# HG changeset patch
# User mmseq
# Date 1313423962 14400
# Node ID 5868599b6b910f5bc63b35bd9ee6ca8aedcc997b
# Parent  a62af63ae8ffd0e673241b3a4f39c9b1985e6f42
Uploaded mmseq analysis pipeline script file

diff -r a62af63ae8ff -r 5868599b6b91 mmseq.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mmseq.sh	Mon Aug 15 11:59:22 2011 -0400
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+TEMP=bam.hits
+bam2hits $1 $2 > $TEMP 2> /dev/null
+mmseq $TEMP output > /dev/null
+mv output.mmseq $3
+mv output.gene.mmseq $4
+mv output.amalgamated.mmseq $5