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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
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