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bugfix: HD line should be printed before SQ #345

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bugfix: HD line should be printed before SQ #345

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13 changes: 9 additions & 4 deletions bwa.c
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Original file line number Diff line number Diff line change
Expand Up @@ -421,7 +421,14 @@ void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
if (p == hdr_line || *(p-1) == '\n') ++n_SQ;
p += 4;
}
// print the header line if @HD is in hdr_line
if (n_HD > 0) err_printf("%s\n", hdr_line);
}
// print a default header line if no @HD has been printed
if (n_HD == 0) {
err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");
}
Comment on lines +428 to +430
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Could be a one-liner in the style of this repo

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if (n_HD == 0) {
err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");
}
if (n_HD == 0) err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");

// print the @SQ lines right after the @HD line
if (n_SQ == 0) {
for (i = 0; i < bns->n_seqs; ++i) {
err_printf("@SQ\tSN:%s\tLN:%d", bns->anns[i].name, bns->anns[i].len);
Expand All @@ -430,10 +437,8 @@ 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);
// print the header line if header line is defined and is not a @HD (e.g. @CO); do this after the @SQ lines.
if (hdr_line && n_HD == 0) err_printf("%s\n", hdr_line);
if (bwa_pg) err_printf("%s\n", bwa_pg);
}

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