From: Derek Date: Fri, 23 Jul 2010 03:09:58 +0000 (-0400) Subject: Mostly cosmetic fixes. A few tweaks to subtool options/settings naming or default... X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=113d4fe3564c2001d0a11b7f7e7bccbfd70cbb79;p=bamtools.git Mostly cosmetic fixes. A few tweaks to subtool options/settings naming or default handling as well. --- diff --git a/BamMultiReader.cpp b/BamMultiReader.cpp index 001df07..005b0b0 100644 --- 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 >::iterator it = readers.begin(); it != readers.end(); ++it) { diff --git a/bamtools_convert.cpp b/bamtools_convert.cpp index de9cc36..ddb3389 100644 --- 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 -out -format "); + Options::SetProgramInfo("bamtools convert", "converts BAM to a number of other formats", "-format [-in -in ...] [-out ] [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 187dc93..4bd7c82 100644 --- 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 8fbb70e..b75f9a0 100644 --- 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 1a58f10..54c4764 100644 --- 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 b18cf58..83584a6 100644 --- a/bamtools_sort.cpp +++ b/bamtools_sort.cpp @@ -70,6 +70,7 @@ class SortTool::SortToolPrivate { // internal methods private: + void ClearBuffer(vector& buffer); bool GenerateSortedRuns(void); bool HandleBufferContents(vector& 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 5ab818f..68ca6d3 100644 --- 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;