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Add the header line to the output SAM #336

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Merged
merged 1 commit into from
Mar 6, 2022
Merged

Add the header line to the output SAM #336

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12 changes: 11 additions & 1 deletion bwa.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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);
}
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