// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
+// Last modified: 30 August 2010
// ---------------------------------------------------------------------------
// Filters a single BAM file (or filters multiple BAM files and merges)
// according to some user-specified criteria.
// ***************************************************************************
+// std includes
+#include <cstdio>
#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 {
+
+// -------------------------------
+// string literal constants
+
+// property names
+const string ALIGNMENTFLAG_PROPERTY = "alignmentFlag";
+const string INSERTSIZE_PROPERTY = "insertSize";
+const string ISDUPLICATE_PROPERTY = "isDuplicate";
+const string ISFAILEDQC_PROPERTY = "isFailedQC";
+const string ISFIRSTMATE_PROPERTY = "isFirstMate";
+const string ISMAPPED_PROPERTY = "isMapped";
+const string ISMATEMAPPED_PROPERTY = "isMateMapped";
+const string ISMATEREVERSESTRAND_PROPERTY = "isMateReverseStrand";
+const string ISPAIRED_PROPERTY = "isPaired";
+const string ISPRIMARYALIGNMENT_PROPERTY = "isPrimaryAlignment";
+const string ISPROPERPAIR_PROPERTY = "isProperPair";
+const string ISREVERSESTRAND_PROPERTY = "isReverseStrand";
+const string ISSECONDMATE_PROPERTY = "isSecondMate";
+const string MAPQUALITY_PROPERTY = "mapQuality";
+const string MATEPOSITION_PROPERTY = "matePosition";
+const string MATEREFERENCE_PROPERTY = "mateReference";
+const string NAME_PROPERTY = "name";
+const string POSITION_PROPERTY = "position";
+const string QUERYBASES_PROPERTY = "queryBases";
+const string REFERENCE_PROPERTY = "reference";
+
+// boolalpha
+const string TRUE_STR = "true";
+const string FALSE_STR = "false";
+
+} // 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;
+ RefVector m_references;
+};
// ---------------------------------------------
// FilterSettings implementation
struct FilterTool::FilterSettings {
+ // ----------------------------------
+ // IO opts
+
// flags
bool HasInputBamFilename;
bool HasOutputBamFilename;
-
+ bool HasRegion;
+ bool HasScriptFilename;
+
// filenames
vector<string> InputFiles;
string OutputFilename;
+ string Region;
+ string ScriptFilename;
+
+ // -----------------------------------
+ // General filter opts
+
+ // flags
+ bool HasAlignmentFlagFilter;
+ bool HasInsertSizeFilter;
+ bool HasMapQualityFilter;
+ bool HasNameFilter;
+ bool HasQueryBasesFilter;
+
+// bool HasTagFilters;
+
+ // filters
+ string AlignmentFlagFilter;
+ string InsertSizeFilter;
+ string NameFilter;
+ string MapQualityFilter;
+ string QueryBasesFilter;
+
+// vector<string> TagFilters;
+
+ // -----------------------------------
+ // AlignmentFlag filter opts
+
+ // flags
+ bool HasIsDuplicateFilter;
+ bool HasIsFailedQCFilter;
+ bool HasIsFirstMateFilter;
+ bool HasIsMappedFilter;
+ bool HasIsMateMappedFilter;
+ bool HasIsMateReverseStrandFilter;
+ bool HasIsPairedFilter;
+ bool HasIsPrimaryAlignmentFilter;
+ bool HasIsProperPairFilter;
+ bool HasIsReverseStrandFilter;
+ bool HasIsSecondMateFilter;
+
+ // filters
+ string IsDuplicateFilter;
+ string IsFailedQCFilter;
+ string IsFirstMateFilter;
+ string IsMappedFilter;
+ string IsMateMappedFilter;
+ string IsMateReverseStrandFilter;
+ string IsPairedFilter;
+ string IsPrimaryAlignmentFilter;
+ string IsProperPairFilter;
+ string IsReverseStrandFilter;
+ string IsSecondMateFilter;
+ // ---------------------------------
// constructor
+
FilterSettings(void)
: HasInputBamFilename(false)
, HasOutputBamFilename(false)
+ , HasRegion(false)
+ , HasScriptFilename(false)
, OutputFilename(Options::StandardOut())
