Make HaplotypeCaller genotype and output spanning deletions#4963

Merged

cwhelan merged 14 commits intomasterfrom cw_haplotypecaller_spanning_deletions

Sep 5, 2018

+2,655-107

Commits on Aug 27, 2018

first steps towards genotyping with spanning deletions
cwhelan
committed
add a flag for including spanning deletions so changes don't affect mutect
cwhelan
committed
cleanup, documentation, remove unused parameters, small bug fix
cwhelan
committed
fix some bugs in the allele mapper; move from fragile order-dependent mapping to a proper check of matching alleles
cwhelan
committed
remove misleading warning when GGA has multple overlapping variants
cwhelan
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fix one more bug in allele mapping when subset of variants in GGA alleles
cwhelan
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fix one more edge case in allele mapper and simplify
cwhelan
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fix a bug in trimming alleles when one or more alleles not supported by haplotypes (GGA mode)
cwhelan
committed
cleanup and add unit test for compose given alleles variant context
cwhelan
committed
Address PR comments
cwhelan
committed
update test resources after merging -- annotations have changed
cwhelan
committed
small doc fix; update imports after merge
cwhelan
committed

Commits on Aug 31, 2018