0.5 0.0 getNextPreArc_pg [732]
[774] 0.0 0.5 0.0 PREARC_FI2P [774]
0.5 0.0 setInsertionMarkers [139]
[775] 0.0 0.5 0.0 [Loop@0x433373 at line 205 in setInsertionMarkers] [775]
0.5 0.0 setPassageMarkerFinish [645]
[776] 0.0 0.5 0.0 PM_FI2P [776]
0.5 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
[777] 0.0 0.5 0.0 writeNucleotideInDescriptor [777]
0.0 0.5 concatenateStringOfNodes [63]
[778] 0.0 0.0 0.5 [Loop@0x40e17c at line 170 in concatenateStringOfNodes] [778]
0.3 0.0 getDestination [248]
0.1 0.1 createAnalogousArc [245]
0.0 0.5 [Loop@0x4160ce at line 1200 in remapNodeInwardReferencesOntoNode] [556]
[779] 0.0 0.0 0.5 getNodePrevious [779]
0.5 0.0 getNodeID [49]
0.5 0.0 setStartOffset [733]
[780] 0.0 0.5 0.0 PM_FI2P [780]
0.4 0.1 arcMergeSort [659]
[781] 0.0 0.4 0.1 arcMergeSort [781]
0.1 0.0 arcMergeSort [1007]
0.0 0.5 reallocateNodeDescriptor [424]
[782] 0.0 0.0 0.5 [Loop@0x408280 at line 708 in reallocateNodeDescriptor] [782]
0.4 0.0 writeNucleotideInDescriptor [809]
0.1 0.0 getNucleotideInDescriptor [969]
0.4 0.1 threadSequenceThroughGraph [7]
[783] 0.0 0.4 0.1 blurLastShortReadMarker [783]
0.1 0.0 setShortReadMarkerPosition [945]
0.1 0.4 tourBusArc [33]
[784] 0.0 0.1 0.4 dfh_insertkey [784]
0.2 0.1 dfhe_newelem [862]
0.0 0.1 dfh_insertel [961]
0.4 0.0 exportGraph [18]
[785] 0.0 0.4 0.0 [Loop@0x407b90 at line 1995 in exportGraph] [785]
0.4 0.0 addBufferToDescriptor [501]
[786] 0.0 0.4 0.0 writeNucleotideInDescriptor [786]
0.4 0.0 appendNegativeDescriptor_pg [748]
[787] 0.0 0.4 0.0 [Loop@0x42fc13 at line 1355 in appendNegativeDescriptor_pg] [787]
0.4 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[788] 0.0 0.4 0.0 min [788]
0.1 0.3 [Loop@0x419ae0 at line 2246 in comparePaths] [231]
[789] 0.0 0.1 0.3 getNodePrevious [789]
0.3 0.0 getNodeID [49]
0.4 0.0 remapNodeTimesOntoTargetNode [474]
[790] 0.0 0.4 0.0 getNodePrevious [790]
0.1 0.3 extractSequence [258]
[791] 0.0 0.1 0.3 setTightStringLength [791]
0.0 0.3 reallocOrExit4 [564]
0.1 0.3 [Loop@0x43034c at line 900 in renumberPreNodes_pg] [366]
[792] 0.0 0.1 0.3 getNextPreArc_pg [792]
0.3 0.0 PREARC_FI2P [829]
0.0 0.4 disconnectNextPassageMarker [656]
[793] 0.0 0.0 0.4 setPreviousInSequence [793]
0.3 0.0 PM_FI2P [833]
0.1 0.0 PM_FI2P [954]
0.3 0.0 [Loop@0x433508 at line 276 in countPreNodes] [296]
0.1 0.0 chooseNextInternalPreNode [739]
[794] 0.0 0.4 0.0 sequenceCount_pg [794]
0.4 0.0 [Loop@0x403978 at line 3743 in spreadReadIDs] [668]
[795] 0.0 0.4 0.0 setShortReadMarkerPosition [795]
0.4 0.0 createReadPairingArray [753]
[796] 0.0 0.4 0.0 [Loop@0x41c05c at line 1385 in createReadPairingArray] [796]
0.2 0.2 remapBackOfNodeMarkersOntoNeighbour [61]
[797] 0.0 0.2 0.2 setNextInSequence [797]
0.2 0.0 PM_FI2P [884]
0.4 0.0 setNextInNode [395]
[798] 0.0 0.4 0.0 PM_FI2P [798]
0.4 0.0 [Loop@0x41aeff at line 311 in dfh_consolidate] [464]
[799] 0.0 0.4 0.0 dfh_compare [799]
0.4 0.0 getPreviousInSequence [658]
[800] 0.0 0.4 0.0 PM_FI2P [800]
0.4 0.0 dfh_consolidate [108]
[801] 0.0 0.4 0.0 [Loop@0x41acc0 at line 328 in dfh_consolidate] [801]
0.1 0.3 expectedNumberOfConnections [675]
[802] 0.0 0.1 0.3 norm [802]
0.3 0.0 exp [735]
0.4 0.0 setPreviousInSequence [690]
[803] 0.0 0.4 0.0 PM_FI2P [803]
0.0 0.4 [Loop@0x416b53 at line 1200 in remapNodeInwardReferencesOntoNode] [549]
[804] 0.0 0.0 0.4 getNodePrevious [804]
0.4 0.0 getNodeID [49]
0.0 0.4 createAnalogousPreArc_pg [511]
[805] 0.0 0.0 0.4 allocatePreArc_pg [805]
0.3 0.1 allocArrayArrayAllocate [289]
0.4 0.0 setPassageMarkerStart [768]
[806] 0.0 0.4 0.0 PM_FI2P [806]
0.2 0.2 [Loop@0x426498 at line 1105 in unmarkInterestingNodes] [695]
[807] 0.0 0.2 0.2 popNodeRecord [807]
0.2 0.0 getNodeID [49]
0.1 0.3 [Loop@0x419a30 at line 112 in comparePaths] [756]
[808] 0.0 0.1 0.3 getNodePrevious [808]
0.3 0.0 getNodeID [49]
0.4 0.0 [Loop@0x408280 at line 708 in reallocateNodeDescriptor] [782]
[809] 0.0 0.4 0.0 writeNucleotideInDescriptor [809]
0.2 0.2 remapBackOfNodeMarkersOntoNeighbour [61]
[810] 0.0 0.2 0.2 getPassageMarkerLength [810]
0.1 0.0 PM_FI2P [1005]
0.1 0.0 PM_FI2P [1027]
0.2 0.2 fh_extractminel [154]
[811] 0.0 0.2 0.2 fh_removerootlist [811]
0.2 0.0 fhe_remove [904]
0.1 0.1 [Loop@0x418ba4 at line 2161 in cleanUpRedundancy] [911]
0.0 0.1 [Loop@0x41852a at line 2001 in concatenateNodesAndVaccinate] [568]
0.0 0.1 [Loop@0x416264 at line 718 in remapNodeMarkersOntoNeighbour] [712]
[812] 0.0 0.1 0.3 isInitial [812]
0.3 0.0 PM_FI2P [861]
0.4 0.0 lockTwoNodes [58]
[813] 0.0 0.4 0.0 [Import thunk omp_test_lock] [813]
0.0 0.3 [Loop@0x428475 at line 1043 in splayToList] [653]
[814] 0.0 0.0 0.3 popConnectionStack [814]
0.0 0.3 deallocateConnectionStack [815]
0.0 0.3 popConnectionStack [814]
[815] 0.0 0.0 0.3 deallocateConnectionStack [815]
0.3 0.0 deallocatePointer [301]
0.3 0.0 PREARC_I2P [817]
[816] 0.0 0.3 0.0 PREARC_FI2P [816]
0.0 0.3 addPreArcToPreNode_pg [442]
[817] 0.0 0.0 0.3 PREARC_I2P [817]
0.3 0.0 PREARC_FI2P [816]
0.3 0.0 [Loop@0x426498 at line 1105 in unmarkInterestingNodes] [695]
[818] 0.0 0.3 0.0 setSingleNodeStatus [818]
0.3 0.0 [Loop@0x41a990 at line 445 in updateNodeStatus] [352]
[819] 0.0 0.3 0.0 setNodeStatus [819]
0.3 0.0 arcMergeSort [667]
[820] 0.0 0.3 0.0 mergeArcLists [820]
0.3 0.0 [Loop@0x403978 at line 3743 in spreadReadIDs] [668]
[821] 0.0 0.3 0.0 setShortReadMarkerOffset [821]
0.3 0.0 mergeDescriptors [468]
[822] 0.0 0.3 0.0 [Loop@0x40626a at line 762 in mergeDescriptors] [822]
0.0 0.3 concatenatePreNodes [220]
[823] 0.0 0.0 0.3 setPreNodeDescriptor_pg [823]
0.3 0.0 _int_free [227]
0.2 0.0 ghostThreadSequenceThroughGraph [11]
0.1 0.0 threadSequenceThroughGraph [7]
[824] 0.0 0.3 0.0 clearKmer [824]
0.3 0.0 threadSequenceThroughGraph [7]
[825] 0.0 0.3 0.0 findReferenceMapping [825]
0.3 0.0 createAnalogousPreArc_pg [511]
[826] 0.0 0.3 0.0 PREARC_FI2P [826]
0.3 0.0 concatenateCommonTodoLists [432]
[827] 0.0 0.3 0.0 [Loop@0x41584e at line 191 in concatenateCommonTodoLists] [827]
0.3 0.0 [Loop@0x40cff0 at line 436 in fh_consolidate] [263]
[828] 0.0 0.3 0.0 fh_compare [828]
0.3 0.0 getNextPreArc_pg [792]
[829] 0.0 0.3 0.0 PREARC_FI2P [829]
0.1 0.1 [Loop@0x433d43 at line 45 in concatenatePreNodes] [335]
0.1 0.0 [Loop@0x434154 at line 146 in concatenatePreGraph_pg] [188]
[830] 0.0 0.2 0.1 isLoop_pg [830]
0.1 0.0 PREARC_FI2P [959]
0.2 0.0 [Loop@0x410bad at line 1797 in usedReads] [857]
0.1 0.0 measureCoOccurences [679]
[831] 0.0 0.3 0.0 sequenceCount [831]
0.3 0.0 destroyPreArc_pg [489]
[832] 0.0 0.3 0.0 PREARC_FI2P [832]
0.3 0.0 setPreviousInSequence [793]
[833] 0.0 0.3 0.0 PM_FI2P [833]
0.1 0.2 [Loop@0x419bb0 at line 2264 in comparePaths] [256]
[834] 0.0 0.1 0.2 getNodePrevious [834]
0.2 0.0 getNodeID [49]
0.3 0.0 transferNodeData [376]
[835] 0.0 0.3 0.0 getNodeTime [835]
0.0 0.3 spreadReadIDs [304]
[836] 0.0 0.0 0.3 [Loop@0x403a78 at line 3779 in spreadReadIDs] [836]
0.2 0.0 setShortReadMarkerPosition [889]
0.1 0.0 setShortReadMarkerOffset [971]
0.3 0.0 [Loop@0x43367f at line 119 in countPreNodes] [446]
[837] 0.0 0.3 0.0 getInsertionMarkerPosition [837]
0.3 0.0 pairedCategories [840]
[838] 0.0 0.3 0.0 [Loop@0x41bb36 at line 1432 in pairedCategories] [838]
0.3 0.0 detachDubiousReads [841]
[839] 0.0 0.3 0.0 [Loop@0x41bbf8 at line 1510 in detachDubiousReads] [839]
0.0 0.3 main [14]
[840] 0.0 0.0 0.3 pairedCategories [840]
0.3 0.0 [Loop@0x41bb36 at line 1432 in pairedCategories] [838]
0.0 0.3 main [14]
[841] 0.0 0.0 0.3 detachDubiousReads [841]
0.3 0.0 [Loop@0x41bbf8 at line 1510 in detachDubiousReads] [839]
0.3 0.0 computeSecondInPair [843]
[842] 0.0 0.3 0.0 [Loop@0x41bedc at line 1468 in computeSecondInPair] [842]
0.0 0.3 importReadSet [98]
[843] 0.0 0.0 0.3 computeSecondInPair [843]
0.3 0.0 [Loop@0x41bedc at line 1468 in computeSecondInPair] [842]
0.3 0.0 getPassageMarkerFinish [616]
[844] 0.0 0.3 0.0 PM_FI2P [844]
