From 743f05bd43459040c4a8f97a1bce38c74c85af8e Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 22 Jun 2011 09:49:09 -0400
Subject: [PATCH] Tweaked Makefile and using GetNextAlignment() in multiBamCov.
---
Makefile | 1 +
genomes/mouse.mm9.genome | 2 +-
src/multiBamCov/multiBamCov.cpp | 2 +-
3 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/Makefile b/Makefile
index 4abfdd2a..b12bb7df 100644
--- a/Makefile
+++ b/Makefile
@@ -77,5 +77,6 @@ all:
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+ @rm -Rf $(BT_ROOT)/lib
.PHONY: clean
diff --git a/genomes/mouse.mm9.genome b/genomes/mouse.mm9.genome
index 84c1e724..9c0955da 100755
--- a/genomes/mouse.mm9.genome
+++ b/genomes/mouse.mm9.genome
@@ -7,7 +7,7 @@ chr6 149517037
chr7 152524553
chr8 131738871
chr9 124076172
-chr10 129993255
+chr10 129993255
chr11 121843856
chr12 121257530
chr13 120284312
diff --git a/src/multiBamCov/multiBamCov.cpp b/src/multiBamCov/multiBamCov.cpp
index 3d53c8ef..e19b3c9f 100644
--- a/src/multiBamCov/multiBamCov.cpp
+++ b/src/multiBamCov/multiBamCov.cpp
@@ -70,7 +70,7 @@ void MultiCovBam::CollectCoverage()
// everything checks out, just iterate through specified region, counting alignments
vector<int> counts(_bam_files.size());
BamAlignment al;
- while ( reader.GetNextAlignmentCore(al) )
+ while ( reader.GetNextAlignment(al) )
{
// lookup the offset of the file name and tabulate coverage
// for the appropriate file
--
GitLab