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Default value for reads.toCoverage(collapse) should be false #1483

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fnothaft opened this Issue Apr 10, 2017 · 0 comments

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fnothaft commented Apr 10, 2017

IMO, it is more common that you're going to run an analysis where you look at the number of reads at a site than where you're going to visualize coverage. As such, I think it makes more sense to not generate the collapsed coverage, which collapses sites that have identical coverage. @akmorrow13 your thoughts?

@fnothaft fnothaft added the discussion label Apr 10, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Apr 17, 2017

[ADAM-1483] Remove collapse parameter from AlignmentRecordRDD.toCoverage
Resolves bigdatagenomics#1483. Instead of providing a parameter in the `toCoverage` method to
allow users to collapse the coverage, makes the `toCoverage` method stupid. This
makes the `toCoverage` method simpler and the behavior easier to reason about.

fnothaft added a commit to fnothaft/adam that referenced this issue May 10, 2017

[ADAM-1483] Remove collapse parameter from AlignmentRecordRDD.toCoverage
Resolves bigdatagenomics#1483. Instead of providing a parameter in the `toCoverage` method to
allow users to collapse the coverage, makes the `toCoverage` method stupid. This
makes the `toCoverage` method simpler and the behavior easier to reason about.

heuermh added a commit that referenced this issue May 10, 2017

[ADAM-1483] Remove collapse parameter from AlignmentRecordRDD.toCoverage
Resolves #1483. Instead of providing a parameter in the `toCoverage` method to
allow users to collapse the coverage, makes the `toCoverage` method stupid. This
makes the `toCoverage` method simpler and the behavior easier to reason about.

@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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