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
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