// ***************************************************************************
// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 31 August 2010
+// Last modified: 3 May 2013
// ---------------------------------------------------------------------------
-// Filters a single BAM file (or filters multiple BAM files and merges)
-// according to some user-specified criteria.
+// Filters BAM file(s) according to some user-specified criteria
// ***************************************************************************
-// std includes
+#include "bamtools_filter.h"
+
+#include <api/BamMultiReader.h>
+#include <api/BamWriter.h>
+#include <utils/bamtools_filter_engine.h>
+#include <utils/bamtools_options.h>
+#include <utils/bamtools_utilities.h>
+using namespace BamTools;
+
+#include <jsoncpp/json.h>
+using namespace Json;
+
#include <cstdio>
+#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <vector>
-
-// BamTools includes
-#include "bamtools_filter.h"
-#include "bamtools_filter_engine.h"
-#include "bamtools_options.h"
-#include "bamtools_utilities.h"
-#include "BamReader.h"
-#include "BamMultiReader.h"
-#include "BamWriter.h"
-
-//JsonCPP includes
-#include "jsoncpp/json.h"
-
using namespace std;
-using namespace BamTools;
-using namespace Json;
namespace BamTools {
// property names
const string ALIGNMENTFLAG_PROPERTY = "alignmentFlag";
+const string CIGAR_PROPERTY = "cigar";
const string INSERTSIZE_PROPERTY = "insertSize";
const string ISDUPLICATE_PROPERTY = "isDuplicate";
const string ISFAILEDQC_PROPERTY = "isFailedQC";
const string ISPROPERPAIR_PROPERTY = "isProperPair";
const string ISREVERSESTRAND_PROPERTY = "isReverseStrand";
const string ISSECONDMATE_PROPERTY = "isSecondMate";
+const string ISSINGLETON_PROPERTY = "isSingleton";
+const string LENGTH_PROPERTY = "length";
const string MAPQUALITY_PROPERTY = "mapQuality";
const string MATEPOSITION_PROPERTY = "matePosition";
const string MATEREFERENCE_PROPERTY = "mateReference";
const string POSITION_PROPERTY = "position";
const string QUERYBASES_PROPERTY = "queryBases";
const string REFERENCE_PROPERTY = "reference";
+const string TAG_PROPERTY = "tag";
// boolalpha
const string TRUE_STR = "true";
const string FALSE_STR = "false";
-} // namespace BamTools
-
-// ---------------------------------------------
-// FilterToolPrivate declaration
-
-class FilterTool::FilterToolPrivate {
+RefVector filterToolReferences;
+
+struct BamAlignmentChecker {
+ bool check(const PropertyFilter& filter, const BamAlignment& al) {
- // 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;
- RefVector m_references;
-};
+ bool keepAlignment = true;
+ const PropertyMap& properties = filter.Properties;
+ PropertyMap::const_iterator propertyIter = properties.begin();
+ PropertyMap::const_iterator propertyEnd = properties.end();
+ for ( ; propertyIter != propertyEnd; ++propertyIter ) {
+
+ // check alignment data field depending on propertyName
+ const string& propertyName = (*propertyIter).first;
+ const PropertyFilterValue& valueFilter = (*propertyIter).second;
+
+ if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= valueFilter.check(al.AlignmentFlag);
+ else if ( propertyName == CIGAR_PROPERTY ) {
+ stringstream cigarSs;
+ const vector<CigarOp>& cigarData = al.CigarData;
+ if ( !cigarData.empty() ) {
+ vector<CigarOp>::const_iterator cigarBegin = cigarData.begin();
+ vector<CigarOp>::const_iterator cigarIter = cigarBegin;
+ vector<CigarOp>::const_iterator cigarEnd = cigarData.end();
+ for ( ; cigarIter != cigarEnd; ++cigarIter ) {
+ const CigarOp& op = (*cigarIter);
+ cigarSs << op.Length << op.Type;
+ }
+ keepAlignment &= valueFilter.check(cigarSs.str());
+ }
+ }
+ else if ( propertyName == INSERTSIZE_PROPERTY ) keepAlignment &= valueFilter.check(al.InsertSize);
+ else if ( propertyName == ISDUPLICATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsDuplicate());
