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Commit 90892a6b authored by Neil Kindlon's avatar Neil Kindlon
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test/closest/a2.bed 0 → 100644
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chr1 10 20 a1 1 -
test/closest/b2.bed 0 → 100644
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chr1 8 9 b1 1 +
chr1 21 22 b2 1 -
test/closest/d4.bed 0 → 100644
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chr1 40 60
chr1 120 140
test/closest/kclosest/d1.bed 0 → 100644
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chr1 10 15
chr1 25 28
chr1 30 40
chr1 35 40
chr1 38 40
chr1 50 60
chr1 70 80
test/closest/kclosest/d2.bed 0 → 100644
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chr1 95 105 2.1 20 +
chr1 98 108 2.2 20 +
chr1 105 115 2.3 20 +
chr1 120 130 2.4 20 +
chr1 140 160 2.5 20 +
chr1 140 155 2.6 20 +
chr1 140 150 2.7 20 +
chr1 170 180 2.8 20 +
chr1 190 200 2.9 20 +
test/closest/kclosest/d3.bed 0 → 100644
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chr1 10 20 3.1 20 -
chr1 30 40 3.2 20 +
chr1 45 60 3.3 20 -
chr1 50 60 3.4 20 -
chr1 55 60 3.5 20 -
chr1 70 80 3.6 20 +
chr1 75 80 3.65 20 +
chr1 90 105 3.7 20 +
chr1 95 110 3.8 20 -
chr1 110 115 3.9 20 +
chr1 120 130 3.10 20 -
chr1 130 140 3.11 20 +
chr1 135 140 3.115 20 +
chr1 150 165 3.12 20 -
chr1 150 160 3.13 20 -
chr1 150 155 3.14 20 -
chr1 170 180 3.15 20 +
chr1 190 200 3.16 20 -
test/closest/kclosest/q1.bed 0 → 100644
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chr1 100 110
test/closest/kclosest/q2.bed 0 → 100644
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chr1 100 110 q2.1 20 +
chr1 105 110 q2.2 20 -
test/closest/kclosest/test-kclosest.sh 0 → 100644
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echo -e \
"\n###########################################################
#
# K CLOSEST HITS TESTS
#
###########################################################\n"
BT=${BT-../../../bin/bedtools}
check()
{
if diff $1 $2; then
echo ok
return 1
else
echo fail
return 0
fi
}
###########################################################
# Test that hits are correctly picked for various values
# of k and tie modes.
###########################################################
echo " kclosest.t1...\c"
echo \
"chr1 100 110 chr1 70 80
chr1 100 110 chr1 50 60
chr1 100 110 chr1 30 40
chr1 100 110 chr1 35 40
chr1 100 110 chr1 38 40" > exp
$BT closest -a q1.bed -b d1.bed -k 3 > obs
check obs exp
rm obs exp
echo " kclosest.t2...\c"
echo \
"chr1 100 110 chr1 70 80
chr1 100 110 chr1 50 60
chr1 100 110 chr1 30 40
chr1 100 110 chr1 35 40
chr1 100 110 chr1 38 40" > exp
$BT closest -a q1.bed -b d1.bed -k 5 > obs
check obs exp
rm obs exp
echo " kclosest.t3...\c"
echo \
"chr1 100 110 chr1 70 80
chr1 100 110 chr1 50 60
chr1 100 110 chr1 30 40
