# HG changeset patch
# User nilesh
# Date 1373335430 14400
# Node ID 4d701c67592a31651164ae6e9a287c1c5e6076d0
# Parent  d9ac0d9cb48ebdac651a1be02ac2b28795a7e260
Uploaded

diff -r d9ac0d9cb48e -r 4d701c67592a samtoolshelper.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtoolshelper.py	Mon Jul 08 22:03:50 2013 -0400
@@ -0,0 +1,20 @@
+import sys
+import subprocess as sp
+import os
+
+# Creates the sorted and indexed bam/bai files that are requried for both bam2wig and RSEQC_count
+def samtools_sorted(bam):
+	sortedbam = bam + ".sorted"
+	indexedbam = ".".join([sortedbam,"bam.bai"])
+	sp.call(['samtools', 'sort', '-m 1000000000', bam, sortedbam])
+	sortedbam = sortedbam + '.bam'
+	sp.call(['samtools', 'index', sortedbam, indexedbam])
+	return sortedbam
+
+def main(args):
+	args[2] = samtools_sorted(args[2])
+	sp.call(args)
+
+
+if __name__ == "__main__":
+	main(sys.argv[1:])
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