From 8a63b8d731ec9252f896bf167cdf1dba174decd5 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 13 Sep 2011 18:57:49 -0400
Subject: [PATCH] Changed error message when BAM is not qeury sorted in
pairToBed
---
src/pairToBed/pairToBed.cpp | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp
index 5640791d..4e534948 100644
--- a/src/pairToBed/pairToBed.cpp
+++ b/src/pairToBed/pairToBed.cpp
@@ -32,6 +32,7 @@ bool IsCorrectMappingForBEDPE (const BamAlignment &bam) {
Constructor
*/
+
BedIntersectPE::BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
string searchType, bool sameStrand, bool diffStrand, bool bamInput,
bool bamOutput, bool uncompressedBam, bool useEditDistance) {
@@ -419,7 +420,7 @@ void BedIntersectPE::IntersectBamPE(string bamFile) {
ProcessBamBlock(bam1, bam2, refs, writer);
}
else {
- cerr << "*****ERROR: -bedpe requires BAM to be sorted or grouped by query name. " << endl;
+ cerr << "*****ERROR: BAM must be sorted by query name. " << endl;
exit(1);
}
}
--
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