From 3b468dd32c97ccc4e9f3831678fd0c5b3afbe65d Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Tue, 12 Feb 2013 17:32:24 -0700
Subject: [PATCH] add n_intersections to jaccard output
---
src/jaccard/jaccard.cpp | 12 ++++++++----
src/jaccard/jaccard.h | 2 +-
test/jaccard/test-jaccard.sh | 20 ++++++++++----------
3 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/src/jaccard/jaccard.cpp b/src/jaccard/jaccard.cpp
index dd0979e9..8df39987 100644
--- a/src/jaccard/jaccard.cpp
+++ b/src/jaccard/jaccard.cpp
@@ -53,7 +53,7 @@ Jaccard::~Jaccard(void) {
}
-unsigned long Jaccard::GetIntersection() {
+unsigned long Jaccard::GetIntersection(size_t &n_intersections) {
_bedA = new BedFile(_bedAFile);
_bedB = new BedFile(_bedBFile);
@@ -70,13 +70,15 @@ unsigned long Jaccard::GetIntersection() {
hit_set.second.reserve(10000);
while (sweep.Next(hit_set)) {
I += GetTotalIntersection(hit_set.first, hit_set.second);
+ n_intersections += hit_set.second.size();
}
return I;
}
void Jaccard::CalculateJaccard() {
- unsigned long I = GetIntersection();
+ size_t n_intersections = 0;
+ unsigned long I = GetIntersection(n_intersections);
unsigned long U = _bedA->getTotalFlattenedLength() + \
_bedB->getTotalFlattenedLength();
@@ -84,13 +86,15 @@ void Jaccard::CalculateJaccard() {
// header
cout << "intersection\t"
<< "union\t"
- << "jaccard"
+ << "jaccard\t"
+ << "n_intersections"
<< endl;
// result
cout << I << "\t"
<< U - I << "\t"
- << (float) I / ((float) U - (float) I)
+ << (float) I / ((float) U - (float) I) << "\t"
+ << n_intersections
<< endl;
}
diff --git a/src/jaccard/jaccard.h b/src/jaccard/jaccard.h
index f0e3fd77..efdd8628 100644
--- a/src/jaccard/jaccard.h
+++ b/src/jaccard/jaccard.h
@@ -57,7 +57,7 @@ private:
//------------------------------------------------
// private methods
//------------------------------------------------
- unsigned long GetIntersection();
+ unsigned long GetIntersection(size_t &n_intersections);
unsigned long GetUnion();
void CalculateJaccard();
diff --git a/test/jaccard/test-jaccard.sh b/test/jaccard/test-jaccard.sh
index d2de0e4a..81e316c5 100644
--- a/test/jaccard/test-jaccard.sh
+++ b/test/jaccard/test-jaccard.sh
@@ -14,8 +14,8 @@ check()
###########################################################
echo " jaccard.t01...\c"
echo \
-"intersection union jaccard
-110 110 1" > exp
+"intersection union jaccard n_intersections
+110 110 1 2" > exp
$BT jaccard -a a.bed -b a.bed > obs
check obs exp
rm obs exp
@@ -23,16 +23,16 @@ rm obs exp
echo " jaccard.t02...\c"
echo \
-"intersection union jaccard
-10 140 0.0714286" > exp
+"intersection union jaccard n_intersections
+10 140 0.0714286 1" > exp
$BT jaccard -a a.bed -b b.bed > obs
check obs exp
rm obs exp
echo " jaccard.t03...\c"
echo \
-"intersection union jaccard
-10 200 0.05" > exp
+"intersection union jaccard n_intersections
+10 200 0.05 1" > exp
$BT jaccard -a a.bed -b c.bed > obs
check obs exp
rm obs exp
@@ -40,8 +40,8 @@ rm obs exp
echo " jaccard.t04...\c"
echo \
-"intersection union jaccard
-0 210 0" > exp
+"intersection union jaccard n_intersections
+0 210 0 0" > exp
$BT jaccard -a a.bed -b d.bed > obs
check obs exp
rm obs exp
@@ -51,8 +51,8 @@ rm obs exp
###########################################################
echo " jaccard.t05...\c"
echo \
-"intersection union jaccard
-10 140 0.0714286" > exp
+"intersection union jaccard n_intersections
+10 140 0.0714286 1" > exp
cat a.bed | $BT jaccard -a - -b b.bed > obs
check obs exp
rm obs exp
--
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