Commit 8df86298 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding index step

parent bf2e950a
......@@ -56,5 +56,5 @@ object SambambaIndex {
apply(root, input, new File(swapExtension(input.getAbsolutePath)))
}
private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bam.bai"
private def swapExtension(inputFile: String) = inputFile.stripSuffix(".bam") + ".bai"
}
......@@ -23,13 +23,7 @@ import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import nl.lumc.sasc.biopet.extensions.picard.{
AddOrReplaceReadGroups,
MarkDuplicates,
MergeSamFiles,
ReorderSam,
SortSam
}
import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.taxextract.TaxExtractExtract
......@@ -45,7 +39,7 @@ import org.broadinstitute.gatk.utils.commandline
import scala.math._
import Mapping.DuplicatesMethod
import nl.lumc.sasc.biopet.extensions.sambamba.SambambaMarkdup
import nl.lumc.sasc.biopet.extensions.sambamba.{SambambaIndex, SambambaMarkdup}
/**
* This pipeline doing a alignment to a given reference genome
......@@ -358,6 +352,7 @@ class Mapping(val parent: Configurable)
case DuplicatesMethod.Sambamba =>
bamFile = new File(outputDir, outputName + ".dedup.bam")
add(SambambaMarkdup(this, mergedBamFile, finalBamFile, !keepFinalBamFile))
add(SambambaIndex(this, finalBamFile))
case DuplicatesMethod.None =>
}
......
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