Download the source code here: bcftools-1.23.3.tar.bz2. (The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)
Changes affecting specific commands:
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bcftools annotate
- Allow annotation of Number=A,R INFO tags from tab-delimited files when alleles are split across multiple records.
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bcftools call
- Fix update of CLR tags
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bcftools convert
- Fix crash when using threads, HAP/LEGEND/SAMPLE output, but suppressing the HAP file by specifying it as '.' (#2528)
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bcftools cnv
-
Fix off-by-one error in reporting HMM qualities
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Fix invalid BAF look-up if no control samples are present
-
-
bcftools csq
-
Fix a segfault caused by incorrect handling of symbolic ALT alleles
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Fix a segfault when the VCF header has no contig lines (#2590)
-
-
bcftools merge
- Fixes in memory access with localized alleles, it could result in printing printing trailing garbage in localized FORMAT fields (#2520)
-
bcftools mpileup
- Fix various bugs in insertion calling (#2531)
-
bcftools norm
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Fix a bug in splitting Type=String FORMAT fields via -a and -m (#2476)
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Check that reference segments match the length expected
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-
bcftools plugin
- Fix plugin link failure when building with --enable-gsl
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bcftools reheader
- Better error reporting on invalid --samples file, don't segfault (#2538)
-
bcftools roh
- Fix off-by-one error in reporting HMM qualities
-
bcftools stats
- Check for failure to load references
Download the source code here: bcftools-1.23.3.tar.bz2. (The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)