https://github.com/CampagneLaboratory/goby
Tip revision: 927660805ccd62f3432b925118afc3cdd142dde6 authored by Fabien Campagne on 31 December 2012, 16:31:19 UTC
updated version numbers for python and c++ APIs
updated version numbers for python and c++ APIs
Tip revision: 9276608
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