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Merge pull request #336 from nh13/patch-5 

Add the header line to the output SAM
This commit is contained in:
Heng Li 2022-03-06 18:06:38 -05:00 committed by GitHub
parent d47f12cddc 56026158d8
commit 4a18837bd2
1 changed files with 11 additions and 1 deletions
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12
bwa.c
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@ -406,10 +406,17 @@ int bwa_idx2mem(bwaidx_t *idx)
void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
{
int i, n_SQ = 0;
int i, n_HD = 0, n_SQ = 0;
extern char *bwa_pg;
if (hdr_line) {
// check for HD line
const char *p = hdr_line;
if ((p = strstr(p, "@HD")) != 0) {
++n_HD;
}
// check for SQ lines
p = hdr_line;
while ((p = strstr(p, "@SQ\t")) != 0) {
if (p == hdr_line || *(p-1) == '\n') ++n_SQ;
p += 4;
@ -423,6 +430,9 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
}
} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
if (n_HD == 0) {
err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");
}
if (hdr_line) err_printf("%s\n", hdr_line);
if (bwa_pg) err_printf("%s\n", bwa_pg);
}