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Oss fuzz 499447432 #1999

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Merged
daviesrob merged 2 commits into from
Apr 20, 2026
Merged

Oss fuzz 499447432 #1999

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b617ed7
Fix extend_ref to not change ref_end on error.
jkbonfield Apr 8, 2026
490b3b3
Improve SQ LN field checking.
jkbonfield Apr 13, 2026
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5 changes: 4 additions & 1 deletion cram/cram_encode.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1504,7 +1504,7 @@ int next_cigar_op(uint32_t *cigar, uint32_t ncigar, int *skip, int *spos,
static inline int extend_ref(char **ref, uint32_t (**hist)[5], hts_pos_t pos,
hts_pos_t ref_start, hts_pos_t *ref_end,
hts_pos_t *ref_end_alloc) {
if (*ref_end < pos)
if (*ref_end < pos && pos < *ref_end_alloc)
*ref_end = pos;
if (pos < ref_start)
return -1;
Expand Down Expand Up @@ -1542,6 +1542,9 @@ static inline int extend_ref(char **ref, uint32_t (**hist)[5], hts_pos_t pos,
memset(&(*ref)[old_end], 0, new_end-old_end);
memset(&(*hist)[old_end], 0, (new_end-old_end)*sizeof(**hist));

if (*ref_end < pos)
*ref_end = pos;

return 0;
}

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4 changes: 2 additions & 2 deletions header.c
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Original file line number Diff line number Diff line change
Expand Up @@ -174,8 +174,8 @@ static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
return -1; // SN should be present, according to spec.
}

if (len == -1) {
hts_log_error("Header includes @SQ line \"%s\" with no LN: tag",
if (len <= 0) {
hts_log_error("Header includes @SQ line \"%s\" with invalid or no LN: tag",
name);
return -1; // LN should be present, according to spec.
}
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