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set -e;
BT=${BT-../../bin/bedtools}
FAILURES=0;
check()
{
if diff $1 $2; then
echo ok
else
FAILURES=$(expr $FAILURES + 1);
echo fail
fi
}
###########################################################
# Test a basic self intersection
############################################################
echo -e " bigchroms.t01...\c"
$BT intersect -sorted -a abig.bed -b abig.bed > obs
check obs abig.bed
rm obs
echo -e " bigchroms.t02...\c"
$BT intersect -a abig.bed -b abig.bed > obs
check obs abig.bed
rm obs
if [[ "$BT_NO_BIG_FILES" != "" ]]; then
python3 make-big-chrom.py
echo -e " bigchroms.t03...big get fasta \c"
$BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
echo "ACTGACCCCGAGACGTTTGCATCCTGCACAGCTAGAGATCCTTTATTAAAAGCACACTGT" > exp
check obs exp
rm obs exp
rm bigx.fasta*
else
echo -e " bigchroms.t03... skip \c"
echo " set env var 'BT_NO_BIG_FILES' to run this test"
fi
echo -e " bigchroms.t04... merge \c"
echo "chr1 1 9000000000" > exp
$BT merge -i big4.bed > obs
check obs exp
rm obs exp
echo -e " bigchroms.t05... closest \c"
$BT closest -a big4c.bed -b big4.bed > obs
echo "chr1 1 10 chr1 1 10
chr1 1 10 chr1 9 8000000000
chr1 8900000000 9000000000 chr1 8000000000 9000000000" > exp
check obs exp
rm obs exp
[[ $FAILURES -eq 0 ]] || exit 1;
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