// ***************************************************************************
// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 March 2011
+// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
-// Filters BAM file(s) according to some user-specified criteria.
+// Filters BAM file(s) according to some user-specified criteria
// ***************************************************************************
#include "bamtools_filter.h"
const string ISPROPERPAIR_PROPERTY = "isProperPair";
const string ISREVERSESTRAND_PROPERTY = "isReverseStrand";
const string ISSECONDMATE_PROPERTY = "isSecondMate";
+const string ISSINGLETON_PROPERTY = "isSingleton";
const string MAPQUALITY_PROPERTY = "mapQuality";
const string MATEPOSITION_PROPERTY = "matePosition";
const string MATEREFERENCE_PROPERTY = "mateReference";
else if ( propertyName == ISPROPERPAIR_PROPERTY ) keepAlignment &= valueFilter.check(al.IsProperPair());
else if ( propertyName == ISREVERSESTRAND_PROPERTY ) keepAlignment &= valueFilter.check(al.IsReverseStrand());
else if ( propertyName == ISSECONDMATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsSecondMate());
+ else if ( propertyName == ISSINGLETON_PROPERTY ) {
+ const bool isSingleton = al.IsPaired() && al.IsMapped() && !al.IsMateMapped();
+ keepAlignment &= valueFilter.check(isSingleton);
+ }
else if ( propertyName == MAPQUALITY_PROPERTY ) keepAlignment &= valueFilter.check(al.MapQuality);
else if ( propertyName == MATEPOSITION_PROPERTY ) keepAlignment &= ( al.IsPaired() && al.IsMateMapped() && valueFilter.check(al.MateRefID) );
else if ( propertyName == MATEREFERENCE_PROPERTY ) {
} // namespace BamTools
-// ---------------------------------------------
-// FilterToolPrivate declaration
-
-class FilterTool::FilterToolPrivate {
-
- // ctor & dtor
- public:
- FilterToolPrivate(FilterTool::FilterSettings* settings);
- ~FilterToolPrivate(void);
-
- // 'public' interface
- public:
- bool Run(void);
-
- // internal methods
- private:
- bool AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens);
- bool CheckAlignment(const BamAlignment& al);
- const string GetScriptContents(void);
- void InitProperties(void);
- bool ParseCommandLine(void);
- bool ParseFilterObject(const string& filterName, const Json::Value& filterObject);
- bool ParseScript(void);
- bool SetupFilters(void);
-
- // data members
- private:
- vector<string> m_propertyNames;
- FilterTool::FilterSettings* m_settings;
- FilterEngine<BamAlignmentChecker> m_filterEngine;
-};
-
// ---------------------------------------------
// FilterSettings implementation
// ----------------------------------
// IO opts
-
+
// flags
bool HasInputBamFilename;
bool HasOutputBamFilename;
bool HasRegion;
bool HasScriptFilename;
bool IsForceCompression;
-
+
// filenames
vector<string> InputFiles;
string OutputFilename;
string Region;
string ScriptFilename;
-
+
// -----------------------------------
// General filter opts
-
+
// flags
bool HasAlignmentFlagFilter;
bool HasInsertSizeFilter;
// -----------------------------------
// AlignmentFlag filter opts
-
+
// flags
bool HasIsDuplicateFilter;
bool HasIsFailedQCFilter;
bool HasIsProperPairFilter;
bool HasIsReverseStrandFilter;
bool HasIsSecondMateFilter;
-
+ bool HasIsSingletonFilter;
+
// filters
string IsDuplicateFilter;
string IsFailedQCFilter;
string IsProperPairFilter;
string IsReverseStrandFilter;
string IsSecondMateFilter;
-
+ string IsSingletonFilter;
+
// ---------------------------------
// constructor
-
+
FilterSettings(void)
: HasInputBamFilename(false)
, HasOutputBamFilename(false)
, HasIsProperPairFilter(false)
, HasIsReverseStrandFilter(false)
, HasIsSecondMateFilter(false)
+ , HasIsSingletonFilter(false)
, IsDuplicateFilter(TRUE_STR)
, IsFailedQCFilter(TRUE_STR)
, IsFirstMateFilter(TRUE_STR)
, IsProperPairFilter(TRUE_STR)
, IsReverseStrandFilter(TRUE_STR)
, IsSecondMateFilter(TRUE_STR)
+ , IsSingletonFilter(TRUE_STR)
{ }
-};
+};
// ---------------------------------------------
-// FilterTool implementation
-
-FilterTool::FilterTool(void)
- : AbstractTool()
- , m_settings(new FilterSettings)
- , m_impl(0)
-{
- // set program details
- Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", "[-in <filename> -in <filename> ...] [-out <filename> | [-forceCompression]] [-region <REGION>] [ [-script <filename] | [filterOptions] ]");
-
- OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