chr1 100 110 chr1 35 40
chr1 100 110 chr1 38 40
chr1 100 110 chr1 25 28" > exp
$BT closest -a q1.bed -b d1.bed -k 6 > obs
check obs exp
rm obs exp
echo " kclosest.t4...\c"
echo \
"chr1 100 110 chr1 70 80
chr1 100 110 chr1 50 60
chr1 100 110 chr1 30 40
chr1 100 110 chr1 35 40
chr1 100 110 chr1 38 40
chr1 100 110 chr1 25 28
chr1 100 110 chr1 10 15" > exp
$BT closest -a q1.bed -b d1.bed -k 7 > obs
check obs exp
rm obs exp
echo " kclosest.t5...\c"
echo \
"chr1 100 110 chr1 70 80
chr1 100 110 chr1 50 60
chr1 100 110 chr1 30 40
chr1 100 110 chr1 25 28" > exp
$BT closest -a q1.bed -b d1.bed -k 4 -t first > obs
check obs exp
rm obs exp
echo " kclosest.t6...\c"
echo \
"chr1 100 110 chr1 70 80
chr1 100 110 chr1 50 60
chr1 100 110 chr1 38 40
chr1 100 110 chr1 25 28" > exp
$BT closest -a q1.bed -b d1.bed -k 4 -t last > obs
check obs exp
rm obs exp
echo " kclosest.t7...\c"
echo \
"chr1 100 110 chr1 95 105 2.1 20 +
chr1 100 110 chr1 98 108 2.2 20 +
chr1 100 110 chr1 105 115 2.3 20 +
chr1 100 110 chr1 120 130 2.4 20 +" > exp
$BT closest -a q1.bed -b d2.bed -k 4 > obs
check obs exp
rm obs exp
echo " kclosest.t8...\c"
echo \
"chr1 100 110 chr1 95 105 2.1 20 +
chr1 100 110 chr1 120 130 2.4 20 +
chr1 100 110 chr1 140 160 2.5 20 +
chr1 100 110 chr1 170 180 2.8 20 +" > exp
$BT closest -a q1.bed -b d2.bed -k 4 -t first > obs
check obs exp
rm obs exp
echo " kclosest.t9...\c"
echo \
"chr1 100 110 chr1 120 130 2.4 20 +
chr1 100 110 chr1 140 160 2.5 20 +
chr1 100 110 chr1 170 180 2.8 20 +
chr1 100 110 chr1 190 200 2.9 20 +" > exp
$BT closest -a q1.bed -b d2.bed -k 4 -t first -io > obs
check obs exp
rm obs exp
echo " kclosest.t10...\c"
echo \
"chr1 100 110 chr1 95 105 2.1 20 +
chr1 100 110 chr1 98 108 2.2 20 +
chr1 100 110 chr1 105 115 2.3 20 +
chr1 100 110 chr1 120 130 2.4 20 +
chr1 100 110 chr1 140 160 2.5 20 +
chr1 100 110 chr1 140 155 2.6 20 +
chr1 100 110 chr1 140 150 2.7 20 +" > exp
$BT closest -a q1.bed -b d2.bed -k 7 > obs
check obs exp
rm obs exp
echo " kclosest.t11...\c"
echo \
"chr1 100 110 chr1 95 105 2.1 20 +
chr1 100 110 chr1 120 130 2.4 20 +
chr1 100 110 chr1 140 160 2.5 20 +
chr1 100 110 chr1 170 180 2.8 20 +
chr1 100 110 chr1 190 200 2.9 20 +" > exp
$BT closest -a q1.bed -b d2.bed -k 7 -t first > obs
check obs exp
rm obs exp
echo " kclosest.t12...\c"
echo \
"chr1 100 110 chr1 105 115 2.3 20 +
chr1 100 110 chr1 120 130 2.4 20 +
chr1 100 110 chr1 140 150 2.7 20 +
chr1 100 110 chr1 170 180 2.8 20 +
chr1 100 110 chr1 190 200 2.9 20 +" > exp
$BT closest -a q1.bed -b d2.bed -k 7 -t last > obs
check obs exp
rm obs exp
echo " kclosest.t13...\c"
echo \
"chr1 100 110 chr1 95 105 2.1 20 + 0
chr1 100 110 chr1 98 108 2.2 20 + 0
chr1 100 110 chr1 105 115 2.3 20 + 0" > exp
$BT closest -a q1.bed -b d2.bed -k 7 -id -D ref > obs
check obs exp
rm obs exp
echo " kclosest.t14...\c"
