From 1d53497e79e3c89b782d3e3ab99723911fdc0146 Mon Sep 17 00:00:00 2001 From: Derek Barnett Date: Wed, 24 Jul 2013 15:02:33 -0400 Subject: [PATCH] Added new '-seed' parameter to 'bamtools random' tool. (issue #73) --- src/api/internal/utils/CMakeLists.txt | 2 +- src/toolkit/bamtools_random.cpp | 24 +++++++++++++++++------- 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/src/api/internal/utils/CMakeLists.txt b/src/api/internal/utils/CMakeLists.txt index d58f95c..4b1e2c2 100644 --- a/src/api/internal/utils/CMakeLists.txt +++ b/src/api/internal/utils/CMakeLists.txt @@ -7,7 +7,7 @@ set( InternalUtilsDir "${InternalDir}/utils" ) -se( InternalUtilsSources +set( InternalUtilsSources ${InternalUtilsDir}/BamException_p.cpp PARENT_SCOPE # <-- leave this last diff --git a/src/toolkit/bamtools_random.cpp b/src/toolkit/bamtools_random.cpp index 5282f15..367ac58 100644 --- a/src/toolkit/bamtools_random.cpp +++ b/src/toolkit/bamtools_random.cpp @@ -2,7 +2,7 @@ // bamtools_random.cpp (c) 2010 Derek Barnett, Erik Garrison // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 10 December 2012 (DB) +// Last modified: 24 July 2013 (DB) // --------------------------------------------------------------------------- // Grab a random subset of alignments (testing tool) // *************************************************************************** @@ -46,6 +46,7 @@ struct RandomTool::RandomSettings { bool HasInput; bool HasInputFilelist; bool HasOutput; + bool HasRandomNumberSeed; bool HasRegion; bool IsForceCompression; @@ -54,6 +55,7 @@ struct RandomTool::RandomSettings { vector InputFiles; string InputFilelist; string OutputFilename; + unsigned int RandomNumberSeed; string Region; // constructor @@ -62,10 +64,12 @@ struct RandomTool::RandomSettings { , HasInput(false) , HasInputFilelist(false) , HasOutput(false) + , HasRandomNumberSeed(false) , HasRegion(false) , IsForceCompression(false) , AlignmentCount(RANDOM_MAX_ALIGNMENT_COUNT) , OutputFilename(Options::StandardOut()) + , RandomNumberSeed(0) { } }; @@ -165,7 +169,10 @@ bool RandomTool::RandomToolPrivate::Run(void) { } // seed our random number generator - srand( time(NULL) ); + if ( m_settings->HasRandomNumberSeed ) + srand( m_settings->RandomNumberSeed ); + else + srand( time(NULL) ); // grab random alignments BamAlignment al; @@ -235,14 +242,17 @@ RandomTool::RandomTool(void) // set up options OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output"); - Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn()); - Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts); - Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut()); + Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn()); + Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts); + Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut()); + Options::AddValueOption("-region", "REGION", "only pull random alignments from within this genomic region. Index file is recommended for better performance, and is used automatically if it exists. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, IO_Opts); Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts); - Options::AddValueOption("-region", "REGION", "only pull random alignments from within this genomic region. Index file is recommended for better performance, and is used automatically if it exists. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, IO_Opts); OptionGroup* SettingsOpts = Options::CreateOptionGroup("Settings"); - Options::AddValueOption("-n", "count", "number of alignments to grab. Note - no duplicate checking is performed", "", m_settings->HasAlignmentCount, m_settings->AlignmentCount, SettingsOpts, RANDOM_MAX_ALIGNMENT_COUNT); + Options::AddValueOption("-n", "count", "number of alignments to grab. Note - no duplicate checking is performed", "", + m_settings->HasAlignmentCount, m_settings->AlignmentCount, SettingsOpts, RANDOM_MAX_ALIGNMENT_COUNT); + Options::AddValueOption("-seed", "unsigned integer", "random number generator seed (for repeatable results). Current time is used if no seed value is provided.", "", + m_settings->HasRandomNumberSeed, m_settings->RandomNumberSeed, SettingsOpts); } RandomTool::~RandomTool(void) { -- 2.39.2