From ab7bbbe407eed1a33f44e20778babfc4f71a61ac Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Sat, 24 Aug 2013 22:30:58 -0400
Subject: [PATCH] [BUG] -split, -tag and BED6 output was not implemented.
---
src/bamToBed/bamToBed.cpp | 27 ++++++++++++++++++++-------
1 file changed, 20 insertions(+), 7 deletions(-)
diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp
index 432a0f63..c89441a0 100644
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -479,13 +479,26 @@ void PrintBed(const BamAlignment &bam, const RefVector &refs,
unsigned int i;
for (i = 0; i < bedBlocks.size(); ++i) {
BED curr = bedBlocks[i];
- printf("%s\t%d\t%d\t\%s\t%d\t%s\n",
- chrom.c_str(),
- curr.start,
- curr.end,
- name.c_str(),
- bam.MapQuality,
- strand.c_str());
+
+ if (bamTag == "") {
+ printf("%s\t%d\t%d\t\%s\t%d\t%s\n",
+ chrom.c_str(),
+ curr.start,
+ curr.end,
+ name.c_str(),
+ bam.MapQuality,
+ strand.c_str());
+ }
+ else {
+ cout << chrom << "\t"
+ << bam.Position << "\t"
+ << curr.start << "\t"
+ << curr.end << "\t"
+ << name << "\t"
+ << PrintTag(bam, bamTag) << "\t"
+ << strand
+ << endl;
+ }
}
}
}
--
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