echo \
"chr1 100 110 chr1 95 105 2.1 20 + 0" > exp
$BT closest -a q1.bed -b d2.bed -k 7 -id -D ref -t first > obs
check obs exp
rm obs exp
###########################################################
# Check strandedness with -iu, -io, -id, and -D ref,
# a, and b.
###########################################################
echo " kclosest.t15...\c"
echo \
"chr1 100 110 chr1 90 105 3.7 20 + 0
chr1 100 110 chr1 95 110 3.8 20 - 0
chr1 100 110 chr1 110 115 3.9 20 + 1
chr1 100 110 chr1 120 130 3.10 20 - 11
chr1 100 110 chr1 130 140 3.11 20 + 21
chr1 100 110 chr1 135 140 3.115 20 + 26
chr1 100 110 chr1 150 165 3.12 20 - 41
chr1 100 110 chr1 150 160 3.13 20 - 41
chr1 100 110 chr1 150 155 3.14 20 - 41
chr1 100 110 chr1 170 180 3.15 20 + 61
chr1 100 110 chr1 190 200 3.16 20 - 81" > exp
$BT closest -a q1.bed -b d3.bed -k 15 -D ref -iu > obs
check obs exp
rm obs exp
echo " kclosest.t16...\c"
echo \
"chr1 100 110 chr1 110 115 3.9 20 + 1
chr1 100 110 chr1 120 130 3.10 20 - 11
chr1 100 110 chr1 70 80 3.6 20 + -21
chr1 100 110 chr1 75 80 3.65 20 + -21
chr1 100 110 chr1 130 140 3.11 20 + 21
chr1 100 110 chr1 135 140 3.115 20 + 26
chr1 100 110 chr1 45 60 3.3 20 - -41
chr1 100 110 chr1 50 60 3.4 20 - -41
chr1 100 110 chr1 55 60 3.5 20 - -41
chr1 100 110 chr1 150 165 3.12 20 - 41
chr1 100 110 chr1 150 160 3.13 20 - 41
chr1 100 110 chr1 150 155 3.14 20 - 41
chr1 100 110 chr1 30 40 3.2 20 + -61
chr1 100 110 chr1 170 180 3.15 20 + 61
chr1 100 110 chr1 10 20 3.1 20 - -81
chr1 100 110 chr1 190 200 3.16 20 - 81" > exp
$BT closest -a q1.bed -b d3.bed -k 15 -D ref -io > obs
check obs exp
rm obs exp
echo " kclosest.t17...\c"
echo \
"chr1 100 110 chr1 90 105 3.7 20 + 0
chr1 100 110 chr1 95 110 3.8 20 - 0
chr1 100 110 chr1 70 80 3.6 20 + -21
chr1 100 110 chr1 75 80 3.65 20 + -21
chr1 100 110 chr1 45 60 3.3 20 - -41
chr1 100 110 chr1 50 60 3.4 20 - -41
chr1 100 110 chr1 55 60 3.5 20 - -41
chr1 100 110 chr1 30 40 3.2 20 + -61
chr1 100 110 chr1 10 20 3.1 20 - -81" > exp
$BT closest -a q1.bed -b d3.bed -k 15 -D ref -id > obs
check obs exp
rm obs exp
echo " kclosest.t18...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + chr1 130 140 3.11 20 + 21
chr1 100 110 q2.1 20 + chr1 135 140 3.115 20 + 26
chr1 100 110 q2.1 20 + chr1 150 165 3.12 20 - 41
chr1 100 110 q2.1 20 + chr1 150 160 3.13 20 - 41
chr1 100 110 q2.1 20 + chr1 150 155 3.14 20 - 41
chr1 100 110 q2.1 20 + chr1 170 180 3.15 20 + 61
chr1 100 110 q2.1 20 + chr1 190 200 3.16 20 - 81
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 90 105 3.7 20 + 1
chr1 105 110 q2.2 20 - chr1 70 80 3.6 20 + 26
chr1 105 110 q2.2 20 - chr1 75 80 3.65 20 + 26
chr1 105 110 q2.2 20 - chr1 45 60 3.3 20 - 46
chr1 105 110 q2.2 20 - chr1 50 60 3.4 20 - 46
chr1 105 110 q2.2 20 - chr1 55 60 3.5 20 - 46
chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + 66
chr1 105 110 q2.2 20 - chr1 10 20 3.1 20 - 86" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D a -iu > obs
check obs exp
rm obs exp
