From 952088e84d0193712340169b8d5118e0467aa1e1 Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Mon, 3 Feb 2014 16:18:14 -0500
Subject: [PATCH] add -valueOnly option to jaccard
---
src/jaccard/jaccard.cpp | 35 ++++++++++++++++++++++-------------
src/jaccard/jaccard.h | 4 +++-
src/jaccard/jaccardMain.cpp | 7 ++++++-
3 files changed, 31 insertions(+), 15 deletions(-)
diff --git a/src/jaccard/jaccard.cpp b/src/jaccard/jaccard.cpp
index 0c22fa8d..147ee4e0 100644
--- a/src/jaccard/jaccard.cpp
+++ b/src/jaccard/jaccard.cpp
@@ -34,12 +34,14 @@ size_t Jaccard::GetTotalIntersection(const BED &a, const vector<BED> &hits)
Constructor
*/
Jaccard::Jaccard(string bedAFile, string bedBFile,
- float overlapFraction, bool reciprocal)
+ float overlapFraction, bool reciprocal,
+ bool valueOnly)
{
_bedAFile = bedAFile;
_bedBFile = bedBFile;
_overlapFraction = overlapFraction;
_reciprocal = reciprocal;
+ _valueOnly = valueOnly;
CalculateJaccard();
@@ -83,19 +85,26 @@ void Jaccard::CalculateJaccard() {
unsigned long U = _bedA->getTotalFlattenedLength() + \
_bedB->getTotalFlattenedLength();
- // header
- cout << "intersection\t"
- << "union-intersection\t"
- << "jaccard\t"
- << "n_intersections"
- << endl;
+ float jaccard_stat = (float) I / ((float) U - (float) I);
- // result
- cout << I << "\t"
- << U - I << "\t"
- << (float) I / ((float) U - (float) I) << "\t"
- << n_intersections
- << endl;
+ if (!_valueOnly) {
+ // header
+ cout << "intersection\t"
+ << "union-intersection\t"
+ << "jaccard\t"
+ << "n_intersections"
+ << endl;
+
+ // result
+ cout << I << "\t"
+ << U - I << "\t"
+ << jaccard_stat << "\t"
+ << n_intersections
+ << endl;
+ }
+ else {
+ cout << jaccard_stat << endl;
+ }
}
diff --git a/src/jaccard/jaccard.h b/src/jaccard/jaccard.h
index efdd8628..2badb00c 100644
--- a/src/jaccard/jaccard.h
+++ b/src/jaccard/jaccard.h
@@ -35,7 +35,8 @@ public:
// constructor
Jaccard(string bedAFile, string bedBFile,
- float overlapFraction, bool reciprocal);
+ float overlapFraction, bool reciprocal,
+ bool valueOnly);
// destructor
~Jaccard(void);
@@ -49,6 +50,7 @@ private:
string _bedBFile;
bool _reciprocal;
+ bool _valueOnly;
float _overlapFraction;
// instance of a bed file class.
diff --git a/src/jaccard/jaccardMain.cpp b/src/jaccard/jaccardMain.cpp
index cc175d17..683306d5 100644
--- a/src/jaccard/jaccardMain.cpp
+++ b/src/jaccard/jaccardMain.cpp
@@ -40,6 +40,7 @@ int jaccard_main(int argc, char* argv[]) {
bool haveBedB = false;
bool haveFraction = false;
bool reciprocalFraction = false;
+ bool valueOnly = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -84,6 +85,9 @@ int jaccard_main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
reciprocalFraction = true;
}
+ else if(PARAMETER_CHECK("-valueOnly", 10, parameterLength)) {
+ valueOnly = true;
+ }
else {
cerr << endl
<< "*****ERROR: Unrecognized parameter: "
@@ -108,7 +112,8 @@ int jaccard_main(int argc, char* argv[]) {
if (!showHelp) {
Jaccard *j = new Jaccard(bedAFile, bedBFile,
- overlapFraction, reciprocalFraction);
+ overlapFraction, reciprocalFraction,
+ valueOnly);
delete j;
return 0;
}
--
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