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r435: bugfix - base not complemented on the rev

This commit is contained in:
Heng Li 2014-02-18 10:32:24 -05:00
parent 14aa43cca0
commit 4adc34eccb
2 changed files with 6 additions and 3 deletions
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7
bwa.c
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@ -93,6 +93,7 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
int i; int i;
int64_t rlen; int64_t rlen;
kstring_t str; kstring_t str;
const char *int2base;
*n_cigar = 0; *NM = -1; *n_cigar = 0; *NM = -1;
if (l_query <= 0 || rb >= re || (rb < l_pac && re > l_pac)) return 0; // reject if negative length or bridging the forward and reverse strand if (l_query <= 0 || rb >= re || (rb < l_pac && re > l_pac)) return 0; // reject if negative length or bridging the forward and reverse strand
@ -127,6 +128,7 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
{// compute NM {// compute NM
int k, x, y, u, n_mm = 0, n_gap = 0; int k, x, y, u, n_mm = 0, n_gap = 0;
str.l = str.m = *n_cigar * 4; str.s = (char*)cigar; // append MD to CIGAR str.l = str.m = *n_cigar * 4; str.s = (char*)cigar; // append MD to CIGAR
int2base = rb < l_pac? "ACGTN" : "TGCAN";
for (k = 0, x = y = u = 0; k < *n_cigar; ++k) { for (k = 0, x = y = u = 0; k < *n_cigar; ++k) {
int op, len; int op, len;
cigar = (uint32_t*)str.s; cigar = (uint32_t*)str.s;
@ -134,7 +136,8 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
if (op == 0) { // match if (op == 0) { // match
for (i = 0; i < len; ++i) { for (i = 0; i < len; ++i) {
if (query[x + i] != rseq[y + i]) { if (query[x + i] != rseq[y + i]) {
kputw(u, &str); kputc("ACGTN"[rseq[y+i]], &str); kputw(u, &str);
kputc(int2base[rseq[y+i]], &str);
++n_mm; u = 0; ++n_mm; u = 0;
} else ++u; } else ++u;
} }
@ -142,7 +145,7 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
} else if (op == 2) { // deletion } else if (op == 2) { // deletion
kputw(u, &str); kputc('^', &str); kputw(u, &str); kputc('^', &str);
for (i = 0; i < len; ++i) for (i = 0; i < len; ++i)
kputc("ACGTN"[rseq[y+i]], &str); kputc(int2base[rseq[y+i]], &str);
u = 0; u = 0;
y += len, n_gap += len; y += len, n_gap += len;
} else if (op == 1) x += len, n_gap += len; // insertion } else if (op == 1) x += len, n_gap += len; // insertion

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.6a-dev-r434" #define PACKAGE_VERSION "0.7.6a+dev-r435"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);