- Options::AddValueOption("-region", "REGION", "only read data from this genomic region (see documentation for more details)", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
- Options::AddValueOption("-script", "filename", "the filter script file (see documentation for more details)", "", m_settings->HasScriptFilename, m_settings->ScriptFilename, 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);
-
- OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters");
- Options::AddValueOption("-alignmentFlag", "int", "keep reads with this *exact* alignment flag (for more detailed queries, see below)", "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
- Options::AddValueOption("-insertSize", "int", "keep reads with insert size that mathces pattern", "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts);
- Options::AddValueOption("-mapQuality", "[0-255]", "keep reads with map quality that matches pattern", "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts);
- Options::AddValueOption("-name", "string", "keep reads with name that matches pattern", "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts);
- Options::AddValueOption("-queryBases", "string", "keep reads with motif that mathces pattern", "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts);
- Options::AddValueOption("-tag", "TAG:VALUE", "keep reads with this key=>value pair", "", m_settings->HasTagFilter, m_settings->TagFilter, FilterOpts);
-
- OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters");
- Options::AddValueOption("-isDuplicate", "true/false", "keep only alignments that are marked as duplicate?", "", m_settings->HasIsDuplicateFilter, m_settings->IsDuplicateFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isFailedQC", "true/false", "keep only alignments that failed QC?", "", m_settings->HasIsFailedQCFilter, m_settings->IsFailedQCFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isFirstMate", "true/false", "keep only alignments marked as first mate?", "", m_settings->HasIsFirstMateFilter, m_settings->IsFirstMateFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isMapped", "true/false", "keep only alignments that were mapped?", "", m_settings->HasIsMappedFilter, m_settings->IsMappedFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isMateMapped", "true/false", "keep only alignments with mates that mapped", "", m_settings->HasIsMateMappedFilter, m_settings->IsMateMappedFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isMateReverseStrand", "true/false", "keep only alignments with mate on reverese strand?", "", m_settings->HasIsMateReverseStrandFilter, m_settings->IsMateReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isPaired", "true/false", "keep only alignments that were sequenced as paired?","", m_settings->HasIsPairedFilter, m_settings->IsPairedFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isPrimaryAlignment", "true/false", "keep only alignments marked as primary?", "", m_settings->HasIsPrimaryAlignmentFilter, m_settings->IsPrimaryAlignmentFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isProperPair", "true/false", "keep only alignments that passed PE resolution?", "", m_settings->HasIsProperPairFilter, m_settings->IsProperPairFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isReverseStrand", "true/false", "keep only alignments on reverse strand?", "", m_settings->HasIsReverseStrandFilter, m_settings->IsReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
- Options::AddValueOption("-isSecondMate", "true/false", "keep only alignments marked as second mate?", "", m_settings->HasIsSecondMateFilter, m_settings->IsSecondMateFilter, AlignmentFlagOpts, TRUE_STR);
-}
-
-FilterTool::~FilterTool(void) {
- delete m_settings;
- m_settings = 0;
-
- delete m_impl;
- m_impl = 0;
-}
-
-int FilterTool::Help(void) {
- Options::DisplayHelp();
- return 0;
-}
+// FilterToolPrivate declaration
-int FilterTool::Run(int argc, char* argv[]) {
-
- // parse command line arguments
- Options::Parse(argc, argv, 1);
-
- // run internal FilterTool implementation, return success/fail
- m_impl = new FilterToolPrivate(m_settings);
-
- if ( m_impl->Run() ) return 0;
- else return 1;
-}
+class FilterTool::FilterToolPrivate {
+
+ // ctor & dtor
+ public:
+ FilterToolPrivate(FilterTool::FilterSettings* settings);
+ ~FilterToolPrivate(void);
+
+ // 'public' interface
+ public:
+ bool Run(void);
+
+ // internal methods