echo " kclosest.t19...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 70 80 3.6 20 + -21
chr1 100 110 q2.1 20 + chr1 75 80 3.65 20 + -21
chr1 100 110 q2.1 20 + chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + chr1 50 60 3.4 20 - -41
chr1 100 110 q2.1 20 + chr1 55 60 3.5 20 - -41
chr1 100 110 q2.1 20 + chr1 30 40 3.2 20 + -61
chr1 100 110 q2.1 20 + chr1 10 20 3.1 20 - -81
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 110 115 3.9 20 + -1
chr1 105 110 q2.2 20 - chr1 120 130 3.10 20 - -11
chr1 105 110 q2.2 20 - chr1 130 140 3.11 20 + -21
chr1 105 110 q2.2 20 - chr1 135 140 3.115 20 + -26
chr1 105 110 q2.2 20 - chr1 150 165 3.12 20 - -41
chr1 105 110 q2.2 20 - chr1 150 160 3.13 20 - -41
chr1 105 110 q2.2 20 - chr1 150 155 3.14 20 - -41
chr1 105 110 q2.2 20 - chr1 170 180 3.15 20 + -61
chr1 105 110 q2.2 20 - chr1 190 200 3.16 20 - -81" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D a -id > obs
check obs exp
rm obs exp
echo " kclosest.t20...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + chr1 70 80 3.6 20 + 21
chr1 100 110 q2.1 20 + chr1 75 80 3.65 20 + 21
chr1 100 110 q2.1 20 + chr1 150 165 3.12 20 - 41
chr1 100 110 q2.1 20 + chr1 150 160 3.13 20 - 41
chr1 100 110 q2.1 20 + chr1 150 155 3.14 20 - 41
chr1 100 110 q2.1 20 + chr1 30 40 3.2 20 + 61
chr1 100 110 q2.1 20 + chr1 190 200 3.16 20 - 81
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 90 105 3.7 20 + 1
chr1 105 110 q2.2 20 - chr1 120 130 3.10 20 - 11
chr1 105 110 q2.2 20 - chr1 70 80 3.6 20 + 26
chr1 105 110 q2.2 20 - chr1 75 80 3.65 20 + 26
chr1 105 110 q2.2 20 - chr1 150 165 3.12 20 - 41
chr1 105 110 q2.2 20 - chr1 150 160 3.13 20 - 41
chr1 105 110 q2.2 20 - chr1 150 155 3.14 20 - 41
chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + 66
chr1 105 110 q2.2 20 - chr1 190 200 3.16 20 - 81" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D b -iu > obs
check obs exp
rm obs exp
echo " kclosest.t21...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 110 115 3.9 20 + -1
chr1 100 110 q2.1 20 + chr1 130 140 3.11 20 + -21
chr1 100 110 q2.1 20 + chr1 135 140 3.115 20 + -26
chr1 100 110 q2.1 20 + chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + chr1 50 60 3.4 20 - -41
chr1 100 110 q2.1 20 + chr1 55 60 3.5 20 - -41
chr1 100 110 q2.1 20 + chr1 170 180 3.15 20 + -61
chr1 100 110 q2.1 20 + chr1 10 20 3.1 20 - -81
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 110 115 3.9 20 + -1
chr1 105 110 q2.2 20 - chr1 130 140 3.11 20 + -21
chr1 105 110 q2.2 20 - chr1 135 140 3.115 20 + -26
chr1 105 110 q2.2 20 - chr1 45 60 3.3 20 - -46
chr1 105 110 q2.2 20 - chr1 50 60 3.4 20 - -46
chr1 105 110 q2.2 20 - chr1 55 60 3.5 20 - -46
chr1 105 110 q2.2 20 - chr1 170 180 3.15 20 + -61
chr1 105 110 q2.2 20 - chr1 10 20 3.1 20 - -86" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D b -id > obs
check obs exp
rm obs exp
echo " kclosest.t22...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + chr1 130 140 3.11 20 + 21
chr1 100 110 q2.1 20 + chr1 135 140 3.115 20 + 26