0.3 0.0 [Loop@0x403f54 at line 3213 in extractBackOfNodeReads] [566]
[845] 0.0 0.3 0.0 setShortReadMarkerPosition [845]
0.3 0.0 remapNodeFibHeapReferencesOntoNode [437]
[846] 0.0 0.3 0.0 dfh_replacedata [846]
0.3 0.0 setPreviousInSequence [690]
[847] 0.0 0.3 0.0 PM_FI2P [847]
0.1 0.2 remapBackOfNodeTimesOntoNeighbour [436]
[848] 0.0 0.1 0.2 setNodePrevious [848]
0.2 0.0 nodeCount [580]
0.0 0.3 remapBackOfNodeMarkersOntoNeighbour [61]
[849] 0.0 0.0 0.3 getPassageMarkerStatus [849]
0.3 0.0 PM_FI2P [850]
0.3 0.0 getPassageMarkerStatus [849]
[850] 0.0 0.3 0.0 PM_FI2P [850]
0.3 0.0 addBufferToDescriptor [501]
[851] 0.0 0.3 0.0 getNucleotideInDescriptor [851]
0.3 0.0 mergeDescriptors [343]
[852] 0.0 0.3 0.0 [Loop@0x4060ac at line 744 in mergeDescriptors] [852]
0.1 0.2 remapBackOfNodeMarkersOntoNeighbour [61]
[853] 0.0 0.1 0.2 passageMarkerDirection [853]
0.2 0.0 PM_FI2P [920]
0.0 0.3 expectedNumberOfConnections [675]
[854] 0.0 0.0 0.3 norm [854]
0.3 0.0 exp [735]
0.3 0.0 setNextInNode [395]
[855] 0.0 0.3 0.0 PM_FI2P [855]
0.1 0.2 newDescriptor_pg [232]
[856] 0.0 0.1 0.2 [Loop@0x42ff74 at line 1025 in newDescriptor_pg] [856]
0.2 0.0 _IO_getc [53]
0.1 0.2 usedReads [371]
[857] 0.0 0.1 0.2 [Loop@0x410bad at line 1797 in usedReads] [857]
0.2 0.0 sequenceCount [831]
0.1 0.2 getPreArcBetweenPreNodes_pg [860]
[858] 0.0 0.1 0.2 getDestination_pg [858]
0.2 0.0 PREARC_FI2P [921]
0.0 0.3 createAnalogousPreArc_pg [511]
[859] 0.0 0.0 0.3 [Loop@0x431bd1 at line 488 in createAnalogousPreArc_pg] [859]
0.0 0.3 getPreArcBetweenPreNodes_pg [860]
0.0 0.3 [Loop@0x431bd1 at line 488 in createAnalogousPreArc_pg] [859]
[860] 0.0 0.0 0.3 getPreArcBetweenPreNodes_pg [860]
0.1 0.2 getDestination_pg [858]
0.3 0.0 isInitial [812]
[861] 0.0 0.3 0.0 PM_FI2P [861]
0.2 0.1 dfh_insertkey [784]
[862] 0.0 0.2 0.1 dfhe_newelem [862]
0.0 0.1 allocateDFibHeapNode [1034]
0.1 0.1 findOrCreateConnection [257]
[863] 0.0 0.1 0.1 allocateConnection [863]
0.1 0.0 [libgomp.so.1.0.0] [94]
0.0 0.2 pushConnectionStack [865]
[864] 0.0 0.0 0.2 allocateConnectionStack [864]
0.2 0.0 allocatePointer [109]
0.0 0.2 [Loop@0x428475 at line 1043 in splayToList] [653]
[865] 0.0 0.0 0.2 pushConnectionStack [865]
0.0 0.2 allocateConnectionStack [864]
0.2 0.0 importRoadMapArray [62]
[866] 0.0 0.2 0.0 [Loop@0x42f1b0 at line 148 in importRoadMapArray] [866]
0.1 0.1 createNodeLocks.omp_fn.2 [868]
[867] 0.0 0.1 0.1 [Loop@0x42c6f0 at line 72 in createNodeLocks.omp_fn.2] [867]
0.1 0.0 omp_init_lock [765]
0.0 0.2 clone [1]
[868] 0.0 0.0 0.2 createNodeLocks.omp_fn.2 [868]
0.1 0.1 [Loop@0x42c6f0 at line 72 in createNodeLocks.omp_fn.2] [867]
0.2 0.0 arcMergeSort [659]
[869] 0.0 0.2 0.0 mergeArcLists [869]
0.2 0.0 [Loop@0x403610 at line 3776 in injectShortReads] [627]
[870] 0.0 0.2 0.0 setShortReadMarkerOffset [870]
0.2 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
[871] 0.0 0.2 0.0 writeNucleotideInDescriptor [871]
0.2 0.0 disconnectNextPassageMarker [656]
[872] 0.0 0.2 0.0 getNextInSequence [872]
0.0 0.2 disconnectNextPassageMarker [656]
[873] 0.0 0.0 0.2 concatenatePassageMarkers [873]
0.1 0.0 PM_FI2P [944]
0.1 0.0 PM_FI2P [956]
0.2 0.0 destroyPreArc_pg [457]
[874] 0.0 0.2 0.0 PREARC_FI2P [874]
0.2 0.0 fh_extractmin [149]
[875] 0.0 0.2 0.0 deallocateFibHeapEl [875]
0.2 0.0 destroyPassageMarker [244]
[876] 0.0 0.2 0.0 deallocatePassageMarker [876]
0.2 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
[877] 0.0 0.2 0.0 writeNucleotideInDescriptor [877]
0.1 0.0 createAnalogousArc [245]
0.1 0.0 createArc [35]
[878] 0.0 0.2 0.0 allocateArc [878]
0.2 0.0 compareSequences [130]
[879] 0.0 0.2 0.0 [Loop@0x419cfa at line 584 in compareSequences] [879]
0.2 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
[880] 0.0 0.2 0.0 writeNucleotideInDescriptor [880]
0.2 0.0 setPassageMarkerFinish [645]
[881] 0.0 0.2 0.0 PM_FI2P [881]
0.2 0.0 getNextInSequence [883]
[882] 0.0 0.2 0.0 PM_FI2P [882]
0.0 0.2 disconnectNextPassageMarker [656]
[883] 0.0 0.0 0.2 getNextInSequence [883]
0.2 0.0 PM_FI2P [882]
0.2 0.0 setNextInSequence [797]
[884] 0.0 0.2 0.0 PM_FI2P [884]
0.0 0.2 emptyNode [763]
[885] 0.0 0.0 0.2 allocateNode [885]
0.0 0.2 allocatePointer [109]
0.2 0.0 getPassageMarkerSequenceID [887]
[886] 0.0 0.2 0.0 PM_FI2P [886]
0.0 0.2 remapBackOfNodeMarkersOntoNeighbour [61]
[887] 0.0 0.0 0.2 getPassageMarkerSequenceID [887]
0.2 0.0 PM_FI2P [886]
0.2 0.0 [Loop@0x4038e6 at line 3339 in spreadReadIDs] [329]
[888] 0.0 0.2 0.0 setShortReadMarkerPosition [888]
0.2 0.0 [Loop@0x403a78 at line 3779 in spreadReadIDs] [836]
[889] 0.0 0.2 0.0 setShortReadMarkerPosition [889]
0.1 0.1 absorbExtensionInScaffold [651]
[890] 0.0 0.1 0.1 [Loop@0x424ad3 at line 131 in absorbExtensionInScaffold] [890]
0.1 0.0 destroyConnection [988]
0.0 0.2 tourBusNode [31]
[891] 0.0 0.0 0.2 velvetLog [891]
0.1 0.0 printf [970]
0.0 0.1 __gettimeofday [983]
0.2 0.0 createReadPairingArray [753]
[892] 0.0 0.2 0.0 [Loop@0x41c020 at line 1380 in createReadPairingArray] [892]
0.2 0.0 renumberNodes [516]
[893] 0.0 0.2 0.0 [Loop@0x404868 at line 1183 in renumberNodes] [893]
0.2 0.0 getPreviousInSequence [658]
[894] 0.0 0.2 0.0 PM_FI2P [894]
0.0 0.2 pushNeighbours [142]
[895] 0.0 0.0 0.2 [Loop@0x425688 at line 928 in pushNeighbours] [895]
0.0 0.2 absorbExtension [344]
0.2 0.0 setPreviousInSequence [690]
[896] 0.0 0.2 0.0 PM_FI2P [896]
0.1 0.0 normInt [972]
0.1 0.0 normInt [1003]
[897] 0.0 0.2 0.0 erf [897]
0.0 0.2 updateNodeStatus [283]
[898] 0.0 0.0 0.2 newFibHeap [898]
0.0 0.2 fh_makekeyheap [901]
0.0 0.2 fh_makekeyheap [901]
[899] 0.0 0.0 0.2 fh_initheap [899]
0.0 0.2 newRecycleBin [900]
0.0 0.2 fh_initheap [899]
[900] 0.0 0.0 0.2 newRecycleBin [900]
0.0 0.2 mallocOrExit3 [67]
0.0 0.2 newFibHeap [898]
[901] 0.0 0.0 0.2 fh_makekeyheap [901]
0.0 0.2 fh_initheap [899]
0.2 0.0 [Loop@0x413330 at line 927 in exportLongNodeSequence] [419]
[902] 0.0 0.2 0.0 getNucleotideChar [902]
0.1 0.1 destroyArc [319]
[903] 0.0 0.1 0.1 deallocateArc [903]
0.1 0.0 deallocatePointer [301]
0.2 0.0 fh_removerootlist [811]
[904] 0.0 0.2 0.0 fhe_remove [904]
0.0 0.2 expandNode [565]
[905] 0.0 0.0 0.2 [Loop@0x405ea6 at line 2681 in expandNode] [905]
0.1 0.1 writeNucleotideAtPosition [632]
0.2 0.0 [Loop@0x40d17f at line 408 in fh_consolidate] [427]
[906] 0.0 0.2 0.0 fh_compare [906]
0.2 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
[907] 0.0 0.2 0.0 writeNucleotideInDescriptor [907]
0.2 0.0 remapBackOfNodeTimesOntoNeighbour [436]
[908] 0.0 0.2 0.0 getNodeTime [908]
0.0 0.2 concatenateNodesAndVaccinate [169]
[909] 0.0 0.0 0.2 [Loop@0x4184e0 at line 1994 in concatenateNodesAndVaccinate] [909]
0.1 0.0 getNextInNode [546]
0.0 0.1 isTerminal [392]
0.1 0.1 addPassageMarker [581]
[910] 0.0 0.1 0.1 allocatePassageMarker [910]
0.1 0.0 allocArrayAllocate [620]
0.0 0.2 [Loop@0x418900 at line 2080 in cleanUpRedundancy] [45]
[911] 0.0 0.0 0.2 [Loop@0x418ba4 at line 2161 in cleanUpRedundancy] [911]
0.1 0.1 isInitial [812]
0.2 0.0 [Loop@0x41983a at line 143 in isPreviousToNode] [373]
[912] 0.0 0.2 0.0 getNodePrevious [912]
0.1 0.1 markInterestingNodes [512]
[913] 0.0 0.1 0.1 resetMiniConnection [913]
0.0 0.1 recordNode [1024]
0.2 0.0 [Loop@0x403f54 at line 3213 in extractBackOfNodeReads] [566]
[914] 0.0 0.2 0.0 setShortReadMarkerOffset [914]
0.2 0.0 remapNodeMarkersOntoNeighbour [104]
[915] 0.0 0.2 0.0 [Loop@0x4164e8 at line 773 in remapNodeMarkersOntoNeighbour] [915]
0.2 0.0 getPreviousInSequence [658]
[916] 0.0 0.2 0.0 PM_FI2P [916]
0.2 0.0 [Loop@0x403f54 at line 3213 in extractBackOfNodeReads] [566]
[917] 0.0 0.2 0.0 setShortReadMarkerPosition [917]
0.0 0.2 concatenatePreNodes [220]
[918] 0.0 0.0 0.2 [Loop@0x4340b8 at line 94 in concatenatePreNodes] [918]
0.0 0.1 appendDescriptors_pg [487]
0.1 0.0 getPreArc_pg [559]
0.2 0.0 concatenatePreNodes [220]
