X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=docs%2FrunSNPAnalysis.sh;h=103b576e73ac450c0af315645abfca41d7abbb40;hp=0e4ff92ffe137759519bce2af3e49b4a33a3b1c2;hb=0d3e3112fd04c2e6b44a25cacef1d591658ad181;hpb=5e4ae21098dba3d1edcf11e7279da0d84c3422e4

diff --git a/docs/runSNPAnalysis.sh b/docs/runSNPAnalysis.sh
index 0e4ff92..103b576 100755
--- a/docs/runSNPAnalysis.sh
+++ b/docs/runSNPAnalysis.sh
@@ -9,19 +9,19 @@
 
 if [ -z "$ERANGEPATH" ]
 then
-    ERANGEPATH='../commoncode'
+    ERANGEPATH='../erange'
 fi
 
-echo 'runSNPAnalysis.sh: version 3.1'
+echo 'runSNPAnalysis.sh: version 3.2'
 
 cachepages=""
 if [ $# -eq 9 ]; then
-    cachepages="-cache "$9
+    cachepages="--cache "$9
 fi
 
 nosplices=""
 if [ $# -eq 10 ]; then
-    nosplices=" -nosplices "
+    nosplices=" --nosplices "
 fi
 
 if [ $# -lt 8 ]; then
@@ -36,7 +36,7 @@ echo 'running with settings: ' $arguments
 python $ERANGEPATH/recordLog.py snp.log runSNPAnalysis.sh "with parameters: $arguments"
 
 # get all SNPs by extracting it from the RDS
-python $ERANGEPATH/getSNPs.py $2 $6 $7 $3.snps.txt -enforceChr $cachepages $nosplices
+python $ERANGEPATH/getSNPs.py $2 $6 $7 $3.snps.txt --enforceChr $cachepages $nosplices
 
 # get SNPs in non-repeat regions only
 python $ERANGEPATH/chkSNPrmask.py $4 $3.snps.txt $3.nr_snps.txt $cachepages