+ , HasAlignmentFlagFilter(false)
+ , HasInsertSizeFilter(false)
+ , HasMapQualityFilter(false)
+ , HasNameFilter(false)
+ , HasQueryBasesFilter(false)
+// , HasTagFilters(false)
+ , HasIsDuplicateFilter(false)
+ , HasIsFailedQCFilter(false)
+ , HasIsFirstMateFilter(false)
+ , HasIsMappedFilter(false)
+ , HasIsMateMappedFilter(false)
+ , HasIsMateReverseStrandFilter(false)
+ , HasIsPairedFilter(false)
+ , HasIsPrimaryAlignmentFilter(false)
+ , HasIsProperPairFilter(false)
+ , HasIsReverseStrandFilter(false)
+ , HasIsSecondMateFilter(false)
+ , IsDuplicateFilter(TRUE_STR)
+ , IsFailedQCFilter(TRUE_STR)
+ , IsFirstMateFilter(TRUE_STR)
+ , IsMappedFilter(TRUE_STR)
+ , IsMateMappedFilter(TRUE_STR)
+ , IsMateReverseStrandFilter(TRUE_STR)
+ , IsPairedFilter(TRUE_STR)
+ , IsPrimaryAlignmentFilter(TRUE_STR)
+ , IsProperPairFilter(TRUE_STR)
+ , IsReverseStrandFilter(TRUE_STR)
+ , IsSecondMateFilter(TRUE_STR)
{ }
};
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> ");
+ Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", "-in <filename> [-in <filename> ... ] -out <filename> -region <REGION> [ [-script <filename] | [filterOptions] ]");
- // set up options
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("-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);
+
+ 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) {
// 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;
+}
+
+// ---------------------------------------------
+// FilterToolPrivate implementation
+
+// constructor
+FilterTool::FilterToolPrivate::FilterToolPrivate(FilterTool::FilterSettings* settings)
+ : m_settings(settings)
+{ }
+
+// destructor
+FilterTool::FilterToolPrivate::~FilterToolPrivate(void) { }
+
+bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens) {
+
+
+ // dummy temp values for token parsing
+ bool boolValue;
+ int32_t int32Value;
+ uint16_t uint16Value;
+ uint32_t uint32Value;
+ string stringValue;
+ PropertyFilterValue::ValueCompareType type;
+
+ // iterate over property token map
+ map<string, string>::const_iterator mapIter = propertyTokens.begin();
+ map<string, string>::const_iterator mapEnd = propertyTokens.end();
+ for ( ; mapIter != mapEnd; ++mapIter ) {
+
+ const string& propertyName = (*mapIter).first;
+ const string& token = (*mapIter).second;
+
+ // ------------------------------
+ // convert token to value & compare type
+ // then add to filter engine
+
+ // bool conversion
+ if ( propertyName == ISDUPLICATE_PROPERTY ||
+ propertyName == ISFAILEDQC_PROPERTY ||
+ propertyName == ISFIRSTMATE_PROPERTY ||
+ propertyName == ISMAPPED_PROPERTY ||
+ propertyName == ISMATEMAPPED_PROPERTY ||
+ propertyName == ISMATEREVERSESTRAND_PROPERTY ||
+ propertyName == ISPAIRED_PROPERTY ||
+ propertyName == ISPRIMARYALIGNMENT_PROPERTY ||
+ propertyName == ISPROPERPAIR_PROPERTY ||
+ propertyName == ISREVERSESTRAND_PROPERTY ||
+ propertyName == ISSECONDMATE_PROPERTY
+ )
+ {
+ FilterEngine::parseToken(token, boolValue, type);
+ FilterEngine::setProperty(filterName, propertyName, boolValue, type);
+ }
+
+ // int32_t conversion
+ else if ( propertyName == INSERTSIZE_PROPERTY ||
+ propertyName == MATEPOSITION_PROPERTY ||
+ propertyName == POSITION_PROPERTY
+ )
+ {
+ FilterEngine::parseToken(token, int32Value, type);
+ 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);
+ }
+
+ // uint32_t conversion
+ else if ( propertyName == ALIGNMENTFLAG_PROPERTY )
+ {
+ FilterEngine::parseToken(token, uint32Value, type);
+ FilterEngine::setProperty(filterName, propertyName, uint32Value, type);
+ }
+
+ // string conversion
