Mostly cosmetic fixes. A few tweaks to subtool options/settings naming or default...

diff --git a/BamMultiReader.cpp b/BamMultiReader.cpp
index 001df075d17fd553e220cc4489a8f3a3fddef25f..005b0b0adc7c6c22c12f4317791785803a974bd6 100644 (file)
--- a/BamMultiReader.cpp
+++ b/BamMultiReader.cpp
@@ -286,7 +286,7 @@ bool BamMultiReader::Rewind(void) {
     return result;
 }
 
-// saves index data to BAM index files (".bai") where necessary, returns success/fail
+// saves index data to BAM index files (".bai"/".bti") where necessary, returns success/fail
 bool BamMultiReader::CreateIndexes(bool useDefaultIndex) {
     bool result = true;
     for (vector<pair<BamReader*, BamAlignment*> >::iterator it = readers.begin(); it != readers.end(); ++it) {

diff --git a/bamtools_convert.cpp b/bamtools_convert.cpp
index de9cc369bab9c32762c8fb2f9e5d1457326970db..ddb338910f535532c319b4159f75932147c67c03 100644 (file)
--- a/bamtools_convert.cpp
+++ b/bamtools_convert.cpp
@@ -76,8 +76,8 @@ struct ConvertTool::ConvertToolPrivate {
 struct ConvertTool::ConvertSettings {
 
     // flags
-    bool HasInputFilenames;
-    bool HasOutputFilename;
+    bool HasInput;
+    bool HasOutput;
     bool HasFormat;
     bool HasRegion;
 
@@ -97,8 +97,8 @@ struct ConvertTool::ConvertSettings {
 
     // constructor
     ConvertSettings(void)
-        : HasInputFilenames(false)
-        , HasOutputFilename(false)
+        : HasInput(false)
+        , HasOutput(false)
         , HasFormat(false)
         , HasRegion(false)
         , HasFastaFilename(false)
@@ -117,12 +117,12 @@ ConvertTool::ConvertTool(void)
     , m_impl(0)
 {
     // set program details
-    Options::SetProgramInfo("bamtools convert", "converts between BAM and a number of other formats", "-in <filename> -out <filename> -format <FORMAT>");
+    Options::SetProgramInfo("bamtools convert", "converts BAM to a number of other formats", "-format <FORMAT> [-in <filename> -in <filename> ...] [-out <filename>] [other options]");
     
     // set up options 
     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
-    Options::AddValueOption("-in",     "BAM filename", "the input BAM file(s)", "", m_settings->HasInputFilenames,  m_settings->InputFiles,     IO_Opts, Options::StandardIn());
-    Options::AddValueOption("-out",    "BAM filename", "the output BAM file",   "", m_settings->HasOutputFilename,  m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+    Options::AddValueOption("-in",     "BAM filename", "the input BAM file(s)", "", m_settings->HasInput,   m_settings->InputFiles,     IO_Opts, Options::StandardIn());
+    Options::AddValueOption("-out",    "BAM filename", "the output BAM file",   "", m_settings->HasOutput,  m_settings->OutputFilename, IO_Opts, Options::StandardOut());
     Options::AddValueOption("-format", "FORMAT", "the output file format - see README for recognized formats", "", m_settings->HasFormat, m_settings->Format, IO_Opts);
    
     OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
@@ -181,7 +181,7 @@ bool ConvertTool::ConvertToolPrivate::Run(void) {
     // initialize conversion input/output
         
     // set to default input if none provided
-    if ( !m_settings->HasInputFilenames ) 
+    if ( !m_settings->HasInput ) 
         m_settings->InputFiles.push_back(Options::StandardIn());
     
     // open input files
@@ -200,7 +200,7 @@ bool ConvertTool::ConvertToolPrivate::Run(void) {
         
     // if output file given
     ofstream outFile;
-    if ( m_settings->HasOutputFilename ) {
+    if ( m_settings->HasOutput ) {
       
