[fix] Add VCF spanning deletion check #569
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Issue: 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 was not considered in angsd VCF reading and led to segfaults. Fix: Add hasSpanningDeletion function to check if there is any spanning deletion and skip the sites with spanning deletion. Fixes #557 Add development-related files to gitignore: -vgcore files from valgrind -commit_message.txt commit message template
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Issue: 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 was not considered in angsd VCF reading and led to segfaults. Fix: Add hasSpanningDeletion function to check if there is any spanning deletion and skip the sites with spanning deletion. Fixes #557Add development-related files to gitignore:
-vgcore files from valgrind
-commit_message.txt commit message template