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Commit c1fb7ab9 authored by Charles Plessy's avatar Charles Plessy
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Call bedtools via the BT variable, allowing to override the location.

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test/map/test-map.sh
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...@@ -694,7 +694,7 @@ echo \ ...@@ -694,7 +694,7 @@ echo \
" "
***** *****
***** ERROR: There are 1 columns given, but there are 2 operations." > exp ***** 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 check obs exp
rm obs exp rm obs exp
...@@ -708,7 +708,7 @@ echo \ ...@@ -708,7 +708,7 @@ echo \
" "
***** *****
***** ERROR: There are 3 columns given, but there are 2 operations." > exp ***** 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 check obs exp
rm obs exp rm obs exp
...@@ -721,7 +721,7 @@ echo \ ...@@ -721,7 +721,7 @@ echo \
" "
***** *****
***** ERROR: Column 1 is not a numeric field for database file values.bed." > exp ***** 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 check obs exp
rm obs exp rm obs exp
...@@ -738,7 +738,7 @@ chr2 0 100 . . ...@@ -738,7 +738,7 @@ chr2 0 100 . .
chr2 100 200 . . chr2 100 200 . .
chr3 0 100 6 7 chr3 0 100 6 7
chr3 100 200 8 23" > exp 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 check obs exp
rm obs exp rm obs exp
...@@ -755,7 +755,7 @@ chr2 0 100 . . . ...@@ -755,7 +755,7 @@ chr2 0 100 . . .
chr2 100 200 . . . chr2 100 200 . . .
chr3 0 100 10 6 7 chr3 0 100 10 6 7
chr3 100 200 120 8 23" > exp 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 check obs exp
rm obs exp rm obs exp
...@@ -771,7 +771,7 @@ chr2 0 100 . ...@@ -771,7 +771,7 @@ chr2 0 100 .
chr2 100 200 . chr2 100 200 .
chr3 0 100 76.2222 chr3 0 100 76.2222
chr3 100 200 0.25" > exp 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 check obs exp
rm obs exp rm obs exp
...@@ -786,7 +786,7 @@ chr2 0 100 . ...@@ -786,7 +786,7 @@ chr2 0 100 .
chr2 100 200 . chr2 100 200 .
chr3 0 100 114.333 chr3 0 100 114.333
chr3 100 200 0.5" > exp 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 check obs exp
rm obs exp rm obs exp
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