Add support for VCFv4.4 / VCFv4.5 Number= fields #1874
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Adds BCF_VL_* types for Number= P, LA, LG, LR and M Upgrades bcf_hdr_register_hrec() so that it sets the appropriate value when it finds one of the new types in a FORMAT header line. Only set number type BCF_VL_FIXED if the value can actually be parsed as an integer. Unknown types will now cause a warning to be printed and will be treated as BCF_VL_VAR. Adds doxygen style comments to describe the meaning of the various BCF_VL_* values.
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Adds
BCF_VL_*types for Number=P,LA,LG,LRandM, and updatesbcf_hdr_register_hrec()so that it sets them.Note that this changes handling of unrecognised
Number=values. Previously htslib would attempt to treat these as numbers, and as it did not check forsscanf()failure they were stored as typeBCF_VL_FIXEDwith count0xfffff. This commit makes it print a warning and store the type asBCF_VL_VARinstead.TODO:
bcf_hdr_check_sanity()bcf_remove_allele_set()work with local alleles