chr1 100 110 q2.1 20 + chr1 170 180 3.15 20 + 61
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 45 60 3.3 20 - 46
chr1 105 110 q2.2 20 - chr1 50 60 3.4 20 - 46
chr1 105 110 q2.2 20 - chr1 55 60 3.5 20 - 46
chr1 105 110 q2.2 20 - chr1 10 20 3.1 20 - 86" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D a -s -iu > obs
check obs exp
rm obs exp
echo " kclosest.t23...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 70 80 3.6 20 + -21
chr1 100 110 q2.1 20 + chr1 75 80 3.65 20 + -21
chr1 100 110 q2.1 20 + chr1 30 40 3.2 20 + -61
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 120 130 3.10 20 - -11
chr1 105 110 q2.2 20 - chr1 150 165 3.12 20 - -41
chr1 105 110 q2.2 20 - chr1 150 160 3.13 20 - -41
chr1 105 110 q2.2 20 - chr1 150 155 3.14 20 - -41
chr1 105 110 q2.2 20 - chr1 190 200 3.16 20 - -81" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D a -s -id > obs
check obs exp
rm obs exp
echo " kclosest.t24...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 70 80 3.6 20 + 21
chr1 100 110 q2.1 20 + chr1 75 80 3.65 20 + 21
chr1 100 110 q2.1 20 + chr1 30 40 3.2 20 + 61
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 120 130 3.10 20 - 11
chr1 105 110 q2.2 20 - chr1 150 165 3.12 20 - 41
chr1 105 110 q2.2 20 - chr1 150 160 3.13 20 - 41
chr1 105 110 q2.2 20 - chr1 150 155 3.14 20 - 41
chr1 105 110 q2.2 20 - chr1 190 200 3.16 20 - 81" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D b -s -iu > obs
check obs exp
rm obs exp
echo " kclosest.t25...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + chr1 110 115 3.9 20 + -1
chr1 100 110 q2.1 20 + chr1 130 140 3.11 20 + -21
chr1 100 110 q2.1 20 + chr1 135 140 3.115 20 + -26
chr1 100 110 q2.1 20 + chr1 170 180 3.15 20 + -61
chr1 105 110 q2.2 20 - chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - chr1 45 60 3.3 20 - -46
chr1 105 110 q2.2 20 - chr1 50 60 3.4 20 - -46
chr1 105 110 q2.2 20 - chr1 55 60 3.5 20 - -46
chr1 105 110 q2.2 20 - chr1 10 20 3.1 20 - -86" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D b -s -id > obs
check obs exp
rm obs exp
echo " kclosest.t26...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + chr1 150 165 3.12 20 - 41
chr1 100 110 q2.1 20 + chr1 150 160 3.13 20 - 41
chr1 100 110 q2.1 20 + chr1 150 155 3.14 20 - 41
chr1 100 110 q2.1 20 + chr1 190 200 3.16 20 - 81
chr1 105 110 q2.2 20 - chr1 90 105 3.7 20 + 1
chr1 105 110 q2.2 20 - chr1 70 80 3.6 20 + 26
chr1 105 110 q2.2 20 - chr1 75 80 3.65 20 + 26
chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + 66" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D a -S -iu > obs
check obs exp
rm obs exp
echo " kclosest.t27...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + chr1 50 60 3.4 20 - -41
chr1 100 110 q2.1 20 + chr1 55 60 3.5 20 - -41
chr1 100 110 q2.1 20 + chr1 10 20 3.1 20 - -81
chr1 105 110 q2.2 20 - chr1 110 115 3.9 20 + -1
chr1 105 110 q2.2 20 - chr1 130 140 3.11 20 + -21
chr1 105 110 q2.2 20 - chr1 135 140 3.115 20 + -26
