Keep unresolved Manta calls #723
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Sometimes an aligner will generate a read mapping with zero aligned bases. When gatk tries to process such a read in the CollectSVEvidence command, it will throw an exception because it gives the read a negative length. This commit adds a read filter when running CollectSVEvidence to ignore such reads.
Merging upstream GATK-SV into forked repo resulted in a flag being added twice because the flag had been introduced in the fork and in the upstream. This commit removes the flag added in the fork.
Create tar files for the tloc and unresolved Manta outputs of TinyResolve instead of an array of files.
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Keep unresolved Manta calls in TinyResolve to assist with resolving ultra complex events.