first pass cleanup of cistematic/genomes; change bamPreprocessing

[erange.git] / docs / runSNPAnalysis.sh

diff --git a/docs/runSNPAnalysis.sh b/docs/runSNPAnalysis.sh
index 0e4ff92ffe137759519bce2af3e49b4a33a3b1c2..51f2e4ccd8bc9ad166cd8f7a5609e6648413c929 100755 (executable)
--- a/docs/runSNPAnalysis.sh
+++ b/docs/runSNPAnalysis.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 #
+# This is no longer supported.  It is recommended that the pythin script of the same name be used instead.
+#
 # runSNPAnalysis.sh
 #
 # Usages: $ERANGEPATH/runSNPAnalysis.sh mouse rdsfile label rmaskdbfile dbsnpfile uniqStartMin totalRatio rpkmfile cachepages
@@ -9,19 +11,19 @@
 
 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 +38,7 @@ 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
@@ -59,4 +61,4 @@ python $ERANGEPATH/getNovelSNPs.py $1 $3.nr_dbsnp_geneinfo.txt $3.nr.final.txt
 
 # make bed file for displaying the snps on UCSC genome browser
 python $ERANGEPATH/makeSNPtrack.py $3.nr_snps.txt $3 $3.nr_snps.bed
-fi
\ No newline at end of file
+fi