From e88f6c388d1b9e67804f998b1423ab9fae6fbdb0 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Fri, 12 Mar 2010 10:34:46 -0500
Subject: [PATCH] Fixed yet another bug in the -nms option in mergeBed.
Now using a map to track the unique names of the features in a merged block.
The consequence is that names will not be reported in the order they were added.
---
src/mergeBed/mergeBed.cpp | 74 ++++++++++++++++++++-------------------
src/mergeBed/mergeBed.h | 2 ++
2 files changed, 40 insertions(+), 36 deletions(-)
diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp
index e1ca8e99..b577e466 100755
--- a/src/mergeBed/mergeBed.cpp
+++ b/src/mergeBed/mergeBed.cpp
@@ -12,6 +12,18 @@
#include "lineFileUtilities.h"
#include "mergeBed.h"
+
+void ReportMergedNames(const map<string, bool> &names) {
+ unsigned int n = 0;
+ map<string, bool>::const_iterator nameItr = names.begin();
+ map<string, bool>::const_iterator nameEnd = names.end();
+ for (; nameItr != nameEnd; ++nameItr) {
+ if (n < (names.size() - 1)) {cout << nameItr->first << ";";}
+ else {cout << nameItr->first;}
+ n++;
+ }
+}
+
// ===============
// = Constructor =
// ===============
@@ -52,37 +64,40 @@ void BedMerge::MergeBed() {
int minStart = INT_MAX;
int maxEnd = 0;
bool OIP = false; // OIP = Overlap In Progress. Lame, I realize.
- unsigned int prev = 0;
+ int prev = -1;
unsigned int curr = 0;
int mergeCount = 1;
- vector<string> names;
+ map<string, bool> names;
// loop through the BED entries for this chromosome
// and look for overlaps
- for (curr = 1; curr < bedList.size(); ++curr) {
+ for (curr = 0; curr < bedList.size(); ++curr) {
+ // make sure prev points to an actual element
+ if (prev < 0) {
+ prev = curr;
+ continue;
+ }
+
// Is there an overlap between the current and previous entries?
if ( overlaps(bedList[prev].start, bedList[prev].end,
bedList[curr].start, bedList[curr].end) >= this->maxDistance) {
-
OIP = true;
mergeCount++;
minStart = min(bedList[prev].start, min(minStart, bedList[curr].start));
maxEnd = max(bedList[prev].end, max(maxEnd, bedList[curr].end));
-
- //names.push_back(bedList[prev].name);
- names.push_back(bedList[curr].name);
+
+ names[bedList[prev].name] = true;
+ names[bedList[curr].name] = true;
}
else if ( overlaps(minStart, maxEnd,
bedList[curr].start, bedList[curr].end) >= this->maxDistance) {
mergeCount++;
minStart = min(minStart, bedList[curr].start);
maxEnd = max(maxEnd, bedList[curr].end);
-
- names.push_back(bedList[curr].name);
+ names[bedList[curr].name] = true;
}
else {
-
// was there an overlap befor the current entry broke it?
if (OIP) {
if (this->numEntries) {
@@ -90,10 +105,7 @@ void BedMerge::MergeBed() {
}
else if (this->reportNames) {
cout << bedList[prev].chrom << "\t" << minStart << "\t" << maxEnd << "\t";
- for (unsigned int n = 0; n < names.size(); ++n) {
- if (n < (names.size() - 1)) {cout << names[n] << ";";}
- else {cout << names[n];}
- }
+ ReportMergedNames(names);
cout << endl;
}
else {
@@ -117,8 +129,9 @@ void BedMerge::MergeBed() {
mergeCount = 1;
minStart = INT_MAX;
maxEnd = 0;
+
names.clear();
- names.push_back(bedList[prev].name);
+ names[bedList[curr].name] = true;
}
prev = curr;
}
@@ -130,10 +143,7 @@ void BedMerge::MergeBed() {
}
else if (this->reportNames) {
cout << bedList[prev].chrom << "\t" << minStart << "\t" << maxEnd << "\t";
- for (unsigned int n = 0; n < names.size(); ++n) {
- if (n < (names.size() - 1)) {cout << names[n] << ";";}
- else {cout << names[n];}
- }
+ ReportMergedNames(names);
cout << endl;
}
else {
@@ -185,7 +195,7 @@ void BedMerge::MergeBedStranded() {
unsigned int curr = 0;
int mergeCount = 1;
int numOnStrand = 0;
- vector<string> names;
+ map<string, bool> names;
// loop through the BED entries for this chromosome
// and look for overlaps
@@ -211,23 +221,21 @@ void BedMerge::MergeBedStranded() {
}
if ( overlaps(bedList[prev].start, bedList[prev].end,
- bedList[curr].start, bedList[curr].end) >= this->maxDistance) {
-
+ bedList[curr].start, bedList[curr].end) >= this->maxDistance) {
OIP = true;
mergeCount++;
minStart = min(bedList[prev].start, min(minStart, bedList[curr].start));
maxEnd = max(bedList[prev].end, max(maxEnd, bedList[curr].end));
- names.push_back(bedList[curr].name);
+ names[bedList[prev].name] = true;
+ names[bedList[curr].name] = true;
}
else if ( overlaps(minStart, maxEnd,
bedList[curr].start, bedList[curr].end) >= this->maxDistance) {
-
mergeCount++;
minStart = min(minStart, bedList[curr].start);
maxEnd = max(maxEnd, bedList[curr].end);
-
- names.push_back(bedList[curr].name);
+ names[bedList[curr].name] = true;
}
else {
@@ -238,10 +246,7 @@ void BedMerge::MergeBedStranded() {
}
else if (this->reportNames) {
cout << bedList[prev].chrom << "\t" << minStart << "\t" << maxEnd << "\t";
- for (unsigned int n = 0; n < names.size(); ++n) {
- if (n < (names.size() - 1)) {cout << names[n] << ";";}
- else {cout << names[n];}
- }
+ ReportMergedNames(names);
cout << "\t" << strands[s] << endl;
}
else {
@@ -267,8 +272,8 @@ void BedMerge::MergeBedStranded() {
maxEnd = 0;
names.clear();
- // add the name of the
- names.push_back(bedList[curr].name);
+ // add the name of the current element in prep for the next block
+ names[bedList[curr].name] = true;
}
prev = curr;
}
@@ -280,10 +285,7 @@ void BedMerge::MergeBedStranded() {
}
else if (this->reportNames) {
cout << bedList[prev].chrom << "\t" << minStart << "\t" << maxEnd << "\t";
- for (unsigned int n = 0; n < names.size(); ++n) {
- if (n < (names.size() - 1)) {cout << names[n] << ";";}
- else {cout << names[n];}
- }
+ ReportMergedNames(names);
cout << "\t" << strands[s] << endl;
}
else {
diff --git a/src/mergeBed/mergeBed.h b/src/mergeBed/mergeBed.h
index d6330985..336c5d55 100755
--- a/src/mergeBed/mergeBed.h
+++ b/src/mergeBed/mergeBed.h
@@ -19,6 +19,8 @@
using namespace std;
+void ReportMergedNames(const map<string, bool> &names);
+
//************************************************
// Class methods and elements
//************************************************
--
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