From b3ba4b983e8a63229218786aebd3697eb434d41c Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 8 Dec 2011 12:31:12 -0500
Subject: [PATCH] bamToBed -bedpe now handles singletons.
---
src/bamToBed/bamToBed.cpp | 22 ++++++++++------------
1 file changed, 10 insertions(+), 12 deletions(-)
diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp
index b825c524..4a4c56c6 100644
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -267,20 +267,18 @@ void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance) {
// rip through the BAM file and convert each mapped entry to BEDPE
BamAlignment bam1, bam2;
while (reader.GetNextAlignment(bam1)) {
- // the alignment must be paired
- if (bam1.IsPaired() == true) {
- // grab the second alignment for the pair.
- reader.GetNextAlignment(bam2);
-
- // require that the alignments are from the same query
- if (bam1.Name == bam2.Name) {
- PrintBedPE(bam1, bam2, refs, useEditDistance);
- }
- else {
- cerr << "*****ERROR: -bedpe requires BAM to be sorted/grouped by query name. " << endl;
- exit(1);
+
+ reader.GetNextAlignment(bam2);
+ if (bam1.Name != bam2.Name) {
+ while (bam1.Name != bam2.Name)
+ {
+ bam1 = bam2;
+ reader.GetNextAlignment(bam2);
}
}
+ else if (bam1.IsPaired() == true) {
+ PrintBedPE(bam1, bam2, refs, useEditDistance);
+ }
}
reader.Close();
}
--
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