From 70ec37661c5fc11229e37913c453ae080b7361f9 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 11 Sep 2009 13:13:23 +0000 Subject: [PATCH] Fix merger command git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1584 348d0f76-0448-11de-a6fe-93d51630548a --- python/RunPilot2Pipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/RunPilot2Pipeline.py b/python/RunPilot2Pipeline.py index 5f6ee69f5..ccf885177 100755 --- a/python/RunPilot2Pipeline.py +++ b/python/RunPilot2Pipeline.py @@ -111,7 +111,7 @@ if __name__ == "__main__": def IndelIntervals(bam, outputFile, intervals): return config.gatkCmd('IndelIntervals') + " -o " + outputFile + " -L " + intervals + " -I " + bam def MergeIntervals(bam, files, outputFile, intervals): - return config.gatkCmd('MergeIntervals') + " -o " + outputFile + " ".join(map( lambda x: " -intervals " + x, files )) + " -L " + intervals + " -I " + bam + return config.gatkCmd('IntervalMerger') + " -o " + outputFile + " ".join(map( lambda x: " -intervals " + x, files )) + " -L " + intervals + " -I " + bam def CleanIntervals(bam, outputFile, intervals, snpfile): return config.gatkCmd('IntervalCleaner') + " -O " + outputFile + " -L " + intervals + " -I " + bam def Injector(bam, outputFile, intervals, inputfile):