chr1 105 110 q2.2 20 - chr1 170 180 3.15 20 + -61" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D a -S -id > obs
check obs exp
rm obs exp
echo " kclosest.t28...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + chr1 150 165 3.12 20 - 41
chr1 100 110 q2.1 20 + chr1 150 160 3.13 20 - 41
chr1 100 110 q2.1 20 + chr1 150 155 3.14 20 - 41
chr1 100 110 q2.1 20 + chr1 190 200 3.16 20 - 81
chr1 105 110 q2.2 20 - chr1 90 105 3.7 20 + 1
chr1 105 110 q2.2 20 - chr1 70 80 3.6 20 + 26
chr1 105 110 q2.2 20 - chr1 75 80 3.65 20 + 26
chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + 66" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D b -S -iu > obs
check obs exp
rm obs exp
echo " kclosest.t29...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + chr1 50 60 3.4 20 - -41
chr1 100 110 q2.1 20 + chr1 55 60 3.5 20 - -41
chr1 100 110 q2.1 20 + chr1 10 20 3.1 20 - -81
chr1 105 110 q2.2 20 - chr1 110 115 3.9 20 + -1
chr1 105 110 q2.2 20 - chr1 130 140 3.11 20 + -21
chr1 105 110 q2.2 20 - chr1 135 140 3.115 20 + -26
chr1 105 110 q2.2 20 - chr1 170 180 3.15 20 + -61" > exp
$BT closest -a q2.bed -b d3.bed -k 15 -D b -S -id > obs
check obs exp
rm obs exp
###########################################################
# Test multiple databases and mdb = all mode
###########################################################
echo " kclosest.t30...\c"
echo \
"chr1 100 110 q2.1 20 + 1 chr1 98 108 2.2 20 + 0
chr1 100 110 q2.1 20 + 1 chr1 105 115 2.3 20 + 0
chr1 100 110 q2.1 20 + 1 chr1 95 105 2.1 20 + 0
chr1 100 110 q2.1 20 + 2 chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + 2 chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + 2 chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + 1 chr1 120 130 2.4 20 + 11
chr1 100 110 q2.1 20 + 2 chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + 2 chr1 70 80 3.6 20 + -21
chr1 100 110 q2.1 20 + 2 chr1 75 80 3.65 20 + -21
chr1 105 110 q2.2 20 - 1 chr1 105 115 2.3 20 + 0
chr1 105 110 q2.2 20 - 1 chr1 98 108 2.2 20 + 0
chr1 105 110 q2.2 20 - 2 chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - 2 chr1 90 105 3.7 20 + -1
chr1 105 110 q2.2 20 - 1 chr1 95 105 2.1 20 + -1
chr1 105 110 q2.2 20 - 2 chr1 110 115 3.9 20 + 1
chr1 105 110 q2.2 20 - 1 chr1 120 130 2.4 20 + 11
chr1 105 110 q2.2 20 - 2 chr1 120 130 3.10 20 - 11
chr1 105 110 q2.2 20 - 2 chr1 130 140 3.11 20 + 21
chr1 105 110 q2.2 20 - 2 chr1 70 80 3.6 20 + -26
chr1 105 110 q2.2 20 - 2 chr1 75 80 3.65 20 + -26" > exp
$BT closest -a q2.bed -b d2.bed d3.bed -mdb all -k 10 -D ref -t all > obs
check obs exp
rm obs exp
echo " kclosest.t31...\c"
echo \
"chr1 100 110 q2.1 20 + 1 chr1 95 105 2.1 20 + 0
chr1 100 110 q2.1 20 + 2 chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + 1 chr1 120 130 2.4 20 + 11
chr1 100 110 q2.1 20 + 2 chr1 70 80 3.6 20 + -21
chr1 100 110 q2.1 20 + 2 chr1 135 140 3.115 20 + 26
chr1 100 110 q2.1 20 + 1 chr1 140 160 2.5 20 + 31
chr1 100 110 q2.1 20 + 2 chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + 2 chr1 30 40 3.2 20 + -61