+ else if ( propertyName == ISFAILEDQC_PROPERTY ) keepAlignment &= valueFilter.check(al.IsFailedQC());
+ else if ( propertyName == ISFIRSTMATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsFirstMate());
+ else if ( propertyName == ISMAPPED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMapped());
+ else if ( propertyName == ISMATEMAPPED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMateMapped());
+ else if ( propertyName == ISMATEREVERSESTRAND_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMateReverseStrand());
+ else if ( propertyName == ISPAIRED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsPaired());
+ else if ( propertyName == ISPRIMARYALIGNMENT_PROPERTY ) keepAlignment &= valueFilter.check(al.IsPrimaryAlignment());
+ 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 == LENGTH_PROPERTY ) keepAlignment &= valueFilter.check(al.Length);
+ 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 ) {
+ if ( !al.IsPaired() || !al.IsMateMapped() ) return false;
+ BAMTOOLS_ASSERT_MESSAGE( (al.MateRefID>=0 && (al.MateRefID<(int)filterToolReferences.size())), "Invalid MateRefID");
+ const string& refName = filterToolReferences.at(al.MateRefID).RefName;
+ keepAlignment &= valueFilter.check(refName);
+ }
+ else if ( propertyName == NAME_PROPERTY ) keepAlignment &= valueFilter.check(al.Name);
+ else if ( propertyName == POSITION_PROPERTY ) keepAlignment &= valueFilter.check(al.Position);
+ else if ( propertyName == QUERYBASES_PROPERTY ) keepAlignment &= valueFilter.check(al.QueryBases);
+ else if ( propertyName == REFERENCE_PROPERTY ) {
+ BAMTOOLS_ASSERT_MESSAGE( (al.RefID>=0 && (al.RefID<(int)filterToolReferences.size())), "Invalid RefID");
+ const string& refName = filterToolReferences.at(al.RefID).RefName;
+ keepAlignment &= valueFilter.check(refName);
+ }
+ else if ( propertyName == TAG_PROPERTY ) keepAlignment &= checkAlignmentTag(valueFilter, al);
+ else BAMTOOLS_ASSERT_UNREACHABLE;
+
+ // if alignment fails at ANY point, just quit and return false
+ if ( !keepAlignment ) return false;
+ }
+
+ BAMTOOLS_ASSERT_MESSAGE( keepAlignment, "Error in BamAlignmentChecker... keepAlignment should be true here");
+ return keepAlignment;
+ }
+
+ bool checkAlignmentTag(const PropertyFilterValue& valueFilter, const BamAlignment& al) {
+
+ // ensure filter contains string data
+ Variant entireTagFilter = valueFilter.Value;
+ if ( !entireTagFilter.is_type<string>() ) return false;
+
+ // localize string from variant
+ const string& entireTagFilterString = entireTagFilter.get<string>();
+
+ // ensure we have at least "XX:x"
+ if ( entireTagFilterString.length() < 4 ) return false;
+
+ // get tagName & lookup in alignment
+ // if found, set tagType to tag type character
+ // if not found, return false
+ const string& tagName = entireTagFilterString.substr(0,2);
+ char tagType = '\0';
+ if ( !al.GetTagType(tagName, tagType) ) return false;
+
+ // remove tagName & ":" from beginning tagFilter
+ string tagFilterString = entireTagFilterString.substr(3);
+
+ // switch on tag type to set tag query value & parse filter token
+ int8_t asciiFilterValue, asciiQueryValue;
+ int32_t intFilterValue, intQueryValue;
+ uint32_t uintFilterValue, uintQueryValue;
+ float realFilterValue, realQueryValue;
+ string stringFilterValue, stringQueryValue;
+
+ PropertyFilterValue tagFilter;
+ PropertyFilterValue::ValueCompareType compareType;
+ bool keepAlignment = false;
+ switch (tagType) {
+
+ // ASCII tag type
+ case 'A':
+ if ( al.GetTag(tagName, asciiQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, asciiFilterValue, compareType) ) {
+ tagFilter.Value = asciiFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(asciiQueryValue);
+ }
+ }
+ break;
+
+ // signed int tag type
+ case 'c' :
+ case 's' :
+ case 'i' :
