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Implemented single line summary mismatches and indels in place of alignment data #112

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merged 6 commits into from
Mar 22, 2016
Merged

Implemented single line summary mismatches and indels in place of alignment data #112

merged 6 commits into from
Mar 22, 2016

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akmorrow13
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erictu
erictu reviewed Mar 21, 2016
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mango-cli/src/main/scala/org/bdgenomics/mango/cli/VizReads.scala
@@ -65,6 +66,7 @@ object VizTimers extends Metrics {

object VizReads extends BDGCommandCompanion with Logging {

var readsRDD: RDD[(ReferenceRegion, AlignmentRecord)] = null
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this goes unused.

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erictu
erictu reviewed Mar 22, 2016
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mango-cli/src/main/scala/org/bdgenomics/mango/cli/VizReads.scala
}
val end: Long = VizReads.getEnd(region.end, seqRecord)
val newRegion = ReferenceRegion(region.referenceName, region.start, end)
Option(refRDD.adamGetReferenceString(region).toUpperCase)
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add in the persist call

@erictu erictu mentioned this pull request Mar 22, 2016
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erictu added a commit that referenced this pull request Mar 22, 2016
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Merge pull request #112 from akmorrow13/master
c02e2ad 
Implemented single line summary mismatches and indels in place of alignment data
@erictu erictu merged commit c02e2ad into bigdatagenomics:master Mar 22, 2016
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erictu commented Mar 22, 2016

Thanks @akmorrow13 !

@erictu erictu mentioned this pull request May 19, 2016
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@akmorrow13 @AmplabJenkins @erictu