chr1 100 110 q2.1 20 + 2 chr1 10 20 3.1 20 - -81
chr1 105 110 q2.2 20 - 1 chr1 98 108 2.2 20 + 0
chr1 105 110 q2.2 20 - 1 chr1 95 105 2.1 20 + -1
chr1 105 110 q2.2 20 - 1 chr1 120 130 2.4 20 + 11
chr1 105 110 q2.2 20 - 2 chr1 130 140 3.11 20 + 21
chr1 105 110 q2.2 20 - 2 chr1 70 80 3.6 20 + -26
chr1 105 110 q2.2 20 - 1 chr1 140 160 2.5 20 + 31
chr1 105 110 q2.2 20 - 2 chr1 150 165 3.12 20 - 41
chr1 105 110 q2.2 20 - 2 chr1 45 60 3.3 20 - -46
chr1 105 110 q2.2 20 - 1 chr1 170 180 2.8 20 + 61
chr1 105 110 q2.2 20 - 2 chr1 30 40 3.2 20 + -66" > exp
$BT closest -a q2.bed -b d2.bed d3.bed -mdb all -k 10 -D ref -t first > obs
check obs exp
rm obs exp
echo " kclosest.t32...\c"
echo \
"chr1 100 110 q2.1 20 + 2 chr1 95 110 3.8 20 - 0
chr1 100 110 q2.1 20 + 2 chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + 2 chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + 2 chr1 130 140 3.11 20 + 21
chr1 100 110 q2.1 20 + 2 chr1 135 140 3.115 20 + 26
chr1 100 110 q2.1 20 + 1 chr1 140 150 2.7 20 + 31
chr1 100 110 q2.1 20 + 2 chr1 150 155 3.14 20 - 41
chr1 100 110 q2.1 20 + 2 chr1 170 180 3.15 20 + 61
chr1 100 110 q2.1 20 + 2 chr1 190 200 3.16 20 - 81
chr1 105 110 q2.2 20 - 2 chr1 95 110 3.8 20 - 0
chr1 105 110 q2.2 20 - 2 chr1 110 115 3.9 20 + 1
chr1 105 110 q2.2 20 - 2 chr1 120 130 3.10 20 - 11
chr1 105 110 q2.2 20 - 2 chr1 130 140 3.11 20 + 21
chr1 105 110 q2.2 20 - 2 chr1 135 140 3.115 20 + 26
chr1 105 110 q2.2 20 - 1 chr1 140 150 2.7 20 + 31
chr1 105 110 q2.2 20 - 2 chr1 150 155 3.14 20 - 41
chr1 105 110 q2.2 20 - 2 chr1 55 60 3.5 20 - -46
chr1 105 110 q2.2 20 - 2 chr1 170 180 3.15 20 + 61
chr1 105 110 q2.2 20 - 2 chr1 30 40 3.2 20 + -66" > exp
$BT closest -a q2.bed -b d2.bed d3.bed -mdb all -k 10 -D ref -t last > obs
check obs exp
rm obs exp
###########################################################
# Test new -fu and -fd features
###########################################################
echo " kclosest.t33...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 70 80 3.6 20 + -21
chr1 100 110 q2.1 20 + chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + chr1 30 40 3.2 20 + -61
chr1 100 110 q2.1 20 + chr1 10 20 3.1 20 - -81
chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 105 110 q2.2 20 - chr1 90 105 3.7 20 + -1
chr1 105 110 q2.2 20 - chr1 70 80 3.6 20 + -26
chr1 105 110 q2.2 20 - chr1 45 60 3.3 20 - -46
chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + -66
chr1 105 110 q2.2 20 - chr1 10 20 3.1 20 - -86" > exp
$BT closest -a q2.bed -b d3.bed -k 5 -D ref -t first -fu > obs
check obs exp
rm obs exp
echo " kclosest.t34...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + chr1 130 140 3.11 20 + 21
chr1 100 110 q2.1 20 + chr1 135 140 3.115 20 + 26
chr1 100 110 q2.1 20 + chr1 150 165 3.12 20 - 41
chr1 105 110 q2.2 20 - chr1 110 115 3.9 20 + 1
chr1 105 110 q2.2 20 - chr1 120 130 3.10 20 - 11
chr1 105 110 q2.2 20 - chr1 130 140 3.11 20 + 21
chr1 105 110 q2.2 20 - chr1 135 140 3.115 20 + 26
chr1 105 110 q2.2 20 - chr1 150 165 3.12 20 - 41" > exp
