From f2209cfc537b21e36eede33247c293cfb16dc3ad Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 22 Mar 2011 08:50:26 -0400
Subject: [PATCH] Unmapped BAM alignments are now captured by -v in
intersectBed and windowBed. Thanks to Davide Cittaro.
---
src/intersectBed/intersectBed.cpp | 8 ++++++++
src/windowBed/windowBed.cpp | 4 ++++
2 files changed, 12 insertions(+)
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index d6ec2c28..53222ebc 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -278,6 +278,10 @@ void BedIntersect::IntersectBam(string bamFile) {
bool overlapsFound = false;
// treat the BAM alignment as a single "block"
if (_obeySplits == false) {
+ // Toying with adding tags. Need new version of FindOverlaps.
+ // FindOverlaps(a, hits);
+ // bam.AddTag("YB", "i", static_cast<int>(hits.size()));
+ // hits.clear();
overlapsFound = FindOneOrMoreOverlap(a);
}
// split the BAM alignment into discrete blocks and
@@ -327,6 +331,10 @@ void BedIntersect::IntersectBam(string bamFile) {
}
}
}
+ // BAM IsMapped() is false
+ else if (_noHit == true) {
+ writer.SaveAlignment(bam);
+ }
}
// close the relevant BAM files.
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index 6b033612..b961f02c 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -204,6 +204,10 @@ void BedWindow::WindowIntersectBam(string bamFile) {
hits.clear();
}
}
+ // BAM IsMapped() is false
+ else if (_noHit == true) {
+ writer.SaveAlignment(bam);
+ }
}
// close the relevant BAM files.
--
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