Path: blob/main/biology/cufflinks/files/patch-src_gdna.cpp
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--- src/gdna.cpp.orig 2022-07-28 03:26:30 UTC1+++ src/gdna.cpp2@@ -11,8 +11,8 @@ const char* IUPAC_COMP ="TtGgAaCcAaKkYyWwSsRrMmBbDdHh3#define G_2BIT 2 // 104#define T_2BIT 3 // 1156-static byte ntCompTable[256];7-static byte nt2bit[256]; //maps any character to a 2bit base value (with N = A)8+static bytex ntCompTable[256];9+static bytex nt2bit[256]; //maps any character to a 2bit base value (with N = A)10static char v_2bit2nt[4] = {'A','C','G','T'};1112//----------------------13@@ -21,9 +21,9 @@ static bool gdna_Ready=gDnaInit();1415//----------------------1617-byte gdna2bit(char* &nt, int n) {18+bytex gdna2bit(char* &nt, int n) {19// Pack n bases into a byte (n can be 1..4)20-byte out = 0;21+bytex out = 0;22while (n && *nt) {23n--;24out <<= 2;25@@ -43,7 +43,7 @@ char ntComplement(char c) {26return ntCompTable[(int)c];27}2829-char g2bit2base(byte v2bit) {30+char g2bit2base(bytex v2bit) {31return v_2bit2nt[v2bit & 0x03 ];32}33343536