$BT closest -a q2.bed -b d3.bed -k 5 -D ref -t first -fd > obs
check obs exp
rm obs exp
echo " kclosest.t35...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 70 80 3.6 20 + -21
chr1 100 110 q2.1 20 + chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + chr1 30 40 3.2 20 + -61
chr1 100 110 q2.1 20 + chr1 10 20 3.1 20 - -81
chr1 100 110 q2.1 20 + chr1 90 105 3.7 20 + 0
chr1 105 110 q2.2 20 - chr1 110 115 3.9 20 + -1
chr1 105 110 q2.2 20 - chr1 120 130 3.10 20 - -11
chr1 105 110 q2.2 20 - chr1 130 140 3.11 20 + -21
chr1 105 110 q2.2 20 - chr1 135 140 3.115 20 + -26
chr1 105 110 q2.2 20 - chr1 150 165 3.12 20 - -41" > exp
$BT closest -a q2.bed -b d3.bed -k 5 -D a -t first -fu > obs
check obs exp
rm obs exp
echo " kclosest.t36...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + chr1 130 140 3.11 20 + 21
chr1 100 110 q2.1 20 + chr1 135 140 3.115 20 + 26
chr1 100 110 q2.1 20 + chr1 150 165 3.12 20 - 41
chr1 105 110 q2.2 20 - chr1 90 105 3.7 20 + 1
chr1 105 110 q2.2 20 - chr1 70 80 3.6 20 + 26
chr1 105 110 q2.2 20 - chr1 45 60 3.3 20 - 46
chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + 66
chr1 105 110 q2.2 20 - chr1 10 20 3.1 20 - 86" > exp
$BT closest -a q2.bed -b d3.bed -k 5 -D a -t first -fd > obs
check obs exp
rm obs exp
echo " kclosest.t37...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 110 115 3.9 20 + -1
chr1 100 110 q2.1 20 + chr1 130 140 3.11 20 + -21
chr1 100 110 q2.1 20 + chr1 135 140 3.115 20 + -26
chr1 100 110 q2.1 20 + chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + chr1 170 180 3.15 20 + -61
chr1 105 110 q2.2 20 - chr1 110 115 3.9 20 + -1
chr1 105 110 q2.2 20 - chr1 130 140 3.11 20 + -21
chr1 105 110 q2.2 20 - chr1 135 140 3.115 20 + -26
chr1 105 110 q2.2 20 - chr1 45 60 3.3 20 - -46
chr1 105 110 q2.2 20 - chr1 170 180 3.15 20 + -61" > exp
$BT closest -a q2.bed -b d3.bed -k 5 -D b -t first -fu > obs
check obs exp
rm obs exp
echo " kclosest.t38...\c"
echo \
"chr1 100 110 q2.1 20 + chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + chr1 70 80 3.6 20 + 21
chr1 100 110 q2.1 20 + chr1 150 165 3.12 20 - 41
chr1 100 110 q2.1 20 + chr1 30 40 3.2 20 + 61
chr1 100 110 q2.1 20 + chr1 190 200 3.16 20 - 81
chr1 105 110 q2.2 20 - chr1 90 105 3.7 20 + 1
chr1 105 110 q2.2 20 - chr1 120 130 3.10 20 - 11
chr1 105 110 q2.2 20 - chr1 70 80 3.6 20 + 26
chr1 105 110 q2.2 20 - chr1 150 165 3.12 20 - 41
chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + 66" > exp
$BT closest -a q2.bed -b d3.bed -k 5 -D b -t first -fd > obs
check obs exp
rm obs exp
test/intersect/bug167_strandSweep.bed 0 → 100644
+ 10
− 0
View file @ 90892a6b
chr1 9550913 9551859 b.C.1 0 -
chr1 9550913 9621173 b 1 -
chr1 9551859 9553903 b.I.1 0 -
chr1 9553903 9553952 b.C.2 0 -
chr1 9553952 9609630 b.I.2 0 -
chr1 9602747 9603392 f.I.1 0 +
chr1 9603392 9603555 f.C.2 0 +
chr1 9603392 9603555 g.C.3 0 +
chr1 9603555 9609916 f.I.2 0 +
chr1 9603555 9609916 g.I.3 0 +
0% or .
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