From f23fb452076cda53e78d64f63d16ba5245d66d9b Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 5 May 2010 12:48:36 -0400
Subject: [PATCH] Fixed bug in sortBed that caused the output to be written
twice.
---
src/sortBed/sortBed.cpp | 2 --
src/utils/bedFile/bedFile.cpp | 6 ++++++
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/src/sortBed/sortBed.cpp b/src/sortBed/sortBed.cpp
index dc79612d..9b0990f5 100755
--- a/src/sortBed/sortBed.cpp
+++ b/src/sortBed/sortBed.cpp
@@ -18,8 +18,6 @@
BedSort::BedSort(string &bedFile) {
_bedFile = bedFile;
_bed = new BedFile(bedFile);
-
- SortBed();
}
//
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index e8e8bf45..38e2ce9d 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -702,6 +702,12 @@ void BedFile::loadBedFileIntoMapNoBin() {
bedStatus = this->GetNextBed(bedEntry, lineNum);
}
Close();
+
+ // sort the BED entries for each chromosome
+ // in ascending order of start position
+ for (masterBedMapNoBin::iterator m = this->bedMapNoBin.begin(); m != this->bedMapNoBin.end(); ++m) {
+ sort(m->second.begin(), m->second.end(), sortByStart);
+ }
}
--
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