+ if ( al.GetTag(tagName, intQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, intFilterValue, compareType) ) {
+ tagFilter.Value = intFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(intQueryValue);
+ }
+ }
+ break;
+
+ // unsigned int tag type
+ case 'C' :
+ case 'S' :
+ case 'I' :
+ if ( al.GetTag(tagName, uintQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, uintFilterValue, compareType) ) {
+ tagFilter.Value = uintFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(uintQueryValue);
+ }
+ }
+ break;
+
+ // 'real' tag type
+ case 'f' :
+ if ( al.GetTag(tagName, realQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, realFilterValue, compareType) ) {
+ tagFilter.Value = realFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(realQueryValue);
+ }
+ }
+ break;
+
+ // string tag type
+
+ case 'Z':
+ case 'H':
+ if ( al.GetTag(tagName, stringQueryValue) ) {
+ if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, stringFilterValue, compareType) ) {
+ tagFilter.Value = stringFilterValue;
+ tagFilter.Type = compareType;
+ keepAlignment = tagFilter.check(stringQueryValue);
+ }
+ }
+ break;
+
+ // unknown tag type
+ default :
+ keepAlignment = false;
+ }
+
+ return keepAlignment;
+ }
+};
+
+} // namespace BamTools
// ---------------------------------------------
// FilterSettings implementation
// ----------------------------------
// IO opts
-
+
// flags
- bool HasInputBamFilename;
- bool HasOutputBamFilename;
+ bool HasInput;
+ bool HasInputFilelist;
+ bool HasOutput;
bool HasRegion;
- bool HasScriptFilename;
+ bool HasScript;
bool IsForceCompression;
-
+
// filenames
vector<string> InputFiles;
+ string InputFilelist;
string OutputFilename;
string Region;
string ScriptFilename;
-
+
// -----------------------------------
// General filter opts
-
+
// flags
bool HasAlignmentFlagFilter;
bool HasInsertSizeFilter;
+ bool HasLengthFilter;
bool HasMapQualityFilter;
bool HasNameFilter;
bool HasQueryBasesFilter;
-
-// bool HasTagFilters;
+ bool HasTagFilter; //(s)
// filters
string AlignmentFlagFilter;
string InsertSizeFilter;
- string NameFilter;
+ string LengthFilter;
string MapQualityFilter;
+ string NameFilter;
string QueryBasesFilter;
-
-// vector<string> TagFilters;
+ string TagFilter; // support multiple ?
// -----------------------------------
// 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)
+ : HasInput(false)
+ , HasInputFilelist(false)
+ , HasOutput(false)
, HasRegion(false)
- , HasScriptFilename(false)
+ , HasScript(false)
, IsForceCompression(false)
, OutputFilename(Options::StandardOut())
, HasAlignmentFlagFilter(false)
, HasInsertSizeFilter(false)
+ , HasLengthFilter(false)
, HasMapQualityFilter(false)
, HasNameFilter(false)
, HasQueryBasesFilter(false)
-// , HasTagFilters(false)
+ , HasTagFilter(false)
, HasIsDuplicateFilter(false)
, HasIsFailedQCFilter(false)
, HasIsFirstMateFilter(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> -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 README for more details)", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
- Options::AddValueOption("-script", "filename", "the filter script file (see README 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. If multiple tags are given, reads must match all", "", m_settings->HasTagFilters, m_settings->TagFilters, 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
// destructor
FilterTool::FilterToolPrivate::~FilterToolPrivate(void) { }
-bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens) {
-
-
+bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName,
+ const map<string,
+ string>& propertyTokens)
+{
// dummy temp values for token parsing
bool boolValue;
int32_t int32Value;
propertyName == ISPRIMARYALIGNMENT_PROPERTY ||
propertyName == ISPROPERPAIR_PROPERTY ||
propertyName == ISREVERSESTRAND_PROPERTY ||
- propertyName == ISSECONDMATE_PROPERTY
