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#!/bin/sh
set -e -x
len=0
if test $# -eq 1
then
len=$1
else
if test $# -ne 0
then
echo "Usage: $0 [len]"
exit 1
fi
fi
encseq2spm()
{
gt encseq decode ${1} | head -n ${2} | grep -v '^>read_5' > tmp.fas
gt encseq encode -indexname sfx tmp.fas
for threads in 1 4
do
GTCALL="env -i bin/gt -j ${threads} encseq2spm"
${GTCALL} -l 32 -singlescan 0 -ii sfx
for len in 32 35
do
opts="-l ${len} -ii sfx -spm count -checksuftab"
${GTCALL} ${opts}
done
done
}
found=0
for indexname in ${HOME}/seqcmpprojects/c22/c22-64bit /local/c22 ${HOME}/c22-64bit
do
if test -f ${indexname}.esq
then
found=1
break
fi
done
if test $found -eq 0
then
echo "$0: cannot find index for c22"
exit 1
else
if test $# -eq 0
then
for len in 100 300 600 900 15000 90000 300000
do
encseq2spm ${indexname} ${len}
done
else
encseq2spm ${indexname} ${len}
fi
fi
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