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 ...@@ -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.core.annotations.AnnotationGtf
import nl.lumc.sasc.biopet.extensions.HtseqCount 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.extensions.samtools.SamtoolsSort
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
...@@ -37,10 +38,10 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement ...@@ -37,10 +38,10 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
case (id, file) => case (id, file) =>
val bamFile = if (sortOnId) { val bamFile = if (sortOnId) {
val samtoolsSort = new SamtoolsSort(this) val samtoolsSort = new SortSam(this)
samtoolsSort.input = file samtoolsSort.input = file
samtoolsSort.output = swapExt(outputDir, file, ".bam", ".idsorted.bam") samtoolsSort.output = swapExt(outputDir, file, ".bam", ".idsorted.bam")
samtoolsSort.sortByName = true samtoolsSort.sortOrder = "queryname"
samtoolsSort.isIntermediate = true samtoolsSort.isIntermediate = true
add(samtoolsSort) add(samtoolsSort)
samtoolsSort.output samtoolsSort.output
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment