From 80f29d23dff7c91573e923d2f19b7c55902ebdf1 Mon Sep 17 00:00:00 2001
From: Aaron Quinlan <aaronquinlan@gmail.com>
Date: Tue, 21 Apr 2009 10:07:41 -0400
Subject: [PATCH] Updated mergeBed reporting logic
1. Changed the cout statements for the last entries for a chromosome.
2. I had forgotten to report the number of merged entries when -n is requested.
3. I also fixed a bug that occassionally caused the last entry for a chromosome
to report the chrom twice in the output.
---
src/intersectBed/intersectBed.cpp | 44 ++++++++++++++++++++++++++++---
src/mergeBed/mergeBed.cpp | 15 ++++++++---
2 files changed, 52 insertions(+), 7 deletions(-)
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index cdce4da2..c6b7dafe 100755
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -1,6 +1,22 @@
+//
+// intersectBed.cpp
+// BEDTools
+//
+// Created by Aaron Quinlan Spring 2009.
+// Copyright 2009 Aaron Quinlan. All rights reserved.
+//
+// Summary: Looks for overlaps between features in two BED files.
+//
+
+/*
+ Includes
+*/
#include "intersectBed.h"
+/*
+ Constructor
+*/
BedIntersect::BedIntersect(string &bedAFile, string &bedBFile, bool &anyHit,
bool &writeB, float &overlapFraction, bool &noHit, bool &writeCount) {
@@ -16,12 +32,20 @@ bool &writeB, float &overlapFraction, bool &noHit, bool &writeCount) {
this->bedB = new BedFile(bedBFile);
}
-
-
+/*
+ Destructor
+*/
BedIntersect::~BedIntersect(void) {
}
+
+/*
+ reportA
+
+ Writes the _original_ BED entry for A.
+ Works for BED3 - BED6.
+*/
void BedIntersect::reportA(const BED &a) {
if (bedA->bedType == 3) {
@@ -39,11 +63,15 @@ void BedIntersect::reportA(const BED &a) {
cout << a.chrom << "\t" << a.start << "\t" << a.end << "\t"
<< a.name << "\t" << a.score << "\t" << a.strand;
}
-
}
-
+/*
+ reportAIntersect
+
+ Writes the base-pair _overlap_ for a BED entry in A.
+ Works for BED3 - BED6.
+*/
void BedIntersect::reportAIntersect(const BED &a, int &start, int &end) {
if (bedA->bedType == 3) {
@@ -64,6 +92,14 @@ void BedIntersect::reportAIntersect(const BED &a, int &start, int &end) {
}
+
+
+/*
+ reportB
+
+ Writes the _original_ BED entry for B.
+ Works for BED3 - BED6.
+*/
void BedIntersect::reportB(const BED &b) {
if (bedB->bedType == 3) {
cout << b.chrom << "\t" << b.start << "\t" << b.end;
diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp
index 499db702..76906f48 100755
--- a/src/mergeBed/mergeBed.cpp
+++ b/src/mergeBed/mergeBed.cpp
@@ -98,12 +98,21 @@ void BedMerge::MergeBed() {
// clean up based on the last entry for the current chromosome
if (OIP) {
- cout << bedList[i-1].chrom << "\t" << minStart << "\t" << maxEnd << endl;
+ if (this->numEntries) {
+ cout << bedList[i-1].chrom << "\t" << minStart << "\t" << maxEnd << "\t" << mergeCount << endl;
+ }
+ else {
+ cout << bedList[i-1].chrom << "\t" << minStart << "\t" << maxEnd << endl;
+ }
}
else {
- cout << m->first << "\t" << bedList[i-1].chrom << "\t" << bedList[i-1].start << "\t" << bedList[i-1].end << endl;
+ if (this->numEntries) {
+ cout << bedList[i-1].chrom << "\t" << bedList[i-1].start << "\t" << bedList[i-1].end << "\t" << mergeCount << endl;
+ }
+ else {
+ cout << bedList[i-1].chrom << "\t" << bedList[i-1].start << "\t" << bedList[i-1].end << endl;
+ }
}
-
}
}
--
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