+ else if ( propertyName == MATEREFERENCE_PROPERTY ||
+ propertyName == NAME_PROPERTY ||
+ propertyName == QUERYBASES_PROPERTY ||
+ propertyName == REFERENCE_PROPERTY
+ )
+ {
+ FilterEngine::parseToken(token, stringValue, type);
+ FilterEngine::setProperty(filterName, propertyName, stringValue, type);
+ }
+
+ // else unknown property
+ else {
+ cerr << "Unknown property: " << propertyName << "!" << endl;
+ return false;
+ }
+ }
+ return true;
+}
+
+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;
+}
+
+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;
+ }
+
+ // read in entire script contents
+ char buffer[1024];
+ ostringstream docStream("");
+ while ( true ) {
+
+ // peek ahead, make sure there is data available
+ char ch = fgetc(inFile);
+ ungetc(ch, inFile);
+ 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;
+ }
+
+ docStream << buffer;
+ }
+
+ // close script file
+ fclose(inFile);
+
+ // import buffer contents to document, return
+ string document = docStream.str();
+ return document;
+}
+
+void FilterTool::FilterToolPrivate::InitProperties(void) {
+
+ // store property names in vector
+ m_propertyNames.push_back(ALIGNMENTFLAG_PROPERTY);
+ m_propertyNames.push_back(INSERTSIZE_PROPERTY);
+ m_propertyNames.push_back(ISDUPLICATE_PROPERTY);
+ m_propertyNames.push_back(ISFAILEDQC_PROPERTY);
+ m_propertyNames.push_back(ISFIRSTMATE_PROPERTY);
+ m_propertyNames.push_back(ISMAPPED_PROPERTY);
+ m_propertyNames.push_back(ISMATEMAPPED_PROPERTY);
+ m_propertyNames.push_back(ISMATEREVERSESTRAND_PROPERTY);
+ m_propertyNames.push_back(ISPAIRED_PROPERTY);
+ m_propertyNames.push_back(ISPRIMARYALIGNMENT_PROPERTY);
+ m_propertyNames.push_back(ISPROPERPAIR_PROPERTY);
+ m_propertyNames.push_back(ISREVERSESTRAND_PROPERTY);
+ m_propertyNames.push_back(ISSECONDMATE_PROPERTY);
+ m_propertyNames.push_back(MAPQUALITY_PROPERTY);
+ m_propertyNames.push_back(MATEPOSITION_PROPERTY);
+ m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
+ m_propertyNames.push_back(NAME_PROPERTY);
+ m_propertyNames.push_back(POSITION_PROPERTY);
+ m_propertyNames.push_back(QUERYBASES_PROPERTY);
+ m_propertyNames.push_back(REFERENCE_PROPERTY);
+
+ // add vector contents to FilterEngine
+ vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
+ vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
+ for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter )
+ FilterEngine::addProperty((*propertyNameIter));
+}
+
+bool FilterTool::FilterToolPrivate::ParseCommandLine(void) {
+
+ // add a rule set to filter engine
+ const string CMD = "COMMAND_LINE";
+ FilterEngine::addFilter(CMD);
+
+ // map property names to command line args
+ map<string, string> propertyTokens;
+ if ( m_settings->HasAlignmentFlagFilter ) propertyTokens.insert( make_pair(ALIGNMENTFLAG_PROPERTY, m_settings->AlignmentFlagFilter) );
+ if ( m_settings->HasInsertSizeFilter ) propertyTokens.insert( make_pair(INSERTSIZE_PROPERTY, m_settings->InsertSizeFilter) );
+ if ( m_settings->HasIsDuplicateFilter ) propertyTokens.insert( make_pair(ISDUPLICATE_PROPERTY, m_settings->IsDuplicateFilter) );
+ if ( m_settings->HasIsFailedQCFilter ) propertyTokens.insert( make_pair(ISFAILEDQC_PROPERTY, m_settings->IsFailedQCFilter) );
+ if ( m_settings->HasIsFirstMateFilter ) propertyTokens.insert( make_pair(ISFIRSTMATE_PROPERTY, m_settings->IsFirstMateFilter) );
+ if ( m_settings->HasIsMappedFilter ) propertyTokens.insert( make_pair(ISMAPPED_PROPERTY, m_settings->IsMappedFilter) );
+ if ( m_settings->HasIsMateMappedFilter ) propertyTokens.insert( make_pair(ISMATEMAPPED_PROPERTY, m_settings->IsMateMappