Mercurial > repos > mvdbeek > dapars

diff dapars.py @ 16:f8bb40b2ff31 draft

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planemo upload for repository https://github.com/mvdbeek/dapars commit b1b007c561ea6c9db145c88b6b128d66ecd05e24-dirty
author mvdbeek
date Fri, 30 Oct 2015 07:31:36 -0400
parents 8af6d4ad2f0a
children 917a2f7ab841
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--- a/dapars.py	Fri Oct 30 07:19:14 2015 -0400
+++ b/dapars.py	Fri Oct 30 07:31:36 2015 -0400
@@ -96,7 +96,7 @@
         cmds = []
         for alignment_file in self.all_alignments:
             cmd = "sort -k1,1 -k2,2n tmp_bedfile.bed | "
-            cmd = cmd + "bedtools coverage -d -s -abam {alignment_file} -b tmp_bedfile.bed |" \
+            cmd = cmd + "bedtools coverage -d -s -abam {alignment_file} -b stdin |" \
                         " cut -f 4,7,8 > coverage_file_{alignment_name}".format(
                 alignment_file = alignment_file, alignment_name= self.alignment_names[alignment_file] )
             cmds.append(cmd)