From 2a16ea92529b07e918e331c13cc56b75e441fb52 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 26 Dec 2012 15:40:42 -0500
Subject: [PATCH] [BUG] Fix regression in reporting all overlapping features
for . Thanks to @jsilter.
---
src/closestBed/closestBed.cpp | 1 +
test/closest/close-a.bed | 8 +++++
test/closest/close-b.bed | 7 ++++
test/closest/test-closest.sh | 66 +++++++++++++++++++++++++++++++++++
4 files changed, 82 insertions(+)
create mode 100644 test/closest/close-a.bed
create mode 100644 test/closest/close-b.bed
diff --git a/src/closestBed/closestBed.cpp b/src/closestBed/closestBed.cpp
index 12279c39..673028aa 100644
--- a/src/closestBed/closestBed.cpp
+++ b/src/closestBed/closestBed.cpp
@@ -126,6 +126,7 @@ void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
closestB.clear();
distances.clear();
}
+ minDistance = 0;
closestB.push_back(*h);
distances.push_back(0);
}
diff --git a/test/closest/close-a.bed b/test/closest/close-a.bed
new file mode 100644
index 00000000..ad2095e3
--- /dev/null
+++ b/test/closest/close-a.bed
@@ -0,0 +1,8 @@
+track name="Test Bed" maxheightpixels=120:120
+chr1 100 101
+chr1 200 201
+chr1 300 301
+chr1 100000 100010
+chr1 100020 100040
+chr2 1 10
+chr2 20 30
diff --git a/test/closest/close-b.bed b/test/closest/close-b.bed
new file mode 100644
index 00000000..65b4e004
--- /dev/null
+++ b/test/closest/close-b.bed
@@ -0,0 +1,7 @@
+track name="Test Bed 2" maxheightpixels=120:120
+chr1 100 101
+chr1 150 201
+chr1 175 375
+chr3 20 30
+chr7 55209979 55210130
+chr7 55210220 55210688
diff --git a/test/closest/test-closest.sh b/test/closest/test-closest.sh
index 58269cf8..7a0ded2d 100644
--- a/test/closest/test-closest.sh
+++ b/test/closest/test-closest.sh
@@ -101,3 +101,69 @@ echo \
$BT closest -a strand-test-a.bed -b strand-test-b.bed -S > obs
check obs exp
rm obs exp
+
+
+###########################################################
+# test reproting of all overlapping features
+###########################################################
+echo " closest.t9...\c"
+echo \
+"chr1 100 101 chr1 100 101
+chr1 200 201 chr1 150 201
+chr1 200 201 chr1 175 375
+chr1 300 301 chr1 175 375
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test reproting of first overlapping feature
+###########################################################
+echo " closest.t10...\c"
+echo \
+"chr1 100 101 chr1 100 101
+chr1 200 201 chr1 150 201
+chr1 300 301 chr1 175 375
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed -t first > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test reproting of last overlapping feature
+###########################################################
+echo " closest.t11...\c"
+echo \
+"chr1 100 101 chr1 100 101
+chr1 200 201 chr1 175 375
+chr1 300 301 chr1 175 375
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed -t last > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test reproting of no overlapping feature
+###########################################################
+echo " closest.t12...\c"
+echo \
+"chr1 100 101 chr1 150 201
+chr1 200 201 chr1 100 101
+chr1 300 301 chr1 150 201
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed -io > obs
+check obs exp
+rm obs exp
--
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