Commit 778ea9d3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-htseqcount_sort_order' into 'develop'

Set default htseq-count sorting order to pos



See merge request !364
parents 0906f14b c4c5dc60
......@@ -26,6 +26,8 @@ import org.broadinstitute.gatk.queue.QScript
class FragmentsPerGene(val root: Configurable) extends QScript with Measurement with AnnotationGtf {
def mergeArgs = MergeArgs(idCols = List(1), valCol = 2, numHeaderLines = 0, fallback = "0")
override def fixedValues: Map[String, Any] = Map("htseqcount" -> Map("order" -> "pos"))
/** Pipeline itself */
def biopetScript(): Unit = {
val jobs = bamFiles.map {
......@@ -38,10 +40,6 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
job.output = new File(outputDir, s"$id.$name.counts")
job.format = Option("bam")
add(job)
// We are forcing the sort order to be ID-sorted, since HTSeq-count often chokes when using position-sorting due
// to its buffer not being large enough.
//TODO: ID sorting job
//job.order = Option("name")
id -> job
}
......
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