X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Ftoolkit%2Fbamtools_index.cpp;h=6e5a86df6b65329e47283a754835d4de55544a30;hb=8c80d760637f8df39262683cd2570f0589423d36;hp=b1e4bc3e00eaf6fd359b35fc081d6147b4ecb0ae;hpb=90bb3691f9aa2a2e8a4dd906c2439c7bc434eb78;p=bamtools.git

diff --git a/src/toolkit/bamtools_index.cpp b/src/toolkit/bamtools_index.cpp
index b1e4bc3..6e5a86d 100644
--- a/src/toolkit/bamtools_index.cpp
+++ b/src/toolkit/bamtools_index.cpp
@@ -3,21 +3,21 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 2 September 2010
+// Last modified: 21 March 2011
 // ---------------------------------------------------------------------------
-// Creates a BAM index (".bai") file for the provided BAM file.
+// Creates a BAM index file.
 // ***************************************************************************
 
-#include <iostream>
-#include <string>
-
 #include "bamtools_index.h"
-#include "bamtools_options.h"
-#include "BamReader.h"
 
-using namespace std;
+#include <api/BamReader.h>
+#include <utils/bamtools_options.h>
 using namespace BamTools;
 
+#include <iostream>
+#include <string>
+using namespace std;
+
 // ---------------------------------------------
 // IndexSettings implementation
 
@@ -51,7 +51,7 @@ IndexTool::IndexTool(void)
     // set up options 
     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
     Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
-    Options::AddOption("-bti", "create (non-standard) BamTools index file", m_settings->IsUsingBamtoolsIndex, IO_Opts);
+    Options::AddOption("-bti", "create (non-standard) BamTools index file (*.bti). Default behavior is to create standard BAM index (*.bai)", m_settings->IsUsingBamtoolsIndex, IO_Opts);
 }
 
 IndexTool::~IndexTool(void) {
@@ -71,11 +71,15 @@ int IndexTool::Run(int argc, char* argv[]) {
     
     // open our BAM reader
     BamReader reader;
-    reader.Open(m_settings->InputBamFilename);
+    if ( !reader.Open(m_settings->InputBamFilename) ) {
+        cerr << "bamtools index ERROR: could not open BAM file: " << m_settings->InputBamFilename << endl;
+        return 1;
+    }
     
     // create index for BAM file
-    bool useDefaultIndex = !m_settings->IsUsingBamtoolsIndex;
-    reader.CreateIndex(useDefaultIndex);
+    const BamIndex::IndexType type = ( m_settings->IsUsingBamtoolsIndex ? BamIndex::BAMTOOLS
+                                                                        : BamIndex::STANDARD );
+    reader.CreateIndex(type);
     
     // clean & exit
     reader.Close();