1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
|
#!/bin/bash
rm deleteme-*
make
src/GsnapParseTest1
java -jar ~gobyweb/reads-for-paper/goby.jar -m att \
-f html deleteme-seq.entries > deleteme-seq.html
java -jar ~gobyweb/reads-for-paper/goby.jar -m sort \
deleteme-seq.entries -o deleteme-seq-sorted
java -jar ~gobyweb/reads-for-paper/goby.jar -m att \
-f html deleteme-seq-sorted.entries > deleteme-seq-sorted.html
java -jar ~gobyweb/reads-for-paper/goby.jar -m ca \
deleteme-seq-sorted.entries -o deleteme-seq-hybrid \
-x MessageChunksWriter:codec=hybrid-1 \
-x AlignmentCollectionHandler:enable-domain-optimizations=false \
-x MessageChunksWriter:template-compression=true \
-x AlignmentCollectionHandler:ignore-read-origin=true \
-x AlignmentWriterImpl:permutate-query-indices=true
java -jar ~gobyweb/reads-for-paper/goby.jar -m att \
-f html deleteme-seq-hybrid.entries > deleteme-seq-hybrid.html
|