Merge pull request #48 from Debian/suggestion-for-testsuite

Patches to make the testsuite easier to move.

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
 

test/reldist/test-reldist.sh

 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
+rm obs exp
\ No newline at end of file