Mercurial > repos > dktanwar > removesnp

diff 01_RemoveSNPs/RemoveSNPs @ 0:12f2a7545ff2 draft

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author dktanwar
date Mon, 16 Oct 2017 13:59:28 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/01_RemoveSNPs/RemoveSNPs	Mon Oct 16 13:59:28 2017 -0400
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#if [ "$1" == "-h" ]; then
+if [[ -z $1 || -z $2 || $1 == "-h" ]]; then
+    echo "This program will remove mismatches from sam file."
+    echo "Usage: `basename $0` test.sam 3"
+    exit 0
+fi
+
+cmd="echo perl -ne 'print if((/XM:i:[0-$2][^0-9]/) || (/^@/));' $1"
+eval `$cmd`
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