Commit 5ff11a3c authored by Peter van 't Hof's avatar Peter van 't Hof

Switch to picard for id sorting

parent b913e017
......@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.measures
import nl.lumc.sasc.biopet.core.annotations.AnnotationGtf
import nl.lumc.sasc.biopet.extensions.HtseqCount
import nl.lumc.sasc.biopet.extensions.picard.SortSam
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsSort
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -37,10 +38,10 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
case (id, file) =>
val bamFile = if (sortOnId) {
val samtoolsSort = new SamtoolsSort(this)
val samtoolsSort = new SortSam(this)
samtoolsSort.input = file
samtoolsSort.output = swapExt(outputDir, file, ".bam", ".idsorted.bam")
samtoolsSort.sortByName = true
samtoolsSort.sortOrder = "queryname"
samtoolsSort.isIntermediate = true
add(samtoolsSort)
samtoolsSort.output
......
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