Commit 51f729f1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'develop' into feature-shiva

parents 85554525 42472f08
......@@ -66,7 +66,7 @@ trait SummaryQScript extends BiopetQScript {
def addSummarizable(summarizable: Summarizable, name: String, sampleId: Option[String], libraryId: Option[String]): Unit = {
if (libraryId.isDefined) require(sampleId.isDefined) // Library always require a sample
summarizables.get((name, sampleId, libraryId)).foreach(summarizables += (name, sampleId, libraryId) -> _)
summarizables += (name, sampleId, libraryId) -> (summarizable :: summarizables.getOrElse((name, sampleId, libraryId), Nil))
......@@ -40,7 +40,8 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var verbose: Boolean = config("verbose", default = false)
var tsize: Option[Int] = config("tsize")
var bandwith: Option[Int] = config("bandwith")
var mfold: Option[Float] = config("mfold")
// TODO: should use List[Float] or Option[List[Float]] here
var mfold: List[String] = config("mfold", default = List.empty[String])
var fixbimodel: Boolean = config("fixbimodel", default = false)
var nomodel: Boolean = config("nomodel", default = false)
var shift: Option[Int] = config("shift")
......@@ -80,7 +81,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
conditional(verbose, "--verbose") + /* Whether to output verbosely */
optional("--tsize", tsize) + /* Sets custom tag length, if not specified macs will use first 10 sequences to estimate the size */
optional("--bw", bandwith) + /* The bandwith to use for model building. Set this parameter as the sonication fragment size estimated in the wetlab */
optional("--mfold", mfold) + /* The parameter to select regions within the model fold. Must be a upper and lower limit. */
optional("'--mfold'", repeat(mfold), escape = false) + /* The parameter to select regions within the model fold. Must be a upper and lower limit. */
conditional(fixbimodel, "--fix-bimodal") + /* Whether turn on the auto paired-peak model process. If it's set, when MACS failed to build paired model, it will use the nomodel settings, the '--extsize' parameter to extend each tags. If set, MACS will be terminated if paried-peak model is failed. */
conditional(nomodel, "--nomodel") + /* While on, MACS will bypass building the shifting model */
optional("--shift", shift) + /* You can set an arbitrary shift in basepairs here */
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