Fix vcfconvert ALT parsing, null deref, and sample compression#2528
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pd3 merged 1 commit intosamtools:developfrom Mar 31, 2026
Merged
Fix vcfconvert ALT parsing, null deref, and sample compression#2528pd3 merged 1 commit intosamtools:developfrom
pd3 merged 1 commit intosamtools:developfrom
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1. _set_chrom_pos_ref_alt (~line 207): The while/if conditions checked isspace_c(*tsv->se) (the constant end pointer) instead of !isspace_c(*se) (the advancing scan pointer), causing the ALT allele scan to terminate immediately or never advance. 2. bgzf_thread_pool calls (~lines 1084, 1234): Added NULL check for hout before calling bgzf_thread_pool, preventing a crash when hap output is suppressed by passing '.' as the filename. 3. sample_compressed assignment (~lines 923, 1048, 1197): Changed `sample_compressed = 0` to `sample_compressed = 1` so that .gz sample filenames actually enable compressed output.
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Summary
_set_chrom_pos_ref_alt— while loop checked*tsv->se(constant end pointer) instead of*se(scan pointer), making it a no-opbgzf_thread_pool(hout, ...)when hap output is suppressed with.sample_compressed = 0to= 1in three places — .gz sample filenames were never actually compressedTest plan
.gzsample output files are compressed