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#!/bin/sh
runall()
{
bin/gt suffixerator -tis -db ${1} -indexname esa
for maxinsertionsort in 1 2 5 10
do
for maxbltriesort in 10 20 30 100
do
for maxdepth in 2 3 4 5 6 7 8 9 10 11 12 13
do
bin/gt dev sfxmap -sortmaxdepth ${maxdepth} -esa esa -v \
-algbds ${maxinsertionsort} ${maxbltriesort} \
1000
done
bin/gt suffixerator -db ${1} -indexname esa2 -suf -v \
-algbds ${maxinsertionsort} ${maxbltriesort} \
1000
bin/gt dev sfxmap -suf -esa esa2
done
done
}
set -e -x
for filename in `ls testdata/[A-Z]*.fna`
do
if test ${filename} != "testdata/corruptpatternfile.fna"
then
runall ${filename}
fi
done
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