[919] 0.0 0.2 0.0 [Loop@0x433f65 at line 103 in concatenatePreNodes] [919]
0.2 0.0 passageMarkerDirection [853]
[920] 0.0 0.2 0.0 PM_FI2P [920]
0.2 0.0 getDestination_pg [858]
[921] 0.0 0.2 0.0 PREARC_FI2P [921]
0.0 0.2 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
[922] 0.0 0.0 0.2 resetMiniConnection [922]
0.1 0.1 recordNode [923]
0.1 0.1 resetMiniConnection [922]
[923] 0.0 0.1 0.1 recordNode [923]
0.0 0.1 allocateNodeList [1028]
0.2 0.0 [Loop@0x404670 at line 1615 in activateArcLookupTable] [189]
[924] 0.0 0.2 0.0 getNodeInGraph [924]
0.2 0.0 fh_insertkey [527]
[925] 0.0 0.2 0.0 fh_insertel [925]
0.2 0.0 appendPositiveDescriptor_pg [517]
[926] 0.0 0.2 0.0 getPreNodeInPreGraph_pg [926]
0.2 0.0 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
[927] 0.0 0.2 0.0 getConnectionDistance [927]
0.1 0.0 convertMarker [700]
0.1 0.0 convertMarker [719]
[928] 0.0 0.2 0.0 setStartID [928]
0.0 0.2 readPreGraphFile [212]
[929] 0.0 0.0 0.2 allocateNodeSpace [929]
0.0 0.2 callocOrExit3 [221]
0.0 0.1 pushNeighbours [142]
[930] 0.0 0.0 0.1 adjustShortReadsByLength [930]
0.0 0.1 [Loop@0x423cd0 at line 741 in adjustShortReadsByLength] [931]
0.0 0.1 adjustShortReadsByLength [930]
[931] 0.0 0.0 0.1 [Loop@0x423cd0 at line 741 in adjustShortReadsByLength] [931]
0.1 0.0 getShortReadMarkerAtIndex [243]
0.1 0.0 integrateDerivativeDistances [514]
[932] 0.0 0.1 0.0 getConnection [932]
0.1 0.0 [Loop@0x413535 at line 748 in lowCoverageRegions] [694]
[933] 0.0 0.1 0.0 newMask [933]
0.0 0.1 destroyGraph [603]
[934] 0.0 0.0 0.1 [Loop@0x4051c0 at line 3792 in destroyGraph] [934]
0.0 0.1 destroyNode [276]
0.0 0.1 remapEmptyPathOntoMiddlePath [298]
[935] 0.0 0.0 0.1 remapEmptyPathArcsOntoMiddlePathSimple [935]
0.0 0.1 [Loop@0x41790d at line 1581 in remapEmptyPathArcsOntoMiddlePathSimple] [936]
0.0 0.1 remapEmptyPathArcsOntoMiddlePathSimple [935]
[936] 0.0 0.0 0.1 [Loop@0x41790d at line 1581 in remapEmptyPathArcsOntoMiddlePathSimple] [936]
0.0 0.1 createAnalogousArc [245]
0.0 0.1 [Loop@0x42bb58 at line 459 in correctGraphLocally] [938]
[937] 0.0 0.0 0.1 tourBus_local [937]
0.1 0.0 dfh_extractmin [81]
0.0 0.1 correctGraphLocally [440]
[938] 0.0 0.0 0.1 [Loop@0x42bb58 at line 459 in correctGraphLocally] [938]
0.0 0.1 tourBus_local [937]
0.0 0.1 [Loop@0x428450 at line 1096 in splayToList] [639]
[939] 0.0 0.0 0.1 pushConnectionStack [939]
0.0 0.1 allocateConnectionStack [940]
0.0 0.1 pushConnectionStack [939]
[940] 0.0 0.0 0.1 allocateConnectionStack [940]
0.1 0.0 allocatePointer [109]
0.1 0.0 [Loop@0x416b53 at line 1200 in remapNodeInwardReferencesOntoNode] [549]
[941] 0.0 0.1 0.0 setNodePrevious [941]
0.0 0.1 removeLowCoverageNodesAndDenounceDubiousReads [66]
[942] 0.0 0.0 0.1 [Loop@0x414bff at line 1260 in removeLowCoverageNodesAndDenounceDubiousReads] [942]
0.1 0.0 getNodeLength [148]
0.1 0.0 remapNodeMarkersOntoNeighbour [104]
[943] 0.0 0.1 0.0 [Loop@0x416590 at line 808 in remapNodeMarkersOntoNeighbour] [943]
0.1 0.0 concatenatePassageMarkers [873]
[944] 0.0 0.1 0.0 PM_FI2P [944]
0.1 0.0 blurLastShortReadMarker [783]
[945] 0.0 0.1 0.0 setShortReadMarkerPosition [945]
0.1 0.0 tourBus [24]
[946] 0.0 0.1 0.0 removeNextNodeFromDHeap [946]
0.1 0.0 dfh_cut [949]
[947] 0.0 0.1 0.0 dfhe_remove [947]
0.0 0.1 dfh_replacekeydata [684]
[948] 0.0 0.0 0.1 [Loop@0x41b327 at line 436 in dfh_replacekeydata] [948]
0.0 0.1 dfh_cascading_cut [950]
0.0 0.1 dfh_cascading_cut [950]
[949] 0.0 0.0 0.1 dfh_cut [949]
0.1 0.0 dfhe_remove [947]
0.0 0.1 [Loop@0x41b327 at line 436 in dfh_replacekeydata] [948]
[950] 0.0 0.0 0.1 dfh_cascading_cut [950]
0.0 0.1 dfh_cut [949]
0.1 0.0 [Loop@0x404255 at line 3082 in extractFrontOfNodeReads] [595]
[951] 0.0 0.1 0.0 setShortReadMarkerOffset [951]
0.1 0.0 addPassageMarker [581]
[952] 0.0 0.1 0.0 PM_FI2P [952]
0.1 0.0 transferNodeData [376]
[953] 0.0 0.1 0.0 getNodeTime [953]
0.1 0.0 setPreviousInSequence [793]
[954] 0.0 0.1 0.0 PM_FI2P [954]
0.1 0.0 setNextInNode [395]
[955] 0.0 0.1 0.0 PM_FI2P [955]
0.1 0.0 concatenatePassageMarkers [873]
[956] 0.0 0.1 0.0 PM_FI2P [956]
0.1 0.0 [Loop@0x43022b at line 942 in renumberPreNodes_pg] [282]
[957] 0.0 0.1 0.0 getPreArc_pg [957]
0.1 0.0 remapNodeFibHeapReferencesOntoNode [437]
[958] 0.0 0.1 0.0 getNodeDHeapNode [958]
0.1 0.0 isLoop_pg [830]
[959] 0.0 0.1 0.0 PREARC_FI2P [959]
0.1 0.0 createAnalogousPreArc_pg [511]
[960] 0.0 0.1 0.0 PREARC_FI2P [960]
0.0 0.1 dfh_insertkey [784]
[961] 0.0 0.0 0.1 dfh_insertel [961]
0.1 0.0 dfh_insertrootlist [962]
0.1 0.0 dfh_insertel [961]
[962] 0.0 0.1 0.0 dfh_insertrootlist [962]
0.1 0.0 reallocOrExit4 [564]
[963] 0.0 0.1 0.0 [Import thunk realloc] [963]
0.1 0.0 [Loop@0x4320d0 at line 154 in orderInsertionMarkers.omp_fn.0] [79]
[964] 0.0 0.1 0.0 qsort [964]
0.1 0.0 destroyPreNode_pg [356]
[965] 0.0 0.1 0.0 [Import thunk free] [965]
0.0 0.1 identifyUniqueNodes [967]
[966] 0.0 0.0 0.1 [Loop@0x434e08 at line 105 in identifyUniqueNodes] [966]
0.0 0.1 isUniqueSolexa [993]
0.0 0.1 readCoherentGraph [994]
[967] 0.0 0.0 0.1 identifyUniqueNodes [967]
0.0 0.1 [Loop@0x434e08 at line 105 in identifyUniqueNodes] [966]
0.1 0.0 [Loop@0x403556 at line 3776 in injectShortReads] [57]
[968] 0.0 0.1 0.0 setShortReadMarkerPosition [968]
0.1 0.0 [Loop@0x408280 at line 708 in reallocateNodeDescriptor] [782]
[969] 0.0 0.1 0.0 getNucleotideInDescriptor [969]
0.1 0.0 velvetLog [891]
[970] 0.0 0.1 0.0 printf [970]
0.1 0.0 [Loop@0x403a78 at line 3779 in spreadReadIDs] [836]
[971] 0.0 0.1 0.0 setShortReadMarkerOffset [971]
0.0 0.1 expectedNumberOfConnections [675]
[972] 0.0 0.0 0.1 normInt [972]
0.1 0.0 erf [897]
0.0 0.1 __gettimeofday [983]
[973] 0.0 0.0 0.1 __vdso_gettimeofday [973]
0.1 0.0 [[vsyscall]] [982]
0.1 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
[974] 0.0 0.1 0.0 writeNucleotideInDescriptor [974]
0.0 0.1 remapNodeTimesOntoTargetNode [474]
[975] 0.0 0.0 0.1 isPreviousToNode [975]
0.1 0.0 getNodeTime [976]
0.1 0.0 isPreviousToNode [975]
[976] 0.0 0.1 0.0 getNodeTime [976]
0.0 0.1 [Loop@0x433570 at line 287 in countPreNodes] [345]
[977] 0.0 0.0 0.1 getInsertionMarkerPosition [977]
0.1 0.0 getStart [143]
0.1 0.0 [Loop@0x403f54 at line 3213 in extractBackOfNodeReads] [566]
[978] 0.0 0.1 0.0 setShortReadMarkerOffset [978]
0.1 0.0 getStartOffset [676]
[979] 0.0 0.1 0.0 PM_FI2P [979]
0.1 0.0 getFinishOffset [981]
[980] 0.0 0.1 0.0 PM_FI2P [980]
0.0 0.1 remapBackOfNodeMarkersOntoNeighbour [61]
[981] 0.0 0.0 0.1 getFinishOffset [981]
0.1 0.0 PM_FI2P [980]
0.1 0.0 __vdso_gettimeofday [973]
[982] 0.0 0.1 0.0 [[vsyscall]] [982]
0.0 0.1 velvetLog [891]
[983] 0.0 0.0 0.1 __gettimeofday [983]
0.0 0.1 __vdso_gettimeofday [973]
0.0 0.1 [Loop@0x4279c0 at line 473 in computeReadToNodeMappings] [985]
[984] 0.0 0.0 0.1 computePartialReadToNodeMappingLong [984]
0.1 0.0 getMarker [624]
0.0 0.1 computeReadToNodeMappings [274]
[985] 0.0 0.0 0.1 [Loop@0x4279c0 at line 473 in computeReadToNodeMappings] [985]
0.0 0.1 computePartialReadToNodeMappingLong [984]
0.0 0.1 computeReadToNodeCounts [379]
[986] 0.0 0.0 0.1 [Loop@0x4276f0 at line 373 in computeReadToNodeCounts] [986]
0.1 0.0 getMarker [624]
0.1 0.0 [Loop@0x42428d at line 201 in integrateDerivativeDistances] [528]
[987] 0.0 0.1 0.0 readjustMiniConnection [987]
0.1 0.0 [Loop@0x424ad3 at line 131 in absorbExtensionInScaffold] [890]
[988] 0.0 0.1 0.0 destroyConnection [988]
0.0 0.1 fillUpGraph [25]
[989] 0.0 0.0 0.1 activateReadStarts [989]
0.0 0.1 callocOrExit3 [221]
0.0 0.1 [Loop@0x4247ed at line 374 in absorbExtensionInScaffold] [678]
[990] 0.0 0.0 0.1 createNewConnection [990]
0.1 0.0 getNodeInGraph [47]
0.1 0.0 [Loop@0x4097c8 at line 548 in splitNodeDescriptor] [992]
[991] 0.0 0.1 0.0 getNucleotideInDescriptor [991]
0.0 0.1 splitNodeDescriptor [588]
[992] 0.0 0.0 0.1 [Loop@0x4097c8 at line 548 in splitNodeDescriptor] [992]
0.1 0.0 getNucleotideInDescriptor [991]
