From ee6104364356cb8dd7578e4ce8fb8eb64dd81bc4 Mon Sep 17 00:00:00 2001
From: Sander van der Zeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 26 Feb 2015 14:39:38 +0100
Subject: [PATCH] change mfold arg parsing, printed empty list when mfold was
not given
---
.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
index 838590f87..6c572f229 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
@@ -81,7 +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'", repeat(mfold), escape = false) + /* The parameter to select regions within the model fold. Must be a upper and lower limit. */
+ (if (mfold.isEmpty) "" else 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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