https://github.com/CampagneLaboratory/goby
Tip revision: c1f4795cdc0b64ae1cacb10ace22ce48d40057b8 authored by Fabien Campagne on 17 December 2013, 23:08:38 UTC
Replace Double.MIN_VALUE with -10. JSON does not like very small double values and they prevent the table from showing in GobyWeb.
Replace Double.MIN_VALUE with -10. JSON does not like very small double values and they prevent the table from showing in GobyWeb.
Tip revision: c1f4795
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