[fix][VCF,indel] Add check for deletion in alleles #562
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Bug: VCF v4.2 introduced the use of asterisk notation (*) in ALTs to represent spanning deletions. If there are alternative alleles at a site, the ‘*’ allele is reserved to indicate that an allele allele is missing due to an upstream deletion. This led to segfaults in angsd VCF reading. Fix: Add hasDelAlt func to check if there is any deletion * in alleles using strcmp. Fixes #557
isinaltinkaya
changed the title
Bug: Apparently [smallBam/small2.bcf](https://github.com/ANGSD/smallBam/blob/master/small2.bcf) contains lots of symbolic alternate alleles, and the sites with only these caused the tests to fail since hasDelAlt was called before isindel. Fix: Add check if record d.allele is NULL before using it. Fixes PR #562 unit tests. Add debugging mode to Makefile to enable debugging-related features easily. Add vgcore to gitignore.
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Bug: VCF v4.2 introduced the use of asterisk notation (*) in ALTs to represent spanning deletions. If there are alternative alleles at a site, the ‘*’ allele is reserved to indicate that an allele allele is missing due to an upstream deletion. This led to segfaults in angsd VCF reading.
Fix: Add hasDelAlt func to check if there is any deletion in alleles using strcmp.
Fixes #557