Should add all logic required to use grumpy rather than gumpy. Big, breaking changes for development, but should have essentially the same interface and outputs; i.e should be a drop in upgrade with higher performance
grumpy is a bit more picky as to which VCFs it supports (as the VCF parsing library isn't quite as mature as pysam). This means the test case for checking samtools VCF compatibility cannot be included as it doesn't actually have a COV field (or something which could build a COV field)
Similarly, with the recent changes and addition of 'frakenVCF', fasta adjudication was already obsolete so was removed. Also, with the performance gains from grumpy, minor alleles can be found anywhere without penalty, so no longer need to be explicitly told where to look
Should add all logic required to use
grumpyrather thangumpy. Big, breaking changes for development, but should have essentially the same interface and outputs; i.e should be a drop in upgrade with higher performancegrumpyis a bit more picky as to which VCFs it supports (as the VCF parsing library isn't quite as mature as pysam). This means the test case for checking samtools VCF compatibility cannot be included as it doesn't actually have a COV field (or something which could build a COV field)Similarly, with the recent changes and addition of 'frakenVCF', fasta adjudication was already obsolete so was removed. Also, with the performance gains from
grumpy, minor alleles can be found anywhere without penalty, so no longer need to be explicitly told where to look