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Permit BAM headers between 2GB and 4GB in size once more. #1421

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merged 1 commit into from
Apr 13, 2022
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Permit BAM headers between 2GB and 4GB in size once more. #1421

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10 changes: 8 additions & 2 deletions sam.c
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Original file line number Diff line number Diff line change
Expand Up @@ -339,17 +339,23 @@ int bam_hdr_write(BGZF *fp, const sam_hdr_t *h)

if (h->hrecs) {
if (sam_hrecs_rebuild_text(h->hrecs, &hdr_ks) != 0) return -1;
if (hdr_ks.l > INT32_MAX) {
if (hdr_ks.l > UINT32_MAX) {
hts_log_error("Header too long for BAM format");
free(hdr_ks.s);
return -1;
} else if (hdr_ks.l > INT32_MAX) {
hts_log_warning("Header too long for BAM specification (>2GB)");
hts_log_warning("Output file may not be portable");
}
text = hdr_ks.s;
l_text = hdr_ks.l;
} else {
if (h->l_text > INT32_MAX) {
if (h->l_text > UINT32_MAX) {
hts_log_error("Header too long for BAM format");
return -1;
} else if (h->l_text > INT32_MAX) {
hts_log_warning("Header too long for BAM specification (>2GB)");
hts_log_warning("Output file may not be portable");
}
text = h->text;
l_text = h->l_text;
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