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Support deduping fragments #1309

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@fnothaft
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fnothaft commented Dec 10, 2016

Resolves #1302 and #1303. Needs more tests and a Pandoc update. Also, I'm thinking the reads2fragments and fragments2reads CLIs should be merged down to a transformFragments CLI. Any disagreement?

@fnothaft fnothaft added this to the 0.21.1 milestone Dec 10, 2016
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AmplabJenkins commented Dec 10, 2016

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1677/
Test PASSed.

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heuermh commented Dec 13, 2016

I'm thinking the reads2fragments and fragments2reads CLIs should be merged down to a transformFragments CLI.

+1

val bamFiles = getFsAndFiles(path)
val filteredFiles = bamFiles.filter(p => {
val pPath = p.getName()
pPath.endsWith(".bam") || pPath.endsWith(".cram") ||

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heuermh Dec 13, 2016

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could split this out into a separate method similar to isVcfExt

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fnothaft Dec 13, 2016

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+1

* @return A new RDD where reads have the duplicate read flag set. Duplicate
* reads are NOT filtered out.
*/
def markDuplicates(): FragmentRDD = MarkDuplicatesInDriver.time {

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heuermh Dec 13, 2016

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is this saying that MarkDuplicates runs solely on the driver, or that the timer is?

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fnothaft Dec 13, 2016

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Just the timer.

@fnothaft fnothaft force-pushed the fnothaft:issues/1302-1303-fragment-mkdups branch from 53eb0d2 to 2c84784 Jan 19, 2017
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fnothaft commented Jan 19, 2017

Rebased. Tests and documentation are good to go now too.

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fnothaft commented Jan 19, 2017

I.e., this PR is good to merge.

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AmplabJenkins commented Jan 19, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1744/
Test PASSed.

@heuermh heuermh merged commit 01297b6 into bigdatagenomics:master Jan 19, 2017
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heuermh commented Jan 19, 2017

Thank you, @fnothaft!

@fnothaft fnothaft deleted the fnothaft:issues/1302-1303-fragment-mkdups branch May 21, 2017
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