From 4dbc38cde7fc4421ce61ec8e9af85cba5b6e663b Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 31 Jan 2011 09:54:03 -0500
Subject: [PATCH] MergeBed now correctly handles a max distance "-d" parameter.
I mistakenly omitted this logic from the new algorithm.
---
src/mergeBed/mergeBed.cpp | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp
index 66af69c3..d0cbb7cb 100644
--- a/src/mergeBed/mergeBed.cpp
+++ b/src/mergeBed/mergeBed.cpp
@@ -37,7 +37,7 @@ BedMerge::BedMerge(string &bedFile, bool &numEntries, int &maxDistance, bool &fo
_bedFile = bedFile;
_numEntries = numEntries;
- _maxDistance = -1 * maxDistance;
+ _maxDistance = maxDistance;
_forceStrand = forceStrand;
_reportNames = reportNames;
@@ -123,7 +123,8 @@ void BedMerge::MergeBed() {
vector<BED>::const_iterator bedItr = bedList.begin();
vector<BED>::const_iterator bedEnd = bedList.end();
for (; bedItr != bedEnd; ++bedItr) {
- if ((int) bedItr->start > end) {
+ // new block, no overlap
+ if ( (((int) bedItr->start - end) > _maxDistance) || (end < 0)) {
if (start >= 0) {
Report(chrom, start, end, names, mergeCount);
// reset
@@ -134,8 +135,9 @@ void BedMerge::MergeBed() {
end = bedItr->end;
names[bedItr->name] = true;
}
+ // same block, overlaps
else {
- end = bedItr->end;
+ if ((int) bedItr-> end > end) end = bedItr->end;
mergeCount++;
names[bedItr->name] = true;
}
@@ -189,7 +191,7 @@ void BedMerge::MergeBedStranded() {
if (bedItr->strand != strands[s]) { continue; }
else { numOnStrand++; }
- if ((int) bedItr->start > end) {
+ if ( (((int) bedItr->start - end) > _maxDistance) || (end < 0)) {
if (start >= 0) {
ReportStranded(chrom, start, end, names, mergeCount, strands[s]);
// reset
@@ -201,7 +203,7 @@ void BedMerge::MergeBedStranded() {
names[bedItr->name] = true;
}
else {
- end = bedItr->end;
+ if ((int) bedItr-> end > end) end = bedItr->end;
mergeCount++;
names[bedItr->name] = true;
}
--
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