diff --git a/test/map/test-map.sh b/test/map/test-map.sh index d9ecbaca890ad1c25b567b97b8c42a0c9cb26604..70d550a92fcc929fccc04e09fbeea7fe86ce93cb 100644 --- a/test/map/test-map.sh +++ b/test/map/test-map.sh @@ -694,7 +694,7 @@ echo \ " ***** ***** ERROR: There are 1 columns given, but there are 2 operations." > exp -../../bin/bedtools map -a ivls.bed -b values.bed -o count,sum 2>&1 > /dev/null | head -3 > obs +$BT map -a ivls.bed -b values.bed -o count,sum 2>&1 > /dev/null | head -3 > obs check obs exp rm obs exp @@ -708,7 +708,7 @@ echo \ " ***** ***** ERROR: There are 3 columns given, but there are 2 operations." > exp -../../bin/bedtools map -a ivls.bed -b values.bed -c 5,1,2 -o count,sum 2>&1 > /dev/null | head -3 > obs +$BT map -a ivls.bed -b values.bed -c 5,1,2 -o count,sum 2>&1 > /dev/null | head -3 > obs check obs exp rm obs exp @@ -721,7 +721,7 @@ echo \ " ***** ***** ERROR: Column 1 is not a numeric field for database file values.bed." > exp -../../bin/bedtools map -a ivls.bed -b values.bed -c 1 -o sum 2>&1 > /dev/null | head -3 > obs +$BT map -a ivls.bed -b values.bed -c 1 -o sum 2>&1 > /dev/null | head -3 > obs check obs exp rm obs exp @@ -738,7 +738,7 @@ chr2 0 100 . . chr2 100 200 . . chr3 0 100 6 7 chr3 100 200 8 23" > exp -../../bin/bedtools map -a ivls.bed -b values4.bed -c 5,7 -o sum > obs +$BT map -a ivls.bed -b values4.bed -c 5,7 -o sum > obs check obs exp rm obs exp @@ -755,7 +755,7 @@ chr2 0 100 . . . chr2 100 200 . . . chr3 0 100 10 6 7 chr3 100 200 120 8 23" > exp -../../bin/bedtools map -a ivls.bed -b values4.bed -c 2,5,7 -o mean,sum,sum > obs +$BT map -a ivls.bed -b values4.bed -c 2,5,7 -o mean,sum,sum > obs check obs exp rm obs exp @@ -771,7 +771,7 @@ chr2 0 100 . chr2 100 200 . chr3 0 100 76.2222 chr3 100 200 0.25" > exp -../../bin/bedtools map -a ivls.bed -b values4.bed -c 7 -o stddev > obs +$BT map -a ivls.bed -b values4.bed -c 7 -o stddev > obs check obs exp rm obs exp @@ -786,7 +786,7 @@ chr2 0 100 . chr2 100 200 . chr3 0 100 114.333 chr3 100 200 0.5" > exp -../../bin/bedtools map -a ivls.bed -b values4.bed -c 7 -o sample_stddev > obs +$BT map -a ivls.bed -b values4.bed -c 7 -o sample_stddev > obs check obs exp rm obs exp diff --git a/test/reldist/test-reldist.sh b/test/reldist/test-reldist.sh index eebde8bda5c3608f9477bd0e91b2028d627e131b..fc315127c1f301e9484891a93c95ee5956d6e16a 100644 --- a/test/reldist/test-reldist.sh +++ b/test/reldist/test-reldist.sh @@ -1,4 +1,5 @@ BT=${BT-../../bin/bedtools} +DATA=${DATA-../../data} check() { @@ -17,8 +18,8 @@ echo " reldist.t01...\c" echo \ "reldist count total fraction 0.00 43424 43424 1.000" > exp -$BT reldist -a ../../data/refseq.chr1.exons.bed.gz \ - -b ../../data/refseq.chr1.exons.bed.gz > obs +$BT reldist -a $DATA/refseq.chr1.exons.bed.gz \ + -b $DATA/refseq.chr1.exons.bed.gz > obs check obs exp rm obs exp @@ -79,8 +80,8 @@ echo \ 0.47 850 43408 0.020 0.48 1006 43408 0.023 0.49 937 43408 0.022" > exp -$BT reldist -a ../../data/refseq.chr1.exons.bed.gz \ - -b ../../data/aluY.chr1.bed.gz > obs +$BT reldist -a $DATA/refseq.chr1.exons.bed.gz \ + -b $DATA/aluY.chr1.bed.gz > obs check obs exp rm obs exp @@ -143,7 +144,7 @@ echo \ 0.48 365 43422 0.008 0.49 336 43422 0.008 0.50 38 43422 0.001" > exp -$BT reldist -a ../../data/refseq.chr1.exons.bed.gz \ - -b ../../data/gerp.chr1.bed.gz > obs +$BT reldist -a $DATA/refseq.chr1.exons.bed.gz \ + -b $DATA/gerp.chr1.bed.gz > obs check obs exp -rm obs exp \ No newline at end of file +rm obs exp