zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix merger command 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1584 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-11 13:13:23 +00:00
parent 45c794d066
commit 70ec37661c
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
python/RunPilot2Pipeline.py
View File

@ -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):