changes to avoid segfault with uncompressed bam #1632
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daviesrob
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Jun 6, 2023
hts.c
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| @@ -866,6 +871,11 @@ htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt) | |||
| *mode_c = format_to_mode[fmt->format]; | |||
| } | |||
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| // Uncompressed bam/bcf is not supported, remove 'u' flag on write | |||
| if (uncomp && *mode_c == 'b' && (strchr(smode, 'w') || strchr(smode, 'a'))) { | |||
| memcpy(uncomp, uncomp + 1, cp2 - uncomp - 1); | |||
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You should use memmove() here because the source and destination buffers overlap, and memcpy() disallows that. But better still would be to turn the 'u' into a '0', as the result will then be uncompressed while still BGZF wrapped.
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Updated accordingly.
vasudeva8
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Aug 17, 2023
Avoids segfault when writing bam/bcf with mode "wbu" by changing "wbu" to "wb0". The ensures the output file will be properly wrapped in BGZF blocks, even though it's not been compressed. Fixes samtools#1617
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Fix for #1617
when bam write is attempted with 'u', the bgzf compression/decompression buffers are not allocated as it denotes uncompressed output. bgzf_flush, called at end, accesses the compression buffers and causes segfault in such case.
Binary data files are implicitly expected to be bgzf compressed and this 'u' flag is not valid / supported.
The fix made is to remove the 'u' flag on write of bam/bcf that the output is written as bgzf compressed with default compression level.