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Rolling back to slower but stable version of bam_to_fastq
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Charles Dietz committed Aug 25, 2016
1 parent 46185a6 commit caad85e
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions pypiper/ngstk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ def markDuplicates(self, aligned_file, out_file, metrics_file, remove_duplicates
cmd += " REMOVE_DUPLICATES=" + remove_duplicates
return cmd

def bam_to_fastq2(self, bam_file, out_fastq_pre, paired_end):
def bam_to_fastq(self, bam_file, out_fastq_pre, paired_end):
self.make_sure_path_exists(os.path.dirname(out_fastq_pre))
cmd = self.tools.java + " -Xmx" + self.pm.javamem
cmd += " -jar " + self.tools.picard + " SamToFastq"
Expand All @@ -111,7 +111,7 @@ def bam_to_fastq2(self, bam_file, out_fastq_pre, paired_end):
cmd += " VALIDATION_STRINGENCY=SILENT"
return cmd

def bam_to_fastq(self, bam_file, out_fastq_pre, paired_end):
def bam_to_fastq2(self, bam_file, out_fastq_pre, paired_end):
self.make_sure_path_exists(os.path.dirname(out_fastq_pre))

if paired_end:
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1 comment on commit caad85e

@nsheff
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@nsheff nsheff commented on caad85e Dec 14, 2016

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for future reference, this was just caused by a missing "+" sign, which was fixed in dev.

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