0.0 0.1 [Loop@0x434e08 at line 105 in identifyUniqueNodes] [966]
[993] 0.0 0.0 0.1 isUniqueSolexa [993]
0.1 0.0 getNodeLength [148]
0.0 0.1 main [14]
[994] 0.0 0.0 0.1 readCoherentGraph [994]
0.0 0.1 identifyUniqueNodes [967]
0.1 0.0 [Loop@0x41ce48 at line 1599 in importReadSet] [204]
[995] 0.0 0.1 0.0 [Import thunk strncpy] [995]
0.1 0.0 [Loop@0x435df8 at line 63 in sortKmerOccurenceTable] [597]
[996] 0.0 0.1 0.0 [Loop@0x435e50 at line 185 in sortKmerOccurenceTable] [996]
0.1 0.0 projectFromShortRead [93]
[997] 0.0 0.1 0.0 getShortReadMarkerOffset [997]
0.1 0.0 findOppositeNode [999]
[998] 0.0 0.1 0.0 [Loop@0x4263db at line 1126 in findOppositeNode] [998]
0.0 0.1 [Loop@0x4263b0 at line 1158 in expandLongNode] [138]
[999] 0.0 0.0 0.1 findOppositeNode [999]
0.1 0.0 [Loop@0x4263db at line 1126 in findOppositeNode] [998]
0.1 0.0 transferNodeData [376]
[1000] 0.0 0.1 0.0 getNodePrevious [1000]
0.1 0.0 setStartOffset [733]
[1001] 0.0 0.1 0.0 PM_FI2P [1001]
0.1 0.0 directlyAppendDescriptors [494]
[1002] 0.0 0.1 0.0 getNodeLength [1002]
0.0 0.1 expectedNumberOfConnections [675]
[1003] 0.0 0.0 0.1 normInt [1003]
0.1 0.0 erf [897]
0.1 0.0 disconnectNextPassageMarker [656]
[1004] 0.0 0.1 0.0 setPreviousInSequence [1004]
0.1 0.0 getPassageMarkerLength [810]
[1005] 0.0 0.1 0.0 PM_FI2P [1005]
0.1 0.0 tourBusArc [33]
[1006] 0.0 0.1 0.0 setNodeTime [1006]
0.1 0.0 arcMergeSort [781]
[1007] 0.0 0.1 0.0 arcMergeSort [1007]
0.0 0.1 expectedNumberOfConnections [675]
[1008] 0.0 0.0 0.1 norm [1008]
0.1 0.0 exp [735]
0.1 0.0 tourBusArc [33]
[1009] 0.0 0.1 0.0 insertNodeIntoDHeap [1009]
0.0 0.1 dfh_extractminel [82]
[1010] 0.0 0.0 0.1 dfh_removerootlist [1010]
0.1 0.0 dfhe_remove [1011]
0.1 0.0 dfh_removerootlist [1010]
[1011] 0.0 0.1 0.0 dfhe_remove [1011]
0.1 0.0 [Loop@0x41990e at line 102 in isPreviousToNode] [412]
[1012] 0.0 0.1 0.0 getNodePrevious [1012]
0.0 0.1 n50 [1014]
[1013] 0.0 0.0 0.1 [Loop@0x41237e at line 1019 in n50] [1013]
0.0 0.1 fh_insertkey [527]
0.0 0.1 logFinalStats [370]
[1014] 0.0 0.0 0.1 n50 [1014]
0.0 0.1 [Loop@0x41237e at line 1019 in n50] [1013]
0.1 0.0 createAnalogousArc [245]
[1015] 0.0 0.1 0.0 getMultiplicity [1015]
0.1 0.0 addPassageMarker [581]
[1016] 0.0 0.1 0.0 PM_FI2P [1016]
0.1 0.0 reverseCatDescriptors [621]
[1017] 0.0 0.1 0.0 writeNucleotideInDescriptor [1017]
0.0 0.1 addPreArcToPreNode_pg [591]
[1018] 0.0 0.0 0.1 PREARC_I2P [1018]
0.1 0.0 PREARC_FI2P [1019]
0.1 0.0 PREARC_I2P [1018]
[1019] 0.0 0.1 0.0 PREARC_FI2P [1019]
0.0 0.1 remapNodeFibHeapReferencesOntoNode [437]
[1020] 0.0 0.0 0.1 dfh_delete [1020]
0.0 0.1 dfh_extractmin [1022]
0.0 0.1 dfh_extractmin [1022]
[1021] 0.0 0.0 0.1 dfh_extractminel [1021]
0.0 0.1 dfh_consolidate [108]
0.0 0.1 dfh_delete [1020]
[1022] 0.0 0.0 0.1 dfh_extractmin [1022]
0.0 0.1 dfh_extractminel [1021]
0.0 0.1 recordNode [1024]
[1023] 0.0 0.0 0.1 allocateNodeList [1023]
0.1 0.0 allocatePointer [109]
0.0 0.1 resetMiniConnection [913]
[1024] 0.0 0.0 0.1 recordNode [1024]
0.0 0.1 allocateNodeList [1023]
0.0 0.1 [Loop@0x4320d0 at line 154 in orderInsertionMarkers.omp_fn.0] [79]
[1025] 0.0 0.0 0.1 msort_with_tmp [1025]
0.0 0.1 compareInsertionMarkers [106]
0.1 0.0 recordKmerOccurence [414]
[1026] 0.0 0.1 0.0 [Import thunk GOMP_critical_start] [1026]
0.1 0.0 getPassageMarkerLength [810]
[1027] 0.0 0.1 0.0 PM_FI2P [1027]
0.0 0.1 recordNode [923]
[1028] 0.0 0.0 0.1 allocateNodeList [1028]
0.1 0.0 allocatePointer [109]
0.1 0.0 [Loop@0x40ab2f at line 2329 in readPreGraphFile] [241]
[1029] 0.0 0.1 0.0 writeNucleotideInDescriptor [1029]
0.1 0.0 callocOrExit3 [221]
[1030] 0.0 0.1 0.0 [Import thunk calloc] [1030]
0.1 0.0 markInterestingNodes [512]
[1031] 0.0 0.1 0.0 readjustMiniConnection [1031]
0.1 0.0 [Loop@0x404255 at line 3082 in extractFrontOfNodeReads] [595]
[1032] 0.0 0.1 0.0 setShortReadMarkerOffset [1032]
0.0 0.1 computeReadToNodeMappings [274]
[1033] 0.0 0.0 0.1 createReadsLocks [1033]
0.0 0.1 mallocOrExit3 [67]
0.0 0.1 dfhe_newelem [862]
[1034] 0.0 0.0 0.1 allocateDFibHeapNode [1034]
0.1 0.0 allocatePointer [109]
Index Function
------ -----------------------------------------------------------------------------
[0] <spontaneous>
[364] GOMP_critical_end
[334] GOMP_critical_start
[438] PM_FI2P
[452] PM_FI2P
[671] PM_FI2P
[894] PM_FI2P
[956] PM_FI2P
[886] PM_FI2P
[798] PM_FI2P
[593] PM_FI2P
[861] PM_FI2P
[844] PM_FI2P
[751] PM_FI2P
[944] PM_FI2P
[554] PM_FI2P
[1001] PM_FI2P
[882] PM_FI2P
[954] PM_FI2P
[952] PM_FI2P
[833] PM_FI2P
[847] PM_FI2P
[612] PM_FI2P
[441] PM_FI2P
[806] PM_FI2P
[1027] PM_FI2P
[608] PM_FI2P
[504] PM_FI2P
[418] PM_FI2P
[500] PM_FI2P
[776] PM_FI2P
[881] PM_FI2P
[920] PM_FI2P
[896] PM_FI2P
[553] PM_FI2P
[855] PM_FI2P
[425] PM_FI2P
[666] PM_FI2P
[979] PM_FI2P
[800] PM_FI2P
[980] PM_FI2P
[884] PM_FI2P
[1016] PM_FI2P
[1005] PM_FI2P
[803] PM_FI2P
[449] PM_FI2P
[955] PM_FI2P
[916] PM_FI2P
[607] PM_FI2P
[757] PM_FI2P
[714] PM_FI2P
[704] PM_FI2P
[703] PM_FI2P
[850] PM_FI2P
[736] PM_FI2P
[780] PM_FI2P
[469] PM_FI2P
[611] PM_FI2P
[959] PREARC_FI2P
[697] PREARC_FI2P
[758] PREARC_FI2P
[921] PREARC_FI2P
[816] PREARC_FI2P
[462] PREARC_FI2P
[774] PREARC_FI2P
[672] PREARC_FI2P
[1019] PREARC_FI2P
[874] PREARC_FI2P
[826] PREARC_FI2P
[648] PREARC_FI2P
[960] PREARC_FI2P
[473] PREARC_FI2P
[158] PREARC_FI2P
[832] PREARC_FI2P
[730] PREARC_FI2P
[716] PREARC_FI2P
[755] PREARC_FI2P
[829] PREARC_FI2P
[537] PREARC_FI2P
[1018] PREARC_I2P
[817] PREARC_I2P
[1026] [Import thunk GOMP_critical_start]
[416] [Import thunk _IO_getc]
[503] [Import thunk __ctype_b_loc]
[759] [Import thunk __isoc99_sscanf]
[1030] [Import thunk calloc]
[767] [Import thunk fgets]
[965] [Import thunk free]
[470] [Import thunk free]
[456] [Import thunk omp_get_thread_num]
[687] [Import thunk omp_set_lock]
[813] [Import thunk omp_test_lock]
[447] [Import thunk omp_unset_lock]
[963] [Import thunk realloc]
[995] [Import thunk strncpy]
[633] [Import thunk vfprintf]
[499] [Loop@0x402310 at line 144 in newTightStringArrayFromStringArray]
[205] [Loop@0x402370 at line 152 in newTightStringArrayFromStringArray]
[226] [Loop@0x402389 at line 124 in newTightStringArrayFromStringArray]
[483] [Loop@0x4027d3 at line 337 in getArcBetweenNodes]
[540] [Loop@0x402980 at line 620 in resetNodeStatus]
[57] [Loop@0x403556 at line 3776 in injectShortReads]
[627] [Loop@0x403610 at line 3776 in injectShortReads]
[234] [Loop@0x403668 at line 3540 in injectShortReads]
[329] [Loop@0x4038e6 at line 3339 in spreadReadIDs]
[668] [Loop@0x403978 at line 3743 in spreadReadIDs]
[836] [Loop@0x403a78 at line 3779 in spreadReadIDs]
[193] [Loop@0x403bad at line 2959 in commonNodeReads]
[506] [Loop@0x403ca0 at line 2997 in commonNodeReads]
[495] [Loop@0x403ce8 at line 3006 in commonNodeReads]
[422] [Loop@0x403d68 at line 2862 in createNodeReadStartArrays]
[529] [Loop@0x403eb1 at line 3155 in extractBackOfNodeReads]
[566] [Loop@0x403f54 at line 3213 in extractBackOfNodeReads]
[562] [Loop@0x4041be at line 3019 in extractFrontOfNodeReads]
[595] [Loop@0x404255 at line 3082 in extractFrontOfNodeReads]
[95] [Loop@0x40449b at line 2881 in orderNodeReadStartArrays]
[189] [Loop@0x404670 at line 1615 in activateArcLookupTable]
[191] [Loop@0x404686 at line 1620 in activateArcLookupTable]
[524] [Loop@0x404760 at line 1139 in renumberNodes]
[893] [Loop@0x404868 at line 1183 in renumberNodes]
[641] [Loop@0x404f40 at line 438 in destroyArc]
[686] [Loop@0x404f80 at line 453 in destroyArc]
[460] [Loop@0x405080 at line 466 in destroyNode]
[399] [Loop@0x4050b0 at line 477 in destroyNode]
[738] [Loop@0x405100 at line 487 in destroyNode]
[934] [Loop@0x4051c0 at line 3792 in destroyGraph]
[431] [Loop@0x4052ef at line 337 in getArcBetweenNodes]
[54] [Loop@0x40553c at line 351 in getArcBetweenNodes]
[222] [Loop@0x40559d at line 357 in getArcBetweenNodes]
[905] [Loop@0x405ea6 at line 2681 in expandNode]