+ propertyName == ISSECONDMATE_PROPERTY ||
+ propertyName == ISSINGLETON_PROPERTY
)
{
- FilterEngine::parseToken(token, boolValue, type);
- FilterEngine::setProperty(filterName, propertyName, boolValue, type);
+ FilterEngine<BamAlignmentChecker>::parseToken(token, boolValue, type);
+ m_filterEngine.setProperty(filterName, propertyName, boolValue, type);
}
// int32_t conversion
else if ( propertyName == INSERTSIZE_PROPERTY ||
+ propertyName == LENGTH_PROPERTY ||
propertyName == MATEPOSITION_PROPERTY ||
propertyName == POSITION_PROPERTY
)
{
- FilterEngine::parseToken(token, int32Value, type);
- FilterEngine::setProperty(filterName, propertyName, int32Value, type);
+ FilterEngine<BamAlignmentChecker>::parseToken(token, int32Value, type);
+ m_filterEngine.setProperty(filterName, propertyName, int32Value, type);
}
// uint16_t conversion
else if ( propertyName == MAPQUALITY_PROPERTY )
{
- FilterEngine::parseToken(token, uint16Value, type);
- FilterEngine::setProperty(filterName, propertyName, uint16Value, type);
+ FilterEngine<BamAlignmentChecker>::parseToken(token, uint16Value, type);
+ m_filterEngine.setProperty(filterName, propertyName, uint16Value, type);
}
// uint32_t conversion
else if ( propertyName == ALIGNMENTFLAG_PROPERTY )
{
- FilterEngine::parseToken(token, uint32Value, type);
- FilterEngine::setProperty(filterName, propertyName, uint32Value, type);
+ FilterEngine<BamAlignmentChecker>::parseToken(token, uint32Value, type);
+ m_filterEngine.setProperty(filterName, propertyName, uint32Value, type);
}
// string conversion
- else if ( propertyName == MATEREFERENCE_PROPERTY ||
+ else if ( propertyName == CIGAR_PROPERTY ||
+ propertyName == MATEREFERENCE_PROPERTY ||
propertyName == NAME_PROPERTY ||
propertyName == QUERYBASES_PROPERTY ||
- propertyName == REFERENCE_PROPERTY
+ propertyName == REFERENCE_PROPERTY
)
{
- FilterEngine::parseToken(token, stringValue, type);
- FilterEngine::setProperty(filterName, propertyName, stringValue, type);
+ FilterEngine<BamAlignmentChecker>::parseToken(token, stringValue, type);
+ m_filterEngine.setProperty(filterName, propertyName, stringValue, type);
+ }
+
+ else if ( propertyName == TAG_PROPERTY ) {
+ // this will be stored directly as the TAG:VALUE token
+ // (VALUE may contain compare ops, will be parsed out later)
+ m_filterEngine.setProperty(filterName, propertyName, token, PropertyFilterValue::EXACT);
}
// else unknown property
else {
- cerr << "Unknown property: " << propertyName << "!" << endl;
+ cerr << "bamtools filter ERROR: unknown property - " << propertyName << endl;
return false;
}
}
}
bool FilterTool::FilterToolPrivate::CheckAlignment(const BamAlignment& al) {
-
- bool keepAlignment = true;
-
- // only consider properties that are actually enabled
- // iterate over these enabled properties
- const vector<string> enabledProperties = FilterEngine::enabledPropertyNames();
- vector<string>::const_iterator propIter = enabledProperties.begin();
- vector<string>::const_iterator propEnd = enabledProperties.end();
- for ( ; propIter != propEnd; ++propIter ) {
-
- // check alignment data field depending on propertyName
- const string& propertyName = (*propIter);
- if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= FilterEngine::check(ALIGNMENTFLAG_PROPERTY, al.AlignmentFlag);
- else if ( propertyName == INSERTSIZE_PROPERTY ) keepAlignment &= FilterEngine::check(INSERTSIZE_PROPERTY, al.InsertSize);
- else if ( propertyName == ISDUPLICATE_PROPERTY ) keepAlignment &= FilterEngine::check(ISDUPLICATE_PROPERTY, al.IsDuplicate());
- else if ( propertyName == ISFAILEDQC_PROPERTY ) keepAlignment &= FilterEngine::check(ISFAILEDQC_PROPERTY, al.IsFailedQC());
- else if ( propertyName == ISFIRSTMATE_PROPERTY ) keepAlignment &= FilterEngine::check(ISFIRSTMATE_PROPERTY, al.IsFirstMate());
