Initial bolus of code #1
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nh13
commented
Feb 2, 2022
nh13
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Feb 3, 2022
nh13
commented
Feb 3, 2022
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| override def execute(): Unit = { | ||
| val source = SamSource(input) | ||
| val writer = bam.map(path => SamWriter(path, header=source.header, sort=Some(SamOrder.Queryname))) |
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fixme: sort is not needed if input is in the correct order.
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tfenne
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Feb 8, 2022
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| // HACK | ||
| SamSource.DefaultUseAsyncIo = true | ||
| SamWriter.DefaultUseAsyncIo = true | ||
| VcfWriter.DefaultUseAsyncIo = true |
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Huh, maybe we should implement a better way to override defaults in FgBioMain?
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Agreed, leaving that to later
src/main/scala/com/fulcrumgenomics/fgsv/util/PutativeBreakpoint.scala
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src/main/scala/com/fulcrumgenomics/fgsv/util/PutativeBreakpoint.scala
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src/main/scala/com/fulcrumgenomics/fgsv/util/PutativeBreakpoint.scala
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| import htsjdk.samtools.util.CoordMath | ||
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| /** A genomic interval and useful methods. */ | ||
| case class GenomicRange(refIndex: Int, start: Int, end: Int) extends Ordered[GenomicRange] { |
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Can we push this back down into fgbio please?
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On re-review, I think we need to think about how to handle refIndex vs. refName more generally before doing that.
src/main/scala/com/fulcrumgenomics/fgsv/util/GenomicRange.scala
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Oh, also meant to say in a comment somewhere, that I think the |
nh13
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Feb 11, 2022
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| // HACK | ||
| SamSource.DefaultUseAsyncIo = true | ||
| SamWriter.DefaultUseAsyncIo = true | ||
| VcfWriter.DefaultUseAsyncIo = true |
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Agreed, leaving that to later
src/main/scala/com/fulcrumgenomics/fgsv/util/PutativeBreakpoint.scala
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src/main/scala/com/fulcrumgenomics/fgsv/util/PutativeBreakpoint.scala
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src/main/scala/com/fulcrumgenomics/fgsv/util/GenomicRange.scala
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| import htsjdk.samtools.util.CoordMath | ||
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| /** A genomic interval and useful methods. */ | ||
| case class GenomicRange(refIndex: Int, start: Int, end: Int) extends Ordered[GenomicRange] { |
| import scala.collection.immutable | ||
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| /** An enumeration over types of SV evidence. */ | ||
| object EvidenceType extends FgBioEnum[EvidenceType] { |
* Attempting to fix breakpoint construction from alignment blocks. * Clean up after a messy rebase.
A bunch of refactoring, most notably of how we accrue counts and assign IDs to breakpoints, so that we are guaranteed to count all evidence for breakpoint the same way and only assign it a single ID.
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