Commit f262d102 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'macs2_change-options' into 'develop'

shift option had wrong var name

See merge request !155
parents 54d5d531 fb03d1c7
......@@ -61,6 +61,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var fixbimodel: Boolean = config("fixbimodel", default = false)
var nomodel: Boolean = config("nomodel", default = false)
var shift: Option[Int] = config("shift")
var extsize: Option[Int] = config("extsize")
var qvalue: Option[Float] = config("qvalue")
var pvalue: Option[Float] = config("pvalue")
var tolarge: Boolean = config("tolarge", default = false)
......@@ -103,7 +104,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
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 */
optional("--extsize", shift) + /* While '--nomodel' is set, MACS uses this parameter to extend reads in 5'->3' direction to fix-sized fragments. For example, if the size of binding region for your transcription factor is 200 bp, and you want to bypass the model building by MACS, this parameter can be set as 200. This option is only valid when --nomodel is set or when MACS fails to build model and --fix-bimodal is on. */
optional("--extsize", extsize) + /* While '--nomodel' is set, MACS uses this parameter to extend reads in 5'->3' direction to fix-sized fragments. For example, if the size of binding region for your transcription factor is 200 bp, and you want to bypass the model building by MACS, this parameter can be set as 200. This option is only valid when --nomodel is set or when MACS fails to build model and --fix-bimodal is on. */
optional("--qvalue", qvalue) + /* the Q-value(FDR) cutoff */
optional("--pvalue", pvalue) + /* The P-value cutoff, if --pvalue is set no Qvalue is calculated */
conditional(tolarge, "--to-large") + /* Whether to scale up the smallest input file to the larger one */
......
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