Mercurial > repos > jeremie > breakdancer_test

changeset 21:199c0c7d3093 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jeremie
date Tue, 01 Jul 2014 10:09:33 -0400
parents b122ca66efc7
children b4f641515363
files breakdancer.py
diffstat 1 files changed, 6 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/breakdancer.py	Tue Jul 01 10:09:05 2014 -0400
+++ b/breakdancer.py	Tue Jul 01 10:09:33 2014 -0400
@@ -5,6 +5,7 @@
 
 parser = argparse.ArgumentParser(description='')
 
+parser.add_argument('-x', dest='binPath')
 parser.add_argument ( '-i1', dest='input_bam', help='the bam input file' )
 parser.add_argument ( '-o1', dest='output_raw', help='the output file' )
 parser.add_argument ( '-o2', dest='output_vcf', help='the output file' )
@@ -14,10 +15,11 @@
 errorFile = tmp_dir+"/errorLog"
 
 currentDir = os.path.dirname(os.path.abspath(__file__))
-bam2cfg = "./bam2cfg.pl"
-# breakdancer = "/usr/bin/breakdancer-max"
-breakdancer = "breakdancer-max"
-breakdancer2vcf = "./breakdancer2vcf.py"
+
+binPath = args.binPath
+bam2cfg = binPath+"/bam2cfg.pl"
+breakdancer = binPath+"/breakdancer-max"
+breakdancer2vcf = binPath+"/breakdancer2vcf.py"
 
 
 def bam2cfg(args):