Mercurial > repos > koen > gbsx
changeset 2:b0d5949b88dd draft
Uploaded gbsx_demultiplexer.sh
| author | koen |
|---|---|
| date | Wed, 13 Jan 2016 10:45:58 -0500 |
| parents | 29fc2bb7bc18 |
| children | 9dc99f2deb3d |
| files | gbsx_demultiplexer.sh |
| diffstat | 1 files changed, 28 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gbsx_demultiplexer.sh Wed Jan 13 10:45:58 2016 -0500 @@ -0,0 +1,28 @@ +#!/usr/bin/env bash + +#export PATH=$PATH:$(dirname $0) +#BASEDIR=$(dirname $0) + + +read1=$1 +read2=$2 +infofile=$3 +barcodeMismatch=$4 +enzymeMismatch=$5 +rad_gbs_select=$6 +demultiplex_stats=$7 + +extra="" +if [ "$read2" != "0" ]; +then + extra="-f2 $read2"; +fi +mkdir gbsx_demultiplex; + +java -jar $GBSX_PATH/GBSX.jar --Demultiplexer -o gbsx_demultiplex -f1 $read1 $extra -i $infofile -mb $barcodeMismatch -me $enzymeMismatch -rad $rad_gbs_select + +cat gbsx_demultiplex/gbsDemultiplex.stats > $demultiplex_stats +rm gbsx_demultiplex/*.log +rm gbsx_demultiplex/*.stats +rm gbsx_demultiplex/undetermined* +