Changed cr.igv.seg output of ModelSegments to give log2 Segment_Mean.

[samuelklee]

Also changed LegacySegmentCollection and CalledLegacySegmentCollection writers to overwrite instead of append. (This was fixed for AbstractRecordCollection writers in an earlier PR but was missed in these collections that override the default writer.)

See https://gatkforums.broadinstitute.org/gatk/discussion/24048/a-few-things-need-help-about-output-of-command-modelsegments#latest for some context. In principle, IGV should be able to handle linear scaling, but it scales automatically for seg files and I'm not sure if you can get around it without some additional steps. Seems easier to just output log2 copy ratios. (Perhaps we initially output linear copy ratios to maintain backwards compatibility with previous versions of GATK CNV? If so, the *LegacySegmentCollections seem to be pulling double duty, since we use them to provide IGV compatibility. In any case, we are currently inconsistent between ModelSegments and CallCopyRatioSegments, as I noted in the forum post.)

@LeeTL1220 any objections? If downstream scripts are consuming the IGV output of ModelSegments, they should be adjusted if necessary.

[codecov]

Codecov Report

Merging #5976 into master will increase coverage by 0.001%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##              master    #5976       +/-   ##
==============================================
+ Coverage     86.929%   86.93%   +0.001%     
  Complexity     32714    32714               
==============================================
  Files           2013     2013               
  Lines         151268   151268               
  Branches       16604    16604               
==============================================
+ Hits          131496   131497        +1     
  Misses         13718    13718               
+ Partials        6054     6053        -1

Impacted Files	Coverage Δ	Complexity Δ
...ute/hellbender/tools/copynumber/ModelSegments.java	97.059% <100%> (ø)	41 <0> (ø)	⬇️
...ats/collections/CalledLegacySegmentCollection.java	63.043% <100%> (ø)	4 <0> (ø)	⬇️
...r/formats/collections/LegacySegmentCollection.java	72.973% <100%> (ø)	4 <0> (ø)	⬇️
...nder/utils/runtime/StreamingProcessController.java	67.773% <0%> (+0.474%)	33% <0%> (ø)	⬇️

[LeeTL1220]

@samuelklee I have no objection. I checked with one collaborator about the change to output format and he had no objection. He nor I knew of any downstream automation that uses the IGV, but this is a pretty informal check.

Please make sure that this change gets included in the release notes!

[LeeTL1220]

Fee free to merge if tests pass.

[samuelklee]

Thanks, @LeeTL1220! @droazen please include in the next release notes.