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fixed a couple bugs identified by gcc 

Recent gcc is better.
This commit is contained in:
Heng Li 2013-02-23 17:15:07 -05:00
parent 6e7903e9f3
commit cda85be059
3 changed files with 4 additions and 3 deletions
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2
bwamem.c
View File

@ -569,7 +569,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
}
if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
if (bwa_rg_id) { kputsn("\tRG:i:", 6, str); kputs(bwa_rg_id, str); }
if (bwa_rg_id[0]) { kputsn("\tRG:i:", 6, str); kputs(bwa_rg_id, str); }
if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
kputc('\n', str);
free(cigar);

4
bwase.c
View File

@ -434,7 +434,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
err_printf("%s", p->qual);
} else err_printf("*");
if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
if (p->type != BWA_TYPE_NO_MATCH) {
@ -482,7 +482,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
err_printf("%s", p->qual);
} else err_printf("*");
if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
putchar('\n');

1
kopen.c
View File

@ -6,6 +6,7 @@
#include <string.h>
#include <stdlib.h>
#include <signal.h>
#include <sys/wait.h>
#include <sys/types.h>
#ifndef _WIN32
#include <netdb.h>