         // open output file stream
         outFile.open(m_settings->OutputFilename.c_str());
@@ -274,7 +274,7 @@ bool ConvertTool::ConvertToolPrivate::Run(void) {
     // ------------------------
     // clean up & exit
     reader.Close();
-    if ( m_settings->HasOutputFilename ) outFile.close();
+    if ( m_settings->HasOutput ) outFile.close();
     return convertedOk;   
 }
 

diff --git a/bamtools_count.cpp b/bamtools_count.cpp
index 187dc9377f35e0442906e87c0835ae6bdc8c7db5..4bd7c82bad7d1bcd8b98151e0b6d85b1b9b99951 100644 (file)
--- a/bamtools_count.cpp
+++ b/bamtools_count.cpp
@@ -57,7 +57,6 @@ CountTool::CountTool(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::AddValueOption("-in",  "BAM filename", "the input BAM file(s)", "", m_settings->HasInput,  m_settings->InputFiles, IO_Opts);
     //Options::AddValueOption("-index", "BAM index filename", "the BAM index file",  "", m_settings->HasBamIndexFilename, m_settings->BamIndexFilename, IO_Opts);
     
@@ -80,6 +79,9 @@ int CountTool::Run(int argc, char* argv[]) {
     // parse command line arguments
     Options::Parse(argc, argv, 1);
 
+    if ( !m_settings->HasInput ) 
+        m_settings->InputFiles.push_back(Options::StandardIn());
+    
     BamMultiReader reader;
     reader.Open(m_settings->InputFiles, false, true);
 

diff --git a/bamtools_header.cpp b/bamtools_header.cpp
index 8fbb70e9b6c08835960a841026103ea11b9e8501..b75f9a0e558b192cdac42350552881158efdc3c9 100644 (file)
--- a/bamtools_header.cpp
+++ b/bamtools_header.cpp
@@ -74,11 +74,11 @@ int HeaderTool::Run(int argc, char* argv[]) {
     
     // open files
     BamMultiReader reader;
-    reader.Open(m_settings->InputFiles, false);
+    if ( reader.Open(m_settings->InputFiles, false) ) {      
+        // dump header contents to stdout
+        cout << reader.GetHeaderText() << endl;
+    }
         
-    // dump header contents to stdout
-    cout << reader.GetHeaderText() << endl;
-    
     // clean up & exit
     reader.Close();
     return 0;

diff --git a/bamtools_options.h b/bamtools_options.h
index 1a58f1080321be0c23380de1ebfef34cadec8084..54c476422accd6221e12127a5138e47b902f26eb 100644 (file)
--- a/bamtools_options.h
+++ b/bamtools_options.h
@@ -32,7 +32,7 @@
 namespace BamTools {
 
 #define ARGUMENT_LENGTH       35
-#define DESC_LENGTH_FIRST_ROW 42
+#define DESC_LENGTH_FIRST_ROW 50
 #define DESC_LENGTH           39
 #define MAX_LINE_LENGTH       78
 

diff --git a/bamtools_sort.cpp b/bamtools_sort.cpp
index b18cf58a711cc5aac98e40bc010603ff4dbc2671..83584a6c8bd9b258bca86a6b4094b2761ceddc82 100644 (file)
--- a/bamtools_sort.cpp
+++ b/bamtools_sort.cpp
@@ -70,6 +70,7 @@ class SortTool::SortToolPrivate {
         
     // internal methods
     private:
+        void ClearBuffer(vector<BamAlignment>& buffer);
         bool GenerateSortedRuns(void);
         bool HandleBufferContents(vector<BamAlignment>& buffer);
         bool MergeSortedRuns(void);
@@ -208,7 +209,7 @@ bool SortTool::SortToolPrivate::GenerateSortedRuns(void) {
     
     // while data available
     BamAlignment al;
-    while ( inputReader.GetNextAlignmentCore(al) ) {
+    while ( inputReader.GetNextAlignmentCore(al)) {
         
         // store alignments in buffer
         buffer.push_back(al);
@@ -262,7 +263,7 @@ bool SortTool::SortToolPrivate::MergeSortedRuns(void) {
     
     // while data available in temp files
     BamAlignment al;
-    while ( multiReader.GetNextAlignment(al) ) {
+    while ( multiReader.GetNextAlignmentCore(al) ) {
         mergedWriter.SaveAlignment(al);
     }
   

diff --git a/bamtools_stats.cpp b/bamtools_stats.cpp
index 5ab818f9142263035a331901585d291da074b58b..68ca6d3e185a29ce1e95d08caa5943a1cf6155db 100644 (file)
--- a/bamtools_stats.cpp
+++ b/bamtools_stats.cpp
@@ -150,7 +150,6 @@ void StatsTool::StatsToolPrivate::PrintStats(void) {
         cout << "Singletons:        " << numSingletons << "\t(" << ((float)numSingletons/numPaired)*100 << "%)" << endl;
     }
     
-    
     if ( settings->IsShowingInsertSizeSummary ) {
       
         double avgInsertSize = 0.0;