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|
#!/bin/sh
set -x
if [ $# -lt 5 ]
then
echo "Usage: $0 <gt-bin> <bothdirections> <idir> <fmindex> <file1> [file2 file3 ..]"
exit 1
fi
gtbin=$1
bothdirections=$2
idir=$3
fmindex=${idir}/$4
shift
shift
shift
shift
rfiles=$*
cerr()
{
$*
if [ $? -ne 0 ]
then
echo "failure: $*"
exit 1
fi
}
suffixerator()
{
cerr "${gtbin} suffixerator -algbds 3 43 120 $*"
}
makesuftab()
{
if [ $1 = 'rev' ]
then
suffixerator -dna -bwt -lcp -tis -suf -pl -dir rev -indexname ${idir}/$2.rev -db $3
else
suffixerator -dna -lcp -tis -suf -pl -dir cpl -indexname ${idir}/$2.cpl -db $3
fi
}
plain()
{
cerr "${gtbin} suffixerator -plain -des no -ssp no -sds no -tis -indexname $1 -smap $1.al1 -db $1.bwt"
}
mkfmindex()
{
indexname=$1
shift
iiargs=$*
cerr "${gtbin} mkfmindex -size small -fmout ${indexname} -ii ${iiargs}"
}
needsrebuild=0
needconstruction1()
{
if [ ! -f ${idir}/$2 ] ||
[ $1 -nt ${idir}/$2 ]
then
$3
needsrebuild=1
else
echo "# ${idir}/$2 is up to date"
fi
}
mkdir -p ${idir}
indexlist=""
for rfile in ${rfiles}
do
indexname=`basename ${rfile}`
needconstruction1 ${rfile} \
"${indexname}.rev.prj" \
"makesuftab rev ${indexname} ${rfile}"
indexlist="${indexlist} ${idir}/${indexname}.rev"
if [ $bothdirections -eq 1 ]
then
needconstruction1 ${rfile} \
"${indexname}.cpl.prj" \
"makesuftab cpl ${indexname} ${rfile}"
indexlist="${indexlist} ${idir}/${indexname}.cpl"
fi
done
if [ $needsrebuild -eq 1 ] ||
[ ! -f ${fmindex}.fma ] ||
[ ! -f ${fmindex}.fmd ] ||
[ ! -f ${fmindex}.bwt ]
then
mkfmindex ${fmindex} ${indexlist}
needsrebuild=1
else
echo "# ${fmindex}.fma is up to date"
echo "# ${fmindex}.fmd is up to date"
echo "# ${fmindex}.bwt is up to date"
fi
if [ $needsrebuild -eq 1 ]
then
needconstruction1 ${fmindex}.bwt ${fmindex}.esq "plain ${fmindex}"
needsrebuild=1
else
echo "# ${fmindex}.esq is up to date"
fi
|
