--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gsmapper2gff.sh	Thu Jun 14 19:29:26 2012 -0400
@@ -0,0 +1,50 @@
+#!/bin/sh
+##convert gsMapper output into gff3/GVF format
+
+#New Zealand Institute for Plant and Food Research
+#This program is free software: you can redistribute it and/or modify
+#     it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+infile=$1
+outfile=$2
+
+awk '
+BEGIN {OFS="\t"}
+/^>/  && sub(/%/,"",$7)  {
+  ID=substr($1,2)
+  if  (length($4) > 1 || match($4,"-") || length($5) > 1 || match($5,"-")) 
+    type="indel"
+    else
+      type="SNP"
+start=$2
+end=$3
+Col9_ID=ID ":gsmapper:" type ":"start
+
+Reference_seq=$4
+Variant_seq=$5
+Total_reads=$6
+Variant_reads=Total_reads * $7 /100 - (Total_reads * $7 % 100)/100 
+
+
+
+ print ID,"gsmapper",type,start,end,".",".",".","ID="Col9_ID";Reference_seq="Reference_seq";Variant_seq="Variant_seq";Total_reads="Total_reads";Variant_reads="Variant_reads
+}' "$infile" > "$outfile" 
+
+
+
+
+
+
+
+