update to work with vcf 4.4 prefixed phasing info #1861
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| * Explicit / prefixed phasing for 1st allele is used only when it is a must to | ||
| * correctly express phasing. | ||
| */ | ||
| static inline int bcf_format_gt1(const bcf_hdr_t *hdr, bcf_fmt_t *fmt, int isample, kstring_t *str) |
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The suffix 1, as used here, is confusing and somewhat conflicting with the convention used throughout the rest of the code. Can you rename so that the 'phase' keyword is included? Or, even better, create an extended function where various flags can be turned on, starting with PHASE_1ST_ALLELE, or something like that?
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I think the name should not be made more specific, and if possible made more generic!
An implementation which supports the newer format should be the 1st choice going forward.
Best would have been to update the current method itself but not possible as it would break the compatibility due to signature change.
Hence chose a name which is in sync with current method. Also we have a few others like index_load/index_build/ etc in same lines.
update to work with vcf 4.4 specification, on prefixed phasing indicators.
vcf files with version < 4.4 are handled as earlier and changes apply only to v4.4 and later.
when explicit phasing indicator present, it is used.
when there are no explicit phasing indicator, phasing status is identified as given in 6.3.3 of vcf4.4 format.
haploids considered implicitly phased and others based on presence of other unphased alleles.
outputs will have prefixed phasing indicator when phasing can not be correctly inferred without it being present.
e.g. unphased haploid - though not found usually, unphased 1st allele with all other alleles phased, phased 1st allele with another unphased allele etc.
A new bcf_format_gt1 method, derived from bcf_format_gt does this output formatting. bcftools may have to use this method to handle vcf 4.4 with prefixed phasing info.
A version enumeration type is added and a method to convert file format header to enumerated version also added.
Fixes #1847