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 a2f975f9659032bed75b5cb280b12a97e97b94df..482fc263a9de4b57edf2d054284341e2b31e0dfd 100644 (file)
--- a/BamReader.cpp
+++ b/BamReader.cpp
@@ -71,7 +71,7 @@ struct BamReader::BamReaderPrivate {
     // "public" interface\r
     // -------------------------------\r
 \r
-    // flie operations\r
+    // file operations\r
     void Close(void);\r
     bool Jump(int refID, int position = 0);\r
     void Open(const string& filename, const string& indexFilename = "");\r
@@ -154,6 +154,7 @@ const string BamReader::GetHeaderText(void) const { return d->HeaderText; }
 int BamReader::GetReferenceCount(void) const { return d->References.size(); }\r
 const RefVector BamReader::GetReferenceData(void) const { return d->References; }\r
 int BamReader::GetReferenceID(const string& refName) const { return d->GetReferenceID(refName); }\r
+const std::string BamReader::GetFilename(void) const { return d->Filename; }
 \r
 // index operations\r
 bool BamReader::CreateIndex(void) { return d->CreateIndex(); }\r

diff --git a/BamReader.h b/BamReader.h
index 8047d7a774e1c516c06d4292784a4adc3805de78..fe28abcc6e07c1799052fec014d00df126132295 100644 (file)
--- a/BamReader.h
+++ b/BamReader.h
@@ -64,6 +64,8 @@ class BamReader {
         const BamTools::RefVector GetReferenceData(void) const;\r
         // returns reference id (used for BamReader::Jump()) for the given reference name\r
         int GetReferenceID(const std::string& refName) const;\r
+        // returns the name of the file associated with this BamReader\r
+        const std::string GetFilename(void) const;\r
 \r
         // ----------------------\r
         // BAM index operations\r

diff --git a/Makefile b/Makefile
index 9c77fb72eaa39dffff33ba416b097ad9eef73ccf..7abd53b5d31e9c8f14472924b8717f3ea4c710b4 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 CXX=           g++\r
 CXXFLAGS=      -Wall -O3\r
-PROG=          BamConversion BamDump BamTrim\r
+PROG=          BamConversion BamDump BamTrim BamMultiMerge\r
 LIBS=          -lz\r
 \r
 all: $(PROG)\r
@@ -14,5 +14,8 @@ BamDump:  BGZF.o BamReader.o BamDumpMain.o
 BamTrim:  BGZF.o BamReader.o BamWriter.o BamTrimMain.o\r
        $(CXX) $(CXXFLAGS) -o $@  BGZF.o BamReader.o BamWriter.o BamTrimMain.o $(LIBS)\r
 \r
+BamMultiMerge: BGZF.o BamMultiReader.o BamReader.o BamWriter.o BamMultiMergeMain.o\r
+       $(CXX) $(CXXFLAGS) -o $@ BGZF.o BamMultiReader.o BamReader.o BamWriter.o BamMultiMergeMain.o $(LIBS)\r
+\r
 clean:\r
        rm -fr gmon.out *.o *.a a.out *~\r