From: barnett <barnett@9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu, 6 May 2010 19:30:12 +0000 (+0000)
Subject: Added BamMultiReader and BamMultiMerge
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=68af22063ff54963fd195cab7daf58c4605629e0;p=bamtools.git

Added BamMultiReader and BamMultiMerge

git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@50 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
---

diff --git a/BamReader.cpp b/BamReader.cpp
index a2f975f..482fc26 100644
--- a/BamReader.cpp
+++ b/BamReader.cpp
@@ -71,7 +71,7 @@ struct BamReader::BamReaderPrivate {
     // "public" interface
     // -------------------------------
 
-    // flie operations
+    // file operations
     void Close(void);
     bool Jump(int refID, int position = 0);
     void Open(const string& filename, const string& indexFilename = "");
@@ -154,6 +154,7 @@ const string BamReader::GetHeaderText(void) const { return d->HeaderText; }
 int BamReader::GetReferenceCount(void) const { return d->References.size(); }
 const RefVector BamReader::GetReferenceData(void) const { return d->References; }
 int BamReader::GetReferenceID(const string& refName) const { return d->GetReferenceID(refName); }
+const std::string BamReader::GetFilename(void) const { return d->Filename; }
 
 // index operations
 bool BamReader::CreateIndex(void) { return d->CreateIndex(); }
diff --git a/BamReader.h b/BamReader.h
index 8047d7a..fe28abc 100644
--- a/BamReader.h
+++ b/BamReader.h
@@ -64,6 +64,8 @@ class BamReader {
         const BamTools::RefVector GetReferenceData(void) const;
         // returns reference id (used for BamReader::Jump()) for the given reference name
         int GetReferenceID(const std::string& refName) const;
+        // returns the name of the file associated with this BamReader
+        const std::string GetFilename(void) const;
 
         // ----------------------
         // BAM index operations
diff --git a/Makefile b/Makefile
index 9c77fb7..7abd53b 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 CXX=		g++
 CXXFLAGS=	-Wall -O3
-PROG=		BamConversion BamDump BamTrim
+PROG=		BamConversion BamDump BamTrim BamMultiMerge
 LIBS=		-lz
 
 all: $(PROG)
@@ -14,5 +14,8 @@ BamDump:  BGZF.o BamReader.o BamDumpMain.o
 BamTrim:  BGZF.o BamReader.o BamWriter.o BamTrimMain.o
 	$(CXX) $(CXXFLAGS) -o $@  BGZF.o BamReader.o BamWriter.o BamTrimMain.o $(LIBS)
 
+BamMultiMerge: BGZF.o BamMultiReader.o BamReader.o BamWriter.o BamMultiMergeMain.o
+	$(CXX) $(CXXFLAGS) -o $@ BGZF.o BamMultiReader.o BamReader.o BamWriter.o BamMultiMergeMain.o $(LIBS)
+
 clean:
 	rm -fr gmon.out *.o *.a a.out *~