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genome / docker-basespace_chromoseq

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Fixed pysam #20

Closed dhspence closed 5 years ago

dhspence commented 5 years ago

Compiled a fork of pysam that fixed the issue in addreadcountstovcfcram.py. This new version is in the source docker container that tagged '5'. Also added explicit refseq fasta argument to the open cram function in this script and reverted some other changes related to this fix. This all needs to be tested to make sure it works.

johnegarza commented 5 years ago

For later reference, this is referring to issue #19