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Work around colons in reference names (GRCh38 HLA). #708
Commits on May 30, 2019
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Work around colons in reference names (GRCh38 HLA).
This extends the callback function used by the hts iterator code to the ref:start-end range parser, permitting the parser to validate whether the whole thing matches a reference name. This works around parsing conflicts when given range queries like "HLA-DRB1*12:17", which is either the whole of "HLA-DRB1*12:17" (this exists in GRCh38) or base 17 onwards of ""HLA-DRB1*12" (which does not). Note there are still some undecided questions here. Do we want to handle the special names used in the iterator at this level to? Eg "*" meaning unmapped data and "." meaning whole file?
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Commits on May 31, 2019
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Now region parsing fails on ambiguous cases.
Also improved return values so NULL is primary way of detecting failure rather than tid. This is more in line with the old hts_parse_reg code. See samtools/hts-specs#124 (comment) for heuristic suggestions.
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Added support for brace-quoting of reference names.
Eg with contigs named "chr1" and "chr1:100-200" we can specify "{chr1}:100-200" and "{chr1:100-200}" to disambiguate.
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Major rewrite of hts_parse_region.
The old function (hts_parse_reg) has been put back, meaning the new API can now have the getid func pointer as a mandatory requirement. Added tests. Tweaked sam_parse_region to have the flags parameter. This is still required as bcftools and samtools use different parameters (parsing style is tool based rather than file format based).
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Changes faidx to use the standard region parser.
Previously it had its own custom parser which nearly, but not quite, matched the old hts_parse_reg code in functionality. Note this changes the fasta coordinate type from long to int, which is a backwards step. However it is expected this will subsequently change to hts_pos_t in another PR.
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Expand hts_parse_region documentation in the header file.
Mainly copied from the useful (but not so visible) comment before the function definition in hts.c.
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Update hts_reglist_create() to use hts_parse_region()
Hash table can now use tid (cast to khash32_t, which is unsigned) as key instead of the region name, avoiding some string copying.
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