https://github.com/CampagneLaboratory/goby
Tip revision: b4f214eb041594c2ffba2c7bfaba751ce2ff60ed authored by Fabien Campagne on 02 March 2015, 20:29:49 UTC
Update change log.
Update change log.
Tip revision: b4f214e
compare.sh
rm -f times.tsv
for symbolModeling in PLUS ORDER_ONE ORDER_ZERO
do
for filename in /data/bam-comparison/EJOYQAZ-gzip.header /data/bam-comparison/XAAOBVT-gzip.header
do
input=`basename ${filename}`
echo Processing ${filename} with method ${symbolModeling}
java -Xmx3g -jar goby.jar --mode ca ${filename} -o discard -x MessageChunksWriter:codec=hybrid-1 \
-x MessageChunksWriter:chunk-size=100000 -x AlignmentCollectionHandler:debug-level=1 \
-x AlignmentCollectionHandler:stats-filename=stats.tsv \
-x AlignmentCollectionHandler:basename=${input}-${symbolModeling} \
-x AlignmentCollectionHandler:symbol-modeling=${symbolModeling} --max-entries 100002 >& /dev/null ;
time -p java -Xmx3g -jar goby.jar --mode cfs discard.entries >& /dev/null
echo ${input}-${symbolModeling}
done
done
#cat times.tsv