DRAFT - ignore me. #1940
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DRAFT - ignore me. #1940
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…mentCollection implementations to use nio paths. Change CleanSam to use getReferencePath. preliminary changes test passing for now CreateSequenceDictionary looks good working on downsamplesam temporary as I fix the issue remove 2 just a commit near ready another checkpoint checkpoint all good except maybe the cram ready chris comments no 1 review edits 1 done proofreading chris edit 2 PicardHtsPath -> IOPath where appropriate another edit another round of edits louis update htsjdk chris suggestion replaceExtension Co-authored-by: Chris Norman <cnorman@broadinstitute.org> chris edit reorganize proofread manually resolve conflicts khalid conflict that was not caught some fix fixed more fails
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Test a fix for Takuto's branch.