[348] [Loop@0x405f5e at line 548 in appendNodeSequence]
[852] [Loop@0x4060ac at line 744 in mergeDescriptors]
[718] [Loop@0x406123 at line 762 in mergeDescriptors]
[724] [Loop@0x406201 at line 744 in mergeDescriptors]
[822] [Loop@0x40626a at line 762 in mergeDescriptors]
[324] [Loop@0x4076f4 at line 548 in exportNode]
[601] [Loop@0x4077b7 at line 548 in exportNode]
[505] [Loop@0x4078f0 at line 1824 in sortNodeArcs]
[574] [Loop@0x407a30 at line 1824 in sortNodeArcs]
[785] [Loop@0x407b90 at line 1995 in exportGraph]
[20] [Loop@0x407c00 at line 2007 in exportGraph]
[21] [Loop@0x407c50 at line 2016 in exportGraph]
[481] [Loop@0x407c80 at line 1987 in exportGraph]
[453] [Loop@0x407cf1 at line 1716 in exportGraph]
[579] [Loop@0x407f3b at line 548 in directlyAppendDescriptors]
[622] [Loop@0x408074 at line 548 in directlyAppendDescriptors]
[782] [Loop@0x408280 at line 708 in reallocateNodeDescriptor]
[699] [Loop@0x408554 at line 548 in appendGap]
[602] [Loop@0x4096a1 at line 548 in splitNodeDescriptor]
[992] [Loop@0x4097c8 at line 548 in splitNodeDescriptor]
[213] [Loop@0x40a990 at line 2309 in readPreGraphFile]
[241] [Loop@0x40ab2f at line 2329 in readPreGraphFile]
[102] [Loop@0x40b8d0 at line 619 in main]
[723] [Loop@0x40cf50 at line 443 in fh_consolidate]
[211] [Loop@0x40cf90 at line 436 in fh_consolidate]
[263] [Loop@0x40cff0 at line 436 in fh_consolidate]
[427] [Loop@0x40d17f at line 408 in fh_consolidate]
[262] [Loop@0x40d280 at line 534 in fh_extractminel]
[326] [Loop@0x40dce0 at line 54 in concatenateReadStarts]
[194] [Loop@0x40dd60 at line 68 in concatenateReadStarts]
[534] [Loop@0x40de14 at line 94 in concatenateStringOfNodes]
[64] [Loop@0x40ded8 at line 109 in concatenateStringOfNodes]
[778] [Loop@0x40e17c at line 170 in concatenateStringOfNodes]
[518] [Loop@0x40e1e4 at line 180 in concatenateStringOfNodes]
[60] [Loop@0x40e270 at line 198 in concatenateGraph]
[103] [Loop@0x40e294 at line 205 in concatenateGraph]
[100] [Loop@0x40e320 at line 217 in concatenateGraph]
[375] [Loop@0x410a59 at line 1797 in usedReads]
[413] [Loop@0x410b08 at line 1816 in usedReads]
[542] [Loop@0x410b70 at line 1824 in usedReads]
[857] [Loop@0x410bad at line 1797 in usedReads]
[1013] [Loop@0x41237e at line 1019 in n50]
[311] [Loop@0x4128ec at line 432 in displayGeneralStatistics]
[316] [Loop@0x412b20 at line 444 in printShortCounts]
[400] [Loop@0x412fad at line 843 in getShortReadCoords]
[445] [Loop@0x413093 at line 857 in getShortReadTwinCoords]
[419] [Loop@0x413330 at line 927 in exportLongNodeSequence]
[694] [Loop@0x413535 at line 748 in lowCoverageRegions]
[705] [Loop@0x4138d2 at line 1419 in removeHighCoverageNodes]
[172] [Loop@0x413aaf at line 980 in exportLongNodeSequences]
[233] [Loop@0x414ada at line 1184 in removeLowCoverageNodesAndDenounceDubiousReads]
[942] [Loop@0x414bff at line 1260 in removeLowCoverageNodesAndDenounceDubiousReads]
[323] [Loop@0x414f6d at line 1193 in removeNodeAndDenounceDubiousReads]
[573] [Loop@0x414fe5 at line 1204 in removeNodeAndDenounceDubiousReads]
[410] [Loop@0x415278 at line 2188 in pathContainsReference]
[590] [Loop@0x415290 at line 2190 in pathContainsReference]
[394] [Loop@0x41530b at line 531 in extractSequence]
[333] [Loop@0x415368 at line 541 in extractSequence]
[523] [Loop@0x4153e7 at line 2435 in getTipLength]
[520] [Loop@0x4157d4 at line 175 in concatenateCommonTodoLists]
[827] [Loop@0x41584e at line 191 in concatenateCommonTodoLists]
[320] [Loop@0x415a00 at line 1851 in destroyPaths]
[337] [Loop@0x415a10 at line 1854 in destroyPaths]
[247] [Loop@0x415a93 at line 2454 in clipTipsHard]
[246] [Loop@0x415aa4 at line 2456 in clipTipsHard]
[286] [Loop@0x415c3e at line 680 in remapNodeArcsOntoTarget]
[556] [Loop@0x4160ce at line 1200 in remapNodeInwardReferencesOntoNode]
[712] [Loop@0x416264 at line 718 in remapNodeMarkersOntoNeighbour]
[915] [Loop@0x4164e8 at line 773 in remapNodeMarkersOntoNeighbour]
[943] [Loop@0x416590 at line 808 in remapNodeMarkersOntoNeighbour]
[332] [Loop@0x4165f8 at line 808 in remapNodeMarkersOntoNeighbour]
[321] [Loop@0x416690 at line 773 in remapNodeMarkersOntoNeighbour]
[374] [Loop@0x416850 at line 894 in remapBackOfNodeOntoNeighbour]
[549] [Loop@0x416b53 at line 1200 in remapNodeInwardReferencesOntoNode]
[439] [Loop@0x416c20 at line 859 in remapBackOfNodeArcsOntoNeighbour]
[471] [Loop@0x4170f0 at line 1033 in remapBackOfNodeMarkersOntoNeighbour]
[536] [Loop@0x417200 at line 1098 in remapBackOfNodeMarkersOntoNeighbour]
[308] [Loop@0x4173f8 at line 1069 in remapBackOfNodeMarkersOntoNeighbour]
[275] [Loop@0x417498 at line 1143 in remapBackOfNodeMarkersOntoNeighbour]
[936] [Loop@0x41790d at line 1581 in remapEmptyPathArcsOntoMiddlePathSimple]
[305] [Loop@0x417bc6 at line 1622 in remapEmptyPathMarkersOntoMiddlePathSimple]
[155] [Loop@0x41816a at line 1975 in simplifyNode]
[486] [Loop@0x418340 at line 112 in simplifyNode]
[709] [Loop@0x418439 at line 1976 in concatenateNodesAndVaccinate]
[433] [Loop@0x418472 at line 1986 in concatenateNodesAndVaccinate]
[909] [Loop@0x4184e0 at line 1994 in concatenateNodesAndVaccinate]
[568] [Loop@0x41852a at line 2001 in concatenateNodesAndVaccinate]
[45] [Loop@0x418900 at line 2080 in cleanUpRedundancy]
[689] [Loop@0x41898d at line 1872 in mapDistancesOntoPaths]
[575] [Loop@0x4189db at line 1881 in mapDistancesOntoPaths]
[46] [Loop@0x418a48 at line 2093 in cleanUpRedundancy]
[660] [Loop@0x418ab0 at line 1896 in markerLeadsToNode]
[492] [Loop@0x418ad8 at line 1896 in markerLeadsToNode]
[911] [Loop@0x418ba4 at line 2161 in cleanUpRedundancy]
[146] [Loop@0x418be0 at line 2070 in concatenatePathNodes]
[570] [Loop@0x418c40 at line 1860 in destroyPaths]
[708] [Loop@0x419340 at line 636 in mapSlowOntoFast]
[69] [Loop@0x4196cb at line 2210 in comparePaths]
[373] [Loop@0x41983a at line 143 in isPreviousToNode]
[412] [Loop@0x41990e at line 102 in isPreviousToNode]
[756] [Loop@0x419a30 at line 112 in comparePaths]
[742] [Loop@0x419a70 at line 112 in comparePaths]
[231] [Loop@0x419ae0 at line 2246 in comparePaths]
[256] [Loop@0x419bb0 at line 2264 in comparePaths]
[879] [Loop@0x419cfa at line 584 in compareSequences]
[131] [Loop@0x419dab at line 589 in comparePaths]
[132] [Loop@0x419ddd at line 590 in compareSequences]
[701] [Loop@0x41a04d at line 2541 in correctGraph]
[325] [Loop@0x41a20d at line 473 in determineEligibleStartingPoints]
[398] [Loop@0x41a240 at line 479 in determineEligibleStartingPoints]
[430] [Loop@0x41a2b7 at line 489 in determineEligibleStartingPoints]
[140] [Loop@0x41a326 at line 497 in determineEligibleStartingPoints]
[266] [Loop@0x41a3a6 at line 2565 in correctGraph]
[278] [Loop@0x41a3eb at line 2359 in correctGraph]
[22] [Loop@0x41a4bf at line 2568 in correctGraph]
[23] [Loop@0x41a640 at line 2570 in correctGraph]
[32] [Loop@0x41a71f at line 2296 in correctGraph]
[771] [Loop@0x41a910 at line 427 in freeDoneTickets]
[285] [Loop@0x41a980 at line 444 in updateNodeStatus]
[352] [Loop@0x41a990 at line 445 in updateNodeStatus]
[801] [Loop@0x41acc0 at line 328 in dfh_consolidate]
[110] [Loop@0x41ad00 at line 321 in dfh_consolidate]
[113] [Loop@0x41ad60 at line 414 in dfh_consolidate]
[464] [Loop@0x41aeff at line 311 in dfh_consolidate]
[126] [Loop@0x41b000 at line 293 in dfh_extractminel]
[948] [Loop@0x41b327 at line 436 in dfh_replacekeydata]
[613] [Loop@0x41b8cb at line 96 in destroyRecycleBin]
[838] [Loop@0x41bb36 at line 1432 in pairedCategories]
[839] [Loop@0x41bbf8 at line 1510 in detachDubiousReads]
[532] [Loop@0x41bce8 at line 1729 in getSequenceLengths]
[842] [Loop@0x41bedc at line 1468 in computeSecondInPair]
[892] [Loop@0x41c020 at line 1380 in createReadPairingArray]
[796] [Loop@0x41c05c at line 1385 in createReadPairingArray]
[216] [Loop@0x41cc29 at line 1545 in importReadSet]
