Mercurial > repos > davidvanzessen > sff_extract_demultiplex

diff wrapper.sh @ 10:5a886d753c0a draft

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author davidvanzessen
date Wed, 25 Nov 2015 05:02:54 -0500
parents cd56ce86c4bf
children b59783f3d3ba
line wrap: on
line diff
--- a/wrapper.sh	Tue Nov 04 09:16:17 2014 -0500
+++ b/wrapper.sh	Wed Nov 25 05:02:54 2015 -0500
@@ -1,11 +1,11 @@
 #!/bin/bash
-input=$1
-output=$2 
-outDir=$3
-mkdir $outDir
-EOL=$4
-mismatches=$5
-partial=$6
+input="$1"
+output="$2"
+outDir="$3"
+mkdir "$outDir"
+EOL="$4"
+mismatches="$5"
+partial="$6"
 name=$(basename "$7")
 ext="${name##*.}"
 name="${name%.*}"
@@ -23,7 +23,7 @@
 	start_int=$((i+2))
 	end_int=$((i+3))
 	id="${!i}"
-	echo "$id"
+	echo "$id, ${start_int}, ${end_int}"
 	trim_start[$id]=${!start_int}
 	trim_end[$id]=${!end_int}
   echo -e "$id\t${!j}" >> $outDir/barcodes.txt