- else if ( propertyName == ISMAPPED_PROPERTY ) keepAlignment &= FilterEngine::check(ISMAPPED_PROPERTY, al.IsMapped());
- else if ( propertyName == ISMATEMAPPED_PROPERTY ) keepAlignment &= FilterEngine::check(ISMATEMAPPED_PROPERTY, al.IsMateMapped());
- else if ( propertyName == ISMATEREVERSESTRAND_PROPERTY ) keepAlignment &= FilterEngine::check(ISMATEREVERSESTRAND_PROPERTY, al.IsMateReverseStrand());
- else if ( propertyName == ISPAIRED_PROPERTY ) keepAlignment &= FilterEngine::check(ISPAIRED_PROPERTY, al.IsPaired());
- else if ( propertyName == ISPRIMARYALIGNMENT_PROPERTY ) keepAlignment &= FilterEngine::check(ISPRIMARYALIGNMENT_PROPERTY, al.IsPrimaryAlignment());
- else if ( propertyName == ISPROPERPAIR_PROPERTY ) keepAlignment &= FilterEngine::check(ISPROPERPAIR_PROPERTY, al.IsProperPair());
- else if ( propertyName == ISREVERSESTRAND_PROPERTY ) keepAlignment &= FilterEngine::check(ISREVERSESTRAND_PROPERTY, al.IsReverseStrand());
- else if ( propertyName == ISSECONDMATE_PROPERTY ) keepAlignment &= FilterEngine::check(ISSECONDMATE_PROPERTY, al.IsSecondMate());
- else if ( propertyName == MAPQUALITY_PROPERTY ) keepAlignment &= FilterEngine::check(MAPQUALITY_PROPERTY, al.MapQuality);
- else if ( propertyName == MATEPOSITION_PROPERTY ) keepAlignment &= ( al.IsPaired() && al.IsMateMapped() && FilterEngine::check(MATEPOSITION_PROPERTY, al.MateRefID) );
- else if ( propertyName == MATEREFERENCE_PROPERTY ) {
- if ( !al.IsPaired() || !al.IsMateMapped() ) return false;
- BAMTOOLS_ASSERT_MESSAGE( (al.MateRefID>=0 && (al.MateRefID<(int)m_references.size())), "Invalid MateRefID");
- const string& refName = m_references.at(al.MateRefID).RefName;
- keepAlignment &= FilterEngine::check(MATEREFERENCE_PROPERTY, refName);
- }
- else if ( propertyName == NAME_PROPERTY ) keepAlignment &= FilterEngine::check(NAME_PROPERTY, al.Name);
- else if ( propertyName == POSITION_PROPERTY ) keepAlignment &= FilterEngine::check(POSITION_PROPERTY, al.Position);
- else if ( propertyName == QUERYBASES_PROPERTY ) keepAlignment &= FilterEngine::check(QUERYBASES_PROPERTY, al.QueryBases);
- else if ( propertyName == REFERENCE_PROPERTY ) {
- BAMTOOLS_ASSERT_MESSAGE( (al.RefID>=0 && (al.RefID<(int)m_references.size())), "Invalid RefID");
- const string& refName = m_references.at(al.RefID).RefName;
- keepAlignment &= FilterEngine::check(REFERENCE_PROPERTY, refName);
- }
- else BAMTOOLS_ASSERT_MESSAGE( false, "Unknown property");
-
- // if alignment fails at ANY point, just quit and return false
- if ( !keepAlignment ) return false;
- }
-
- // return success (should still be true at this point)
- return keepAlignment;
+ return m_filterEngine.check(al);
}
const string FilterTool::FilterToolPrivate::GetScriptContents(void) {
// open script for reading
FILE* inFile = fopen(m_settings->ScriptFilename.c_str(), "rb");
if ( !inFile ) {
- cerr << "FilterTool error: Could not open script: " << m_settings->ScriptFilename << " for reading" << endl;
- return false;
+ cerr << "bamtools filter ERROR: could not open script: "
+ << m_settings->ScriptFilename << " for reading" << endl;
+ return string();
}
// read in entire script contents
// peek ahead, make sure there is data available
char ch = fgetc(inFile);
ungetc(ch, inFile);
- if( feof(inFile) ) break;
+ if( feof(inFile) )
+ break;
// read next block of data
if ( fgets(buffer, 1024, inFile) == 0 ) {
- cerr << "FilterTool error : could not read from script" << endl;
- return false;
+ cerr << "bamtools filter ERROR: could not read script contents" << endl;
+ return string();
}
docStream << buffer;
fclose(inFile);
// import buffer contents to document, return
- string document = docStream.str();
- return document;
+ return docStream.str();
}
void FilterTool::FilterToolPrivate::InitProperties(void) {
// store property names in vector
m_propertyNames.push_back(ALIGNMENTFLAG_PROPERTY);
+ m_propertyNames.push_back(CIGAR_PROPERTY);
