diff export2sam.sh @ 0:61f3089ddc74 default tip

commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export2sam.sh	Tue Dec 30 18:53:23 2014 +0900
@@ -0,0 +1,42 @@
+#!/bin/sh
+# SET TOOL DIRECTORY
+
+CMDNAME=`basename $0`
+
+while getopts a:b:o:gr OPT
+do
+  case $OPT in
+    "a" ) FLG_A="TRUE" ; VALUE_A="$OPTARG" ;;
+    "b" ) FLG_B="TRUE" ; VALUE_B="$OPTARG" ;;
+    "o" ) FLG_O="TRUE" ; VALUE_O="$OPTARG" ;;
+    "g" ) FLG_G="TRUE" ;;
+    "r" ) FLG_R="TRUE" ;;
+      * ) echo "Usage: $CMDNAME [-a VALUE] [-b] [-o VALUE] [-gr]" 1>&2
+          exit 1 ;;
+  esac
+done
+
+# SINGLE END OR PAIR END
+if [ ! $FLG_B ] ; then
+  ARGS="--read1=$VALUE_A"
+else
+  ARGS="--read1=$VALUE_A --read2=$VALUE_B"
+fi
+
+# GZIPPED OR NOT
+if [ $FLG_G ] ; then
+  CMD1="./illumina_export2sam_gz.pl $ARGS"
+else
+  CMD1="./illumina_export2sam.pl $ARGS"
+fi
+
+# MODIFY ACCORDING TO THE REFERENCE
+if [ $FLG_R ] ; then
+  CMD2='$tmp=$_;$tmp=~s/chr_fragments\.fa\///g;$tmp=~s/(chr\w+)\.fa/$1/g;print $tmp;'
+  CMD="$CMD1 | perl -ne '$CMD2'"
+else
+  CMD=$CMD1
+fi
+
+echo $CMD
+eval $CMD > $VALUE_O