[121] [Loop@0x41cce8 at line 1564 in importReadSet]
[183] [Loop@0x41cd0e at line 1568 in importReadSet]
[498] [Loop@0x41cd15 at line 1580 in importReadSet]
[204] [Loop@0x41ce48 at line 1599 in importReadSet]
[631] [Loop@0x41ce71 at line 1612 in importReadSet]
[931] [Loop@0x423cd0 at line 741 in adjustShortReadsByLength]
[528] [Loop@0x42428d at line 201 in integrateDerivativeDistances]
[678] [Loop@0x4247ed at line 374 in absorbExtensionInScaffold]
[890] [Loop@0x424ad3 at line 131 in absorbExtensionInScaffold]
[895] [Loop@0x425688 at line 928 in pushNeighbours]
[513] [Loop@0x4261eb at line 131 in expandLongNode]
[138] [Loop@0x4263b0 at line 1158 in expandLongNode]
[998] [Loop@0x4263db at line 1126 in findOppositeNode]
[695] [Loop@0x426498 at line 1105 in unmarkInterestingNodes]
[135] [Loop@0x426660 at line 1229 in exploitShortReadPairs]
[134] [Loop@0x426669 at line 1178 in exploitShortReadPairs]
[691] [Loop@0x4269dc at line 566 in estimateMissingInsertLengths]
[680] [Loop@0x426b58 at line 631 in estimateMissingInsertLengths]
[254] [Loop@0x4270fb at line 1670 in countShortReads]
[253] [Loop@0x42715e at line 1678 in countShortReads]
[73] [Loop@0x42729b at line 441 in computeReadToNodeMappings.omp_fn.1]
[71] [Loop@0x427310 at line 445 in computePartialReadToNodeMappingShort]
[118] [Loop@0x427558 at line 343 in computeReadToNodeCounts.omp_fn.0]
[116] [Loop@0x4275b0 at line 358 in computeReadToNodeCounts.omp_fn.0]
[986] [Loop@0x4276f0 at line 373 in computeReadToNodeCounts]
[654] [Loop@0x427878 at line 423 in allocateReadToNodeTables]
[985] [Loop@0x4279c0 at line 473 in computeReadToNodeMappings]
[637] [Loop@0x428420 at line 1093 in computeNodeToNodeMappings.omp_fn.5]
[639] [Loop@0x428450 at line 1096 in splayToList]
[653] [Loop@0x428475 at line 1043 in splayToList]
[312] [Loop@0x4286e4 at line 882 in splayConnection]
[90] [Loop@0x429963 at line 1429 in projectFromNode]
[156] [Loop@0x429a08 at line 1442 in projectFromShortRead]
[180] [Loop@0x429af0 at line 1464 in projectFromShortRead]
[88] [Loop@0x429de4 at line 1593 in computeNodeToNodeMappings.omp_fn.3]
[626] [Loop@0x42a990 at line 1814 in buildScaffold]
[625] [Loop@0x42a9b5 at line 1701 in buildScaffold]
[477] [Loop@0x42ba95 at line 423 in correctGraphLocally]
[677] [Loop@0x42bab8 at line 513 in correctGraphLocally]
[938] [Loop@0x42bb58 at line 459 in correctGraphLocally]
[478] [Loop@0x42bdb5 at line 396 in clipTipsVeryHardLocally]
[583] [Loop@0x42be0b at line 396 in isLocalDeadEnd]
[698] [Loop@0x42be4c at line 407 in isLocalTwinDeadEnd]
[249] [Loop@0x42c130 at line 502 in referenceGraphKmers]
[251] [Loop@0x42c13c at line 502 in referenceGraphKmers]
[207] [Loop@0x42c240 at line 536 in referenceGraphKmers]
[302] [Loop@0x42c2d8 at line 571 in referenceGraphKmers]
[293] [Loop@0x42c4a0 at line 543 in referenceGraphKmers]
[867] [Loop@0x42c6f0 at line 72 in createNodeLocks.omp_fn.2]
[6] [Loop@0x42ccd5 at line 1141 in fillUpGraph.omp_fn.4]
[8] [Loop@0x42cf80 at line 863 in fillUpGraph.omp_fn.4]
[215] [Loop@0x42d0be at line 226 in isNodeMemorized]
[287] [Loop@0x42d69c at line 188 in unMemorizeNodes]
[218] [Loop@0x42d820 at line 848 in threadSequenceThroughGraph]
[12] [Loop@0x42d940 at line 642 in ghostThreadSequenceThroughGraph]
[186] [Loop@0x42db42 at line 226 in isNodeMemorized]
[292] [Loop@0x42dc11 at line 188 in unMemorizeNodes]
[217] [Loop@0x42de10 at line 683 in ghostThreadSequenceThroughGraph]
[9] [Loop@0x42df3f at line 1101 in fillUpGraph.omp_fn.3]
[157] [Loop@0x42f110 at line 127 in importRoadMapArray]
[866] [Loop@0x42f1b0 at line 148 in importRoadMapArray]
[76] [Loop@0x42f1e8 at line 154 in importRoadMapArray]
[642] [Loop@0x42f690 at line 374 in destroyPreGraph_pg]
[151] [Loop@0x42f787 at line 1217 in exportPreGraph_pg]
[166] [Loop@0x42f7ce at line 1149 in exportPreGraph_pg]
[563] [Loop@0x42fb19 at line 1321 in appendPositiveDescriptor_pg]
[787] [Loop@0x42fc13 at line 1355 in appendNegativeDescriptor_pg]
[261] [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg]
[224] [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg]
[271] [Loop@0x42fcb0 at line 1003 in addPreNodeToPreGraph_pg]
[391] [Loop@0x42fd7d at line 1015 in newDescriptor_pg]
[856] [Loop@0x42ff74 at line 1025 in newDescriptor_pg]
[393] [Loop@0x4300ff at line 83 in simplePreArcCount_pg]
[272] [Loop@0x4301b8 at line 923 in renumberPreNodes_pg]
[282] [Loop@0x43022b at line 942 in renumberPreNodes_pg]
[353] [Loop@0x43023c at line 900 in renumberPreNodes_pg]
[366] [Loop@0x43034c at line 900 in renumberPreNodes_pg]
[493] [Loop@0x43055a at line 453 in removePreArcFromList_pg]
[488] [Loop@0x430640 at line 310 in destroyPreNode_pg]
[458] [Loop@0x4306a6 at line 310 in destroyPreNode_pg]
[38] [Loop@0x431967 at line 83 in createPreArc_pg]
[859] [Loop@0x431bd1 at line 488 in createAnalogousPreArc_pg]
[766] [Loop@0x432040 at line 63 in createNodeLocks.omp_fn.1]
[79] [Loop@0x4320d0 at line 154 in orderInsertionMarkers.omp_fn.0]
[27] [Loop@0x4321b0 at line 867 in connectPreNodes.omp_fn.2]
[28] [Loop@0x432270 at line 699 in connectPreNodes.omp_fn.2]
[307] [Loop@0x43227f at line 891 in connectPreNodes.omp_fn.2]
[34] [Loop@0x432390 at line 705 in connectAnnotation]
[84] [Loop@0x432850 at line 390 in createPreNodes]
[350] [Loop@0x432907 at line 427 in createPreNodes]
[120] [Loop@0x4329dc at line 461 in createPreNodes]
[125] [Loop@0x432a00 at line 461 in createPreNodes]
[128] [Loop@0x432a08 at line 461 in createPreNodes]
[119] [Loop@0x432bfd at line 430 in createPreNodes]
[163] [Loop@0x432bfd at line 506 in createPreNodes]
[164] [Loop@0x432bfd at line 506 in createPreNodes]
[161] [Loop@0x432bfd at line 506 in createPreNodes]
[355] [Loop@0x432cb2 at line 119 in createPreNodes]
[239] [Loop@0x432de1 at line 554 in createPreNodes]
[415] [Loop@0x432ee1 at line 565 in createPreNodes]
[303] [Loop@0x432faa at line 602 in createPreNodes]
[357] [Loop@0x4332b7 at line 177 in setInsertionMarkers]
[362] [Loop@0x4332db at line 185 in setInsertionMarkers]
[775] [Loop@0x433373 at line 205 in setInsertionMarkers]
[196] [Loop@0x4333ac at line 214 in setInsertionMarkers]
[197] [Loop@0x4333d6 at line 222 in setInsertionMarkers]
[296] [Loop@0x433508 at line 276 in countPreNodes]
[345] [Loop@0x433570 at line 287 in countPreNodes]
[388] [Loop@0x4335be at line 119 in countPreNodes]
[598] [Loop@0x433611 at line 309 in countPreNodes]
[446] [Loop@0x43367f at line 119 in countPreNodes]
[268] [Loop@0x4337dd at line 341 in newPreGraph_pg]
[731] [Loop@0x4338dc at line 846 in connectPreNodes]
[387] [Loop@0x433bd2 at line 195 in isEligibleTip]
[335] [Loop@0x433d43 at line 45 in concatenatePreNodes]
[543] [Loop@0x433e80 at line 83 in concatenatePreNodes]
[451] [Loop@0x433f15 at line 109 in concatenatePreNodes]
[919] [Loop@0x433f65 at line 103 in concatenatePreNodes]
[358] [Loop@0x433f90 at line 123 in concatenatePreNodes]
[918] [Loop@0x4340b8 at line 94 in concatenatePreNodes]
[159] [Loop@0x434140 at line 142 in concatenatePreGraph_pg]
[188] [Loop@0x434154 at line 146 in concatenatePreGraph_pg]
[327] [Loop@0x4341ba at line 165 in concatenatePreGraph_pg]
[330] [Loop@0x434278 at line 235 in clipTips_pg]
[331] [Loop@0x43428c at line 242 in clipTips_pg]
[966] [Loop@0x434e08 at line 105 in identifyUniqueNodes]
[3] [Loop@0x435cf0 at line 84 in findKmerInKmerOccurenceTable]
[597] [Loop@0x435df8 at line 63 in sortKmerOccurenceTable]
[996] [Loop@0x435e50 at line 185 in sortKmerOccurenceTable]
[643] [Loop@0x435f4b at line 157 in sortKmerOccurenceTable]
[605] [Loop@0x436210 at line 242 in destroyAllocArrayArray]
[982] [[vsyscall]]
[94] [libgomp.so.1.0.0]
[538] _IO_fclose
[547] _IO_fflush
[53] _IO_getc
[19] _IO_vfprintf
[448] __ctype_b_loc
[983] __gettimeofday
[70] __isoc99_sscanf
[225] __libc_calloc
[572] __libc_realloc
[13] __libc_start_main
[569] __strlen_sse42
[558] __strncpy_ssse3
