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Jkbonfield vcf int64 #1003
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Jkbonfield vcf int64 #1003
Commits on Dec 9, 2019
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Fixes BCF in-memory decoding with 64-bit integers.
Any 64-bit INFO field that wasn't the last in the list would cause subsequent fields to be decoded incorrectly. This commit fixes that, plus updates the tests accordingly so the bug could be triggered. Fixes the first part of samtools#999 (test1.vcf), but doesn't fix the second part (BCF output silently being broken). Fixes samtools/bcftools#1123
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Commits on Dec 10, 2019
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Make 64-bit optional and don't compile by default.
This commit addresses several problems introduced by the recently added support of 64-bit coordinates: - 64-bit positions were silently modified on BCF output - any erroneous out-of-range INFO value resulted in unparseable BCF output (in contrast to the previous behavior of a silent under/overflow) - conversion between VCF and BCF is no longer possible Large genomes is a niche area and can be easily worked around by splitting the largest chromosome into two. This commit makes the compilation of 64-bit values optional, favoring the interroperability of BCF with VCF, a feature heavily relied on in many pipelines. The support of large genomes in this commit is limited to POS and INFO tags defined as Number=1 (motivated by INFO/END), all other extreme values are replaced with a missing value ("."). This changes the original ad-hoc approach which supported first field of any INFO tag array. The default 32-bit mode adds checks to prevent under/overflow of INFO and FORMAT integer values and prints a warning when extreme values are replaced with a missing value. An additional check is added to prevent overflow of 64-bit coordinates on BCF output. Note that the 64-bit support is not compiled in by default because: - it breaks VCF/BCF specification - it works only for VCF but cannot produce a functional BCF - there is currently no front-end capable of indexing VCFs with 64bit coordinates (n_lvls is not accessible via `bcftools index`) Note that a full 64-bit support for BCF would require significantly more work and large changes of the codebase, API, and the BCF specification, therefore it is not planned at the moment. The limited POS and INFO/END support for VCF can be compiled in by editing htslib/vcf.c and setting #define ALLOW_INT64 1
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Commits on Dec 11, 2019
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Commits on Dec 12, 2019
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Allow compilation w/o modifying vcf.c
and temporarily comment out failing tests which assume 64 bit positions are compiled in by default.
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Commits on Dec 13, 2019
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Commits on Dec 16, 2019
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- bug fix in `bcf_dec_typed_int1_safe()`, 64-bit values could not have been read correctly by this function - cosmetic change to declare val1 always as int64_t and explicit cast to int32_t and add explicit LL to a 64-bit constant in case some compilers were fussy
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