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r303: bugfix - wrong band width when CIGAR

This commit is contained in:
Heng Li 2013-02-27 15:39:15 -05:00
parent e620f0ff4e
commit 292e92b602
3 changed files with 7 additions and 7 deletions
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2
bwa.1
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@ -229,8 +229,6 @@ supported throughout BWA. Ideally, a value 0 for disabling all the output to
stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for
all normal messages; 4 or higher for debugging. When this option takes value
4, the output is not SAM. [3]
.RE
.RE
.TP

10
bwa.c
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@ -74,7 +74,7 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
{
uint32_t *cigar = 0;
uint8_t tmp, *rseq;
int i, w;
int i, w, max_gap, min_w;
int64_t rlen;
*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
@ -89,10 +89,12 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
//printf("[Q] "); for (i = 0; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
//printf("[R] "); for (i = 0; i < re - rb; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');
// set the band-width
w = (int)((double)(l_query * mat[0] - q) / r + 1.);
w = w < 1? w : 1;
max_gap = (int)((double)(((l_query+1)>>1) * mat[0] - q) / r + 1.);
max_gap = max_gap > 1? max_gap : 1;
w = (max_gap + abs(rlen - l_query) + 1) >> 1;
w = w < w_? w : w_;
w += abs(rlen - l_query);
min_w = abs(rlen - l_query) + 3;
w = w > min_w? w : min_w;
// NW alignment
*score = ksw_global(l_query, query, rlen, rseq, 5, mat, q, r, w, n_cigar, &cigar);
{// compute NM

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.6.2-r302-beta"
#define PACKAGE_VERSION "0.6.2-r303-beta"
#endif
static int usage()