[973] __vdso_gettimeofday
[227] _int_free
[344] absorbExtension
[651] absorbExtensionInScaffold
[190] activateArcLookupTable
[989] activateReadStarts
[501] addBufferToDescriptor
[762] addEmptyNodeToGraph
[581] addPassageMarker
[591] addPreArcToPreNode_pg
[442] addPreArcToPreNode_pg
[772] addPreArcToPreNode_pg
[223] addPreNodeToPreGraph_pg
[56] addReadStart
[202] addUncertainPassageMarker
[930] adjustShortReadsByLength
[620] allocArrayAllocate
[289] allocArrayArrayAllocate
[610] allocArrayArrayFree
[423] allocArrayFree
[702] allocArrayGetElement
[519] allocArrayGetElement
[878] allocateArc
[585] allocateConnection
[863] allocateConnection
[864] allocateConnectionStack
[940] allocateConnectionStack
[1034] allocateDFibHeapNode
[761] allocateFibHeapEl
[885] allocateNode
[1023] allocateNodeList
[1028] allocateNodeList
[929] allocateNodeSpace
[720] allocatePassageMarker
[713] allocatePassageMarker
[910] allocatePassageMarker
[109] allocatePointer
[291] allocatePreArc_pg
[805] allocatePreArc_pg
[655] allocateReadToNodeTables
[182] allocateSmallNodeList
[167] allocateSmallNodeList
[317] appendDescriptors
[487] appendDescriptors_pg
[502] appendGap
[748] appendNegativeDescriptor_pg
[349] appendNodeSequence
[517] appendPositiveDescriptor_pg
[781] arcMergeSort
[659] arcMergeSort
[667] arcMergeSort
[1007] arcMergeSort
[783] blurLastShortReadMarker
[141] buildScaffold
[221] callocOrExit3
[578] catDescriptors
[717] chooseNextInternalPreNode
[739] chooseNextInternalPreNode
[40] cleanUpRedundancy
[824] clearKmer
[144] clipTipsHard
[476] clipTipsVeryHardLocally
[200] clipTips_pg
[1] clone
[173] commonNodeReads
[336] compareCoords
[628] compareIDnums
[106] compareInsertionMarkers
[482] compareKmerOccurences
[674] compareKmerOccurences
[4] compareKmers
[50] comparePaths
[130] compareSequences
[192] compareShortReadMarkers
[338] computeNodeToNodeMappings
[89] computeNodeToNodeMappings.omp_fn.3
[636] computeNodeToNodeMappings.omp_fn.5
[984] computePartialReadToNodeMappingLong
[72] computePartialReadToNodeMappingShort
[379] computeReadToNodeCounts
[117] computeReadToNodeCounts.omp_fn.0
[274] computeReadToNodeMappings
[74] computeReadToNodeMappings.omp_fn.1
[843] computeSecondInPair
[432] concatenateCommonTodoLists
[59] concatenateGraph
[169] concatenateNodesAndVaccinate
[873] concatenatePassageMarkers
[147] concatenatePathNodes
[127] concatenatePreGraph_pg
[220] concatenatePreNodes
[77] concatenateReadStarts
[63] concatenateStringOfNodes
[741] concatenateTodoListIntoActive
[461] concatenateTodoLists
[606] concatenateTodoLists
[30] connectAnnotation
[378] connectPassageMarkers
[29] connectPreNodeToTheNext
[99] connectPreNodes
[26] connectPreNodes.omp_fn.2
[650] connectionSingleRotateWithLeft
[685] connectionSingleRotateWithRight
[269] convertInsertionMarkers
[700] convertMarker
[719] convertMarker
[198] convertSequences
[609] copyKmers
[15] correctGraph
[440] correctGraphLocally
[692] countCoOccurences
[295] countPreNodes
[255] countShortReads
[245] createAnalogousArc
[511] createAnalogousPreArc_pg
[35] createArc
[162] createConnection
[990] createNewConnection
[764] createNodeLocks.omp_fn.1
[868] createNodeLocks.omp_fn.2
[421] createNodeReadStartArrays
[36] createPreArc_pg
[51] createPreNodes
[753] createReadPairingArray
[1033] createReadsLocks
[617] createTwinConnectionInTree
[903] deallocateArc
[815] deallocateConnectionStack
[875] deallocateFibHeapEl
[876] deallocatePassageMarker
[510] deallocatePassageMarker
[301] deallocatePointer
[683] deallocatePreArc_pg
[746] deallocatePreArc_pg
[306] deallocateSmallNodeList
[294] deallocateSmallNodeList
[604] destroyAllocArrayArray
[319] destroyArc
[988] destroyConnection
[603] destroyGraph
[276] destroyNode
[244] destroyPassageMarker
[479] destroyPaths
[236] destroyPaths
[457] destroyPreArc_pg
[489] destroyPreArc_pg
[525] destroyPreGraph_pg
[356] destroyPreNode_pg
[615] destroyRecycleBin
[614] destroyRecycleBinChunks
[841] detachDubiousReads
[122] determineEligibleStartingPoints
[950] dfh_cascading_cut
[799] dfh_compare
[725] dfh_compare
[521] dfh_compare
[108] dfh_consolidate
[949] dfh_cut
[1020] dfh_delete
[1022] dfh_extractmin
[81] dfh_extractmin
[82] dfh_extractminel
[1021] dfh_extractminel
[115] dfh_heaplink
[961] dfh_insertel
[784] dfh_insertkey
[618] dfh_insertrootlist
[129] dfh_insertrootlist
[962] dfh_insertrootlist
[1010] dfh_removerootlist
[386] dfh_removerootlist
[846] dfh_replacedata
[629] dfh_replacekey
[684] dfh_replacekeydata
[647] dfhe_insertafter
[576] dfhe_insertafter
[124] dfhe_insertafter
[123] dfhe_insertbefore
[862] dfhe_newelem
[1011] dfhe_remove
[420] dfhe_remove
[947] dfhe_remove
[494] directlyAppendDescriptors
[656] disconnectNextPassageMarker
[310] displayGeneralStatistics
[763] emptyNode
[897] erf
[589] estimateMissingInsertLengths
[735] exp
[136] expandLongNode
[133] expandLongNodes
[565] expandNode
[675] expectedNumberOfConnections
[101] exploitShortReadPairs
[485] exportArc
[454] exportArc
[18] exportGraph
[170] exportLongNodeSequence
[171] exportLongNodeSequences
[210] exportNode
[152] exportPreGraph_pg
[150] exportPreNode_pg
[406] extractBackOfNodeReads
[404] extractFrontOfNodeReads
[368] extractPassageMarker
[258] extractSequence
[85] fgets
[906] fh_compare
[828] fh_compare
[195] fh_consolidate
[149] fh_extractmin
[154] fh_extractminel
[277] fh_heaplink
[899] fh_initheap
[925] fh_insertel
[527] fh_insertkey
[265] fh_insertrootlist
[507] fh_insertrootlist
[901] fh_makekeyheap
[811] fh_removerootlist
[409] fh_removerootlist
[567] fhe_initelem
[552] fhe_insertafter
[288] fhe_insertafter
[480] fhe_insertafter
[284] fhe_insertbefore
[541] fhe_newelem
[904] fhe_remove
[435] fhe_remove
[206] fillTightStringWithString
[25] fillUpGraph
[10] fillUpGraph.omp_fn.3
[5] fillUpGraph.omp_fn.4
[2] findKmerInKmerOccurenceTable
[187] findLowCoverageRegions
[999] findOppositeNode
[257] findOrCreateConnection
[825] findReferenceMapping
[497] free
[770] freeDoneTickets
[328] getAnnotSequenceID
[681] getAnnotationCount
[428] getAnnotationLength
[351] getArc
[314] getArcBetweenNodes
[179] getArcBetweenNodes
[52] getArcBetweenNodes
[932] getConnection
[665] getConnectionDestination
[927] getConnectionDistance
[248] getDestination
[42] getDestination_pg
[858] getDestination_pg
[484] getDestination_pg
[230] getFinish
[490] getFinishID
[981] getFinishOffset
[721] getInsertLength
[160] getInsertionMarkerPosition
[201] getInsertionMarkerPosition
[649] getInsertionMarkerPosition
[977] getInsertionMarkerPosition
[367] getInsertionMarkerPosition
[837] getInsertionMarkerPosition
[390] getInsertionMarkerPosition
[463] getInsertionMarkerPosition
[726] getInsertionMarkerPosition
[174] getKmerKey
[177] getKmerOccurenceNodeID
[264] getKmerOccurencePosition
[381] getLength
[624] getMarker
[346] getMultiplicity
[1015] getMultiplicity
[682] getNextAnnotation
[522] getNextArc
[546] getNextInNode
[883] getNextInSequence
[347] getNextInSequence
[872] getNextInSequence
[396] getNextPreArc_pg
[734] getNextPreArc_pg
[732] getNextPreArc_pg
[531] getNextPreArc_pg
[577] getNextPreArc_pg
[472] getNextPreArc_pg
[792] getNextPreArc_pg
[235] getNextPreArc_pg
[360] getNode
[557] getNodeDHeapNode
[958] getNodeDHeapNode
[544] getNodeID
[49] getNodeID
[924] getNodeInGraph
[47] getNodeInGraph
[1002] getNodeLength
[148] getNodeLength
[594] getNodePrevious
[808] getNodePrevious
[779] getNodePrevious
[1000] getNodePrevious
[640] getNodePrevious
[790] getNodePrevious
[789] getNodePrevious
[912] getNodePrevious
[1012] getNodePrevious
[834] getNodePrevious
[804] getNodePrevious
[363] getNodePrevious
[743] getNodePrevious
[707] getNodeReadCount
[688] getNodeReads
[365] getNodeStatus
[137] getNodeTime
[711] getNodeTime
[112] getNodeTime
[976] getNodeTime
[835] getNodeTime
[619] getNodeTime
[953] getNodeTime
[715] getNodeTime
[455] getNodeTime
