…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 <[email protected]>

chris edit

reorganize

proofread

manually resolve conflicts

khalid conflict that was not caught

some fix

fixed more fails