m_propertyNames.push_back(INSERTSIZE_PROPERTY);
m_propertyNames.push_back(ISDUPLICATE_PROPERTY);
m_propertyNames.push_back(ISFAILEDQC_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(LENGTH_PROPERTY);
m_propertyNames.push_back(MAPQUALITY_PROPERTY);
m_propertyNames.push_back(MATEPOSITION_PROPERTY);
m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
m_propertyNames.push_back(POSITION_PROPERTY);
m_propertyNames.push_back(QUERYBASES_PROPERTY);
m_propertyNames.push_back(REFERENCE_PROPERTY);
+ m_propertyNames.push_back(TAG_PROPERTY);
- // add vector contents to FilterEngine
+ // add vector contents to FilterEngine<BamAlignmentChecker>
vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter )
- FilterEngine::addProperty((*propertyNameIter));
+ m_filterEngine.addProperty((*propertyNameIter));
}
bool FilterTool::FilterToolPrivate::ParseCommandLine(void) {
// add a rule set to filter engine
const string CMD = "COMMAND_LINE";
- FilterEngine::addFilter(CMD);
+ m_filterEngine.addFilter(CMD);
// map property names to command line args
map<string, string> propertyTokens;
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->HasLengthFilter ) propertyTokens.insert( make_pair(LENGTH_PROPERTY, m_settings->LengthFilter) );
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) );
-
+ if ( m_settings->HasTagFilter ) propertyTokens.insert( make_pair(TAG_PROPERTY, m_settings->TagFilter) );
+
// send add these properties to filter set "COMMAND_LINE"
return AddPropertyTokensToFilter(CMD, propertyTokens);
}
}
// add this filter to engin
- FilterEngine::addFilter(filterName);
+ m_filterEngine.addFilter(filterName);
// add token list to this filter
return AddPropertyTokensToFilter(filterName, propertyTokens);
Json::Reader reader;
if ( !reader.parse(document, root) ) {
// use built-in error reporting mechanism to alert user what was wrong with the script
- cerr << "Failed to parse configuration\n" << reader.getFormatedErrorMessages();
+ cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl
+ << reader.getFormatedErrorMessages();
return false;
}
// if id tag supplied
const Json::Value id = filter["id"];
- if ( !id.isNull() ) {
+ if ( !id.isNull() )
filterName = id.asString();
- }
// use array index
else {
success &= ParseFilterObject(filterName, filter);
}
- // see if user defined "rule" for these filters
+ // see if user defined a "rule" for these filters
+ // otherwise, use filter engine's default rule behavior
+ string ruleString("");
const Json::Value rule = root["rule"];
- if ( !rule.isNull() ) {
- cout << "found rule: " << rule.asString() << endl;
- } else {
- cout << "no rule found!" << endl;
- }
+ if ( rule.isString() )
+ ruleString = rule.asString();
+ m_filterEngine.setRule(ruleString);
+ // return success/fail
return success;
}
return success;
}
-
bool FilterTool::FilterToolPrivate::Run(void) {
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename )
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
-
+
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools filter ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// initialize defined properties & user-specified filters
// quit if failed
- if ( !SetupFilters() ) return 1;
+ if ( !SetupFilters() )
+ return false;
// open reader without index
BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false, true);
+ if ( !reader.Open(m_settings->InputFiles) ) {
+ cerr << "bamtools filter ERROR: could not open input files for reading." << endl;
+ return false;
+ }
+
+ // retrieve reader header & reference data
const string headerText = reader.GetHeaderText();
- m_references = reader.GetReferenceData();
+ filterToolReferences = reader.GetReferenceData();
- // open writer
+ // determine compression mode for BamWriter
+ bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
+ !m_settings->IsForceCompression );
+ BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
+ if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
+
+ // open BamWriter
BamWriter writer;
- bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
- writer.Open(m_settings->OutputFilename, headerText, m_references, writeUncompressed);
-
- BamAlignment al;
-
+ writer.SetCompressionMode(compressionMode);
+ if ( !writer.Open(m_settings->OutputFilename, headerText, filterToolReferences) ) {
+ cerr << "bamtools filter ERROR: could not open " << m_settings->OutputFilename << " for writing." << endl;
+ reader.Close();
+ return false;
+ }
+
// if no region specified, filter entire file
+ BamAlignment al;
if ( !m_settings->HasRegion ) {
while ( reader.GetNextAlignment(al) ) {
if ( CheckAlignment(al) )
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
- // attempt to re-open reader with index files
- reader.Close();
- bool openedOK = reader.Open(m_settings->InputFiles, true, true );
-
- // if error
- if ( !openedOK ) {
- cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
- return 1;
- }
-
- // if index data available, we can use SetRegion
- if ( reader.IsIndexLoaded() ) {
-
+ // attempt to find index files
+ reader.LocateIndexes();
+
+ // if index data available for all BAM files, we can use SetRegion
+ if ( reader.HasIndexes() ) {
+
// attempt to use SetRegion(), if failed report error
if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
- cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
+ cerr << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl;
reader.Close();
- return 1;
+ return false;
}
// everything checks out, just iterate through specified region, filtering alignments
- while ( reader.GetNextAlignmentCore(al) )
+ while ( reader.GetNextAlignment(al) )
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
- }
+ }
// no index data available, we have to iterate through until we
// find overlapping alignments
else {
- while( reader.GetNextAlignmentCore(al) ) {
- if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
- (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ while ( reader.GetNextAlignment(al) ) {
+ if ( (al.RefID >= region.LeftRefID) && ((al.Position + al.Length) >= region.LeftPosition) &&
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
// error parsing REGION string
else {
- cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
- cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ cerr << "bamtools filter ERROR: could not parse REGION: " << m_settings->Region << endl;
+ cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
+ << endl;
reader.Close();
- return 1;
+ return false;
}
}
// clean up & exit
reader.Close();
writer.Close();
- return 0;
+ return true;
}
bool FilterTool::FilterToolPrivate::SetupFilters(void) {
- // add known properties to FilterEngine
+ // set up filter engine with supported properties
InitProperties();
// parse script for filter rules, if given
- if ( m_settings->HasScriptFilename ) return ParseScript();
+ if ( m_settings->HasScript )
+ return ParseScript();
// 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> ... | -list <filelist>] "
+ "[-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 listDesc = "the input BAM file list, one line per file";
+ 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->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", listDesc, "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
+ Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutput, 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->HasScript, 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 lengthDesc = "keep reads with length 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("-length", "int", lengthDesc, "", m_settings->HasLengthFilter, m_settings->LengthFilter, 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