[496] getNodeTime
[561] getNodeTime
[908] getNodeTime
[551] getNodeTime
[107] getNucleotide
[902] getNucleotideChar
[969] getNucleotideInDescriptor
[630] getNucleotideInDescriptor
[710] getNucleotideInDescriptor
[634] getNucleotideInDescriptor
[851] getNucleotideInDescriptor
[571] getNucleotideInDescriptor
[644] getNucleotideInDescriptor
[991] getNucleotideInDescriptor
[361] getNucleotideInDescriptor
[530] getNucleotideInDescriptor_pg
[592] getOtherEnd_pg
[616] getPassageMarkerFinish
[810] getPassageMarkerLength
[887] getPassageMarkerSequenceID
[752] getPassageMarkerStart
[849] getPassageMarkerStatus
[584] getPosition
[39] getPreArcBetweenPreNodes_pg
[860] getPreArcBetweenPreNodes_pg
[957] getPreArc_pg
[559] getPreArc_pg
[219] getPreArc_pg
[508] getPreNodeInPreGraph_pg
[926] getPreNodeInPreGraph_pg
[111] getPreNodeLength_pg
[658] getPreviousInSequence
[408] getRecycleBinInArray
[533] getSequenceLengths
[401] getShortReadCoords
[243] getShortReadMarkerAtIndex
[465] getShortReadMarkerID
[997] getShortReadMarkerOffset
[260] getShortReadMarkerPosition
[444] getShortReadTwinCoords
[143] getStart
[600] getStartID
[676] getStartOffset
[722] getTightStringInArray
[515] getTipLength
[417] getTwinMarker
[545] getTwinMarker
[228] getTwinNode
[760] getUniqueness
[727] getWordLength
[11] ghostThreadSequenceThroughGraph
[208] hasSinglePreArc_pg
[967] identifyUniqueNodes
[16] importPreGraph
[98] importReadSet
[62] importRoadMapArray
[596] incrementAnnotationCoordinates
[322] incrementOriginalVirtualCoverage
[214] incrementReadStartCount
[240] incrementVirtualCoverage
[267] initializeTodoLists
[41] injectShortReads
[1009] insertNodeIntoDHeap
[729] insertPassageMarker
[514] integrateDerivativeDistances
[359] isEligibleTip
[812] isInitial
[582] isLocalDeadEnd
[657] isLocalTwinDeadEnd
[830] isLoop_pg
[168] isNodeMemorized
[209] isNodeMemorized
[975] isPreviousToNode
[411] isPreviousToNode
[372] isPreviousToNode
[466] isSecondInPair
[392] isTerminal
[993] isUniqueSolexa
[175] keyInAccelerationTable
[623] keyInAccelerationTable
[68] lockNode
[80] lockNode
[237] lockRead
[281] lockTwoNodes
[75] lockTwoNodes
[58] lockTwoNodes
[370] logFinalStats
[693] lowCoverageRegions
[14] main
[65] malloc
[67] mallocOrExit3
[526] mapDistancesOntoPaths
[673] mapSlowOntoFast
[512] markInterestingNodes
[491] markerLeadsToNode
[661] markerLeadsToNode
[259] max
[679] measureCoOccurences
[178] memorizeNode
[165] memorizeNode
[820] mergeArcLists
[869] mergeArcLists
[343] mergeDescriptors
[468] mergeDescriptors
[754] mergeNodeReads
[788] min
[769] min_short
[1025] msort_with_tmp
[1014] n50
[232] newDescriptor_pg
[898] newFibHeap
[933] newMask
[37] newPreGraph_pg
[900] newRecycleBin
[586] newTightString
[199] newTightStringArrayFromStringArray
[434] nextStartingPoint
[229] nextTodoTicket
[580] nodeCount
[854] norm
[802] norm
[1008] norm
[972] normInt
[1003] normInt
[380] omp_get_thread_num
[765] omp_init_lock
[44] omp_set_lock
[91] omp_test_lock
[48] omp_unset_lock
[279] orderInsertionMarkers
[78] orderInsertionMarkers.omp_fn.0
[96] orderNodeReadStartArrays
[840] pairedCategories
[853] passageMarkerDirection
[407] pathContainsReference
[814] popConnectionStack
[807] popNodeRecord
[652] popNucleotide
[662] preNodeCount_pg
[315] printShortCounts
[970] printf
[87] projectFromNode
[184] projectFromReadPair
[93] projectFromShortRead
[203] projectFromSingleRead
[939] pushConnectionStack
[865] pushConnectionStack
[142] pushNeighbours
[185] pushNucleotide
[964] qsort
[43] qsort_r
[994] readCoherentGraph
[212] readPreGraphFile
[382] readjustConnectionInTree
[987] readjustMiniConnection
[1031] readjustMiniConnection
[564] reallocOrExit4
[424] reallocateNodeDescriptor
[414] recordKmerOccurence
[1024] recordNode
[923] recordNode
[83] referenceGraphKmers
[313] remapBackOfNodeArcsOntoNeighbour
[587] remapBackOfNodeDescriptorOntoNeighbour
[61] remapBackOfNodeMarkersOntoNeighbour
[55] remapBackOfNodeOntoNeighbour
[436] remapBackOfNodeTimesOntoNeighbour
[935] remapEmptyPathArcsOntoMiddlePathSimple
[299] remapEmptyPathMarkersOntoMiddlePathSimple
[298] remapEmptyPathOntoMiddlePath
[342] remapNodeArcsOntoNeighbour
[252] remapNodeArcsOntoTarget
[437] remapNodeFibHeapReferencesOntoNode
[555] remapNodeInwardReferencesOntoNode
[550] remapNodeInwardReferencesOntoNode
[104] remapNodeMarkersOntoNeighbour
[97] remapNodeOntoNeighbour
[475] remapNodeTimesOntoNeighbour
[474] remapNodeTimesOntoTargetNode
[706] removeHighCoverageNodes
[66] removeLowCoverageNodesAndDenounceDubiousReads
[946] removeNextNodeFromDHeap
[238] removeNodeAndDenounceDubiousReads
[426] removePreArcFromList_pg
[250] removeUnreliableConnections
[516] renumberNodes
[273] renumberPreNodes_pg
[913] resetMiniConnection
[922] resetMiniConnection
[539] resetNodeStatus
[621] reverseCatDescriptors
[114] reversePushNucleotide
[831] sequenceCount
[794] sequenceCount_pg
[744] setFinishID
[139] setInsertionMarkers
[354] setMarker
[395] setNextInNode
[797] setNextInSequence
[670] setNextInSequence
[941] setNodePrevious
[773] setNodePrevious
[848] setNodePrevious
[663] setNodePrevious
[819] setNodeStatus
[1006] setNodeTime
[645] setPassageMarkerFinish
[768] setPassageMarkerStart
[403] setPassageMarkerStatus
[823] setPreNodeDescriptor_pg
[793] setPreviousInSequence
[690] setPreviousInSequence
[389] setPreviousInSequence
[1004] setPreviousInSequence
[176] setShortReadMarkerOffset
[1032] setShortReadMarkerOffset
[971] setShortReadMarkerOffset
[669] setShortReadMarkerOffset
[599] setShortReadMarkerOffset
[870] setShortReadMarkerOffset
[951] setShortReadMarkerOffset
[914] setShortReadMarkerOffset
[635] setShortReadMarkerOffset
[341] setShortReadMarkerOffset
[978] setShortReadMarkerOffset
[397] setShortReadMarkerOffset
[749] setShortReadMarkerOffset
[821] setShortReadMarkerOffset
[467] setShortReadMarkerOffset
[429] setShortReadMarkerPosition
[968] setShortReadMarkerPosition
[845] setShortReadMarkerPosition
[443] setShortReadMarkerPosition
[745] setShortReadMarkerPosition
[945] setShortReadMarkerPosition
[340] setShortReadMarkerPosition
[888] setShortReadMarkerPosition
[535] setShortReadMarkerPosition
[560] setShortReadMarkerPosition
[242] setShortReadMarkerPosition
[402] setShortReadMarkerPosition
[795] setShortReadMarkerPosition
[889] setShortReadMarkerPosition
[917] setShortReadMarkerPosition
[818] setSingleNodeStatus
[928] setStartID
[733] setStartOffset
[791] setTightStringLength
[405] setTopOfTheNode
[737] shiftRight
[548] shiftRight
[459] simpleArcCount
[385] simplePreArcCount_pg
[153] simplifyNode
[300] sortCoords
[318] sortCoords
[105] sortKmerOccurenceTable
[450] sortNodeArcs
[509] sortNodeArcs
[297] splayConnection
[638] splayToList
[588] splitNodeDescriptor
[304] spreadReadIDs
[646] testConnection
[7] threadSequenceThroughGraph
[24] tourBus
[33] tourBusArc
[31] tourBusNode
[937] tourBus_local
[376] transferNodeData
[728] transposePassageMarker
[270] unLockNode
[145] unLockNode
[86] unLockRead
[383] unLockTwoNodes
[92] unLockTwoNodes
[181] unLockTwoNodes
[290] unMemorizeNodes
[280] unMemorizeNodes
[696] unmarkInterestingNodes
[283] updateNodeStatus
[369] updatePreArcData_pg
[377] updatePreArcData_pg
[371] usedReads
[17] velvetFprintf
[891] velvetLog
[309] writeNucleotide
[632] writeNucleotideAtPosition
[809] writeNucleotideInDescriptor
[1017] writeNucleotideInDescriptor
[974] writeNucleotideInDescriptor
[877] writeNucleotideInDescriptor
[907] writeNucleotideInDescriptor
[1029] writeNucleotideInDescriptor
[740] writeNucleotideInDescriptor
[747] writeNucleotideInDescriptor
[786] writeNucleotideInDescriptor
[777] writeNucleotideInDescriptor
[880] writeNucleotideInDescriptor
[871] writeNucleotideInDescriptor
[384] writeNucleotideInDescriptor_pg
[664] writeNucleotideInDescriptor_pg
[750] writeNucleotideNumber
[339] writeNucleotideNumber
