From 0e2b20aec3269d9a2a95d51c6117d306a1a2c9bf Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 2 Apr 2012 21:04:54 -0400
Subject: [PATCH] fixed logic bug in bedtobam's -bed12 mode.
---
src/bedToBam/bedToBam.cpp | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/bedToBam/bedToBam.cpp b/src/bedToBam/bedToBam.cpp
index d6fc5cde..59406e0b 100644
--- a/src/bedToBam/bedToBam.cpp
+++ b/src/bedToBam/bedToBam.cpp
@@ -247,7 +247,7 @@ void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int, std::le
else{
// does it smell like BED12? if so, process it.
- if (bed.fields.size() == 6) {
+ if (bed.fields.size() == 12) {
// extract the relevant BED fields to convert BED12 to BAM
// namely: blockCount, blockStarts, blockEnds
@@ -344,9 +344,9 @@ int bedtobam_reg2bin(int beg, int end) {
--end;
if (beg>>14 == end>>14) return ((1<<15)-1)/7 + (beg>>14);
if (beg>>17 == end>>17) return ((1<<12)-1)/7 + (beg>>17);
- if (beg>>20 == end>>20) return ((1<<9)-1)/7 + (beg>>20);
- if (beg>>23 == end>>23) return ((1<<6)-1)/7 + (beg>>23);
- if (beg>>26 == end>>26) return ((1<<3)-1)/7 + (beg>>26);
+ if (beg>>20 == end>>20) return ((1<<9)-1)/7 + (beg>>20);
+ if (beg>>23 == end>>23) return ((1<<6)-1)/7 + (beg>>23);
+ if (beg>>26 == end>>26) return ((1<<3)-1)/7 + (beg>>26);
return 0;
}
--
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