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Fixed bug in NGSTK bam_conversions
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Charles Dietz committed Aug 30, 2016
1 parent caad85e commit a26a02c
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion pypiper/ngstk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -613,7 +613,7 @@ def bam_conversions(self, bam, depth=True):
:param depth: also calculate coverage over each position
"""
cmd = self.tools.samtools + " view -h " + bam + " > " + bam.replace(".bam", ".sam") + "\n"
cmd += self.tools.samtools + " sort " + bam + " " + bam.replace(".bam", "_sorted") + "\n"
cmd += self.tools.samtools + " sort " + bam + " " + bam.replace(".bam", "_sorted.bam") + "\n"
cmd += self.tools.samtools + " index " + bam.replace(".bam", "_sorted.bam") + "\n"
if depth:
cmd += self.tools.samtools + " depth " + bam.replace(".bam", "_sorted.bam") + " > " + bam.replace(".bam", "_sorted.depth") + "\n"
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2 comments on commit a26a02c

@nsheff
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@nsheff nsheff commented on a26a02c Nov 3, 2016

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yes.

@nsheff
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@nsheff nsheff commented on a26a02c Dec 14, 2016

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charles, these replace functions are also bad because they would change "cancer.sample.1" to "cancer.bample.1", since they don't require the .bam to be trailing.

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