+ private:
+ bool AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens);
+ bool CheckAlignment(const BamAlignment& al);
+ const string GetScriptContents(void);
+ void InitProperties(void);
+ bool ParseCommandLine(void);
+ bool ParseFilterObject(const string& filterName, const Json::Value& filterObject);
+ bool ParseScript(void);
+ bool SetupFilters(void);
+
+ // data members
+ private:
+ vector<string> m_propertyNames;
+ FilterTool::FilterSettings* m_settings;
+ FilterEngine<BamAlignmentChecker> m_filterEngine;
+};
// ---------------------------------------------
// FilterToolPrivate implementation
propertyName == ISPRIMARYALIGNMENT_PROPERTY ||
propertyName == ISPROPERPAIR_PROPERTY ||
propertyName == ISREVERSESTRAND_PROPERTY ||
- propertyName == ISSECONDMATE_PROPERTY
+ propertyName == ISSECONDMATE_PROPERTY ||
+ propertyName == ISSINGLETON_PROPERTY
)
{
FilterEngine<BamAlignmentChecker>::parseToken(token, boolValue, type);
// string conversion
else if ( propertyName == CIGAR_PROPERTY ||
- propertyName == MATEREFERENCE_PROPERTY ||
+ propertyName == MATEREFERENCE_PROPERTY ||
propertyName == NAME_PROPERTY ||
propertyName == QUERYBASES_PROPERTY ||
propertyName == REFERENCE_PROPERTY
m_propertyNames.push_back(ISPROPERPAIR_PROPERTY);
m_propertyNames.push_back(ISREVERSESTRAND_PROPERTY);
m_propertyNames.push_back(ISSECONDMATE_PROPERTY);
+ m_propertyNames.push_back(ISSINGLETON_PROPERTY);
m_propertyNames.push_back(MAPQUALITY_PROPERTY);
m_propertyNames.push_back(MATEPOSITION_PROPERTY);
m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
if ( m_settings->HasIsProperPairFilter ) propertyTokens.insert( make_pair(ISPROPERPAIR_PROPERTY, m_settings->IsProperPairFilter) );
if ( m_settings->HasIsReverseStrandFilter ) propertyTokens.insert( make_pair(ISREVERSESTRAND_PROPERTY, m_settings->IsReverseStrandFilter) );
if ( m_settings->HasIsSecondMateFilter ) propertyTokens.insert( make_pair(ISSECONDMATE_PROPERTY, m_settings->IsSecondMateFilter) );
+ if ( m_settings->HasIsSingletonFilter ) propertyTokens.insert( make_pair(ISSINGLETON_PROPERTY, m_settings->IsSingletonFilter) );
if ( m_settings->HasMapQualityFilter ) propertyTokens.insert( make_pair(MAPQUALITY_PROPERTY, m_settings->MapQualityFilter) );
if ( m_settings->HasNameFilter ) propertyTokens.insert( make_pair(NAME_PROPERTY, m_settings->NameFilter) );
if ( m_settings->HasQueryBasesFilter ) propertyTokens.insert( make_pair(QUERYBASES_PROPERTY, m_settings->QueryBasesFilter) );
// otherwise check command line for filters
else return ParseCommandLine();
}
+
+// ---------------------------------------------
+// FilterTool implementation
+
+FilterTool::FilterTool(void)
+ : AbstractTool()
+ , m_settings(new FilterSettings)
+ , m_impl(0)
+{
+ // ----------------------------------
+ // set program details
+
+ const string usage = "[-in <filename> -in <filename> ...] "
+ "[-out <filename> | [-forceCompression]] [-region <REGION>] "
+ "[ [-script <filename] | [filterOptions] ]";
+ Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", usage );
+
+ // ----------------------------------
+ // I/O options
+
+ OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
+
+ const string inDesc = "the input BAM file(s)";
+ const string outDesc = "the output BAM file";
+ const string regionDesc = "only read data from this genomic region (see documentation for more details)";
+ const string scriptDesc = "the filter script file (see documentation for more details)";
+ const string forceDesc = "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";
+
+ Options::AddValueOption("-in", "BAM filename", inDesc, "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-region", "REGION", regionDesc, "", m_settings->HasRegion, m_settings->Region, IO_Opts);
+ Options::AddValueOption("-script", "filename", scriptDesc, "", m_settings->HasScriptFilename, m_settings->ScriptFilename, IO_Opts);
+ Options::AddOption("-forceCompression",forceDesc, m_settings->IsForceCompression, IO_Opts);
+
+ // ----------------------------------
+ // general filter options
+
+ OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters");
+
+ const string flagDesc = "keep reads with this *exact* alignment flag (for more detailed queries, see below)";
+ const string insertDesc = "keep reads with insert size that matches pattern";
+ const string mapQualDesc = "keep reads with map quality that matches pattern";
+ const string nameDesc = "keep reads with name that matches pattern";
+ const string queryDesc = "keep reads with motif that matches pattern";
+ const string tagDesc = "keep reads with this key=>value pair";
+
+ Options::AddValueOption("-alignmentFlag", "int", flagDesc, "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
+ Options::AddValueOption("-insertSize", "int", insertDesc, "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts);
+ Options::AddValueOption("-mapQuality", "[0-255]", mapQualDesc, "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts);
+ Options::AddValueOption("-name", "string", nameDesc, "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts);
+ Options::AddValueOption("-queryBases", "string", queryDesc, "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts);
+ Options::AddValueOption("-tag", "TAG:VALUE", tagDesc, "", m_settings->HasTagFilter, m_settings->TagFilter, FilterOpts);
+
+ // ----------------------------------
+ // alignment flag filter options
+
+ OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters");
+
+ const string boolArg = "true/false";
+ const string isDupDesc = "keep only alignments that are marked as duplicate?";
+ const string isFailQcDesc = "keep only alignments that failed QC?";
+ const string isFirstMateDesc = "keep only alignments marked as first mate?";
+ const string isMappedDesc = "keep only alignments that were mapped?";
+ const string isMateMappedDesc = "keep only alignments with mates that mapped";
+ const string isMateReverseDesc = "keep only alignments with mate on reverese strand?";
+ const string isPairedDesc = "keep only alignments that were sequenced as paired?";
+ const string isPrimaryDesc = "keep only alignments marked as primary?";
+ const string isProperPairDesc = "keep only alignments that passed PE resolution?";
+ const string isReverseDesc = "keep only alignments on reverse strand?";
+ const string isSecondMateDesc = "keep only alignments marked as second mate?";
+ const string isSingletonDesc = "keep only singletons";
+
+ Options::AddValueOption("-isDuplicate", boolArg, isDupDesc, "", m_settings->HasIsDuplicateFilter, m_settings->IsDuplicateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isFailedQC", boolArg, isFailQcDesc, "", m_settings->HasIsFailedQCFilter, m_settings->IsFailedQCFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isFirstMate", boolArg, isFirstMateDesc, "", m_settings->HasIsFirstMateFilter, m_settings->IsFirstMateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMapped", boolArg, isMappedDesc, "", m_settings->HasIsMappedFilter, m_settings->IsMappedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMateMapped", boolArg, isMateMappedDesc, "", m_settings->HasIsMateMappedFilter, m_settings->IsMateMappedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMateReverseStrand", boolArg, isMateReverseDesc, "", m_settings->HasIsMateReverseStrandFilter, m_settings->IsMateReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isPaired", boolArg, isPairedDesc, "", m_settings->HasIsPairedFilter, m_settings->IsPairedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isPrimaryAlignment", boolArg, isPrimaryDesc, "", m_settings->HasIsPrimaryAlignmentFilter, m_settings->IsPrimaryAlignmentFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isProperPair", boolArg, isProperPairDesc, "", m_settings->HasIsProperPairFilter, m_settings->IsProperPairFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isReverseStrand", boolArg, isReverseDesc, "", m_settings->HasIsReverseStrandFilter, m_settings->IsReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isSecondMate", boolArg, isSecondMateDesc, "", m_settings->HasIsSecondMateFilter, m_settings->IsSecondMateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isSingleton", boolArg, isSingletonDesc, "", m_settings->HasIsSingletonFilter, m_settings->IsSingletonFilter, AlignmentFlagOpts, TRUE_STR);
+}
+
+FilterTool::~FilterTool(void) {
+
+ delete m_settings;
+ m_settings = 0;
+
+ delete m_impl;
+ m_impl = 0;
+}
+
+int FilterTool::Help(void) {
+ Options::DisplayHelp();
+ return 0;
+}
+
+int FilterTool::Run(int argc, char* argv[]) {
+
+ // parse command line arguments
+ Options::Parse(argc, argv, 1);
+
+ // initialize FilterTool with settings
+ m_impl = new FilterToolPrivate(m_settings);
+
+ // run FilterTool, return success/fail
+ if ( m_impl->Run() )
+ return 0;
+ else
+ return 1;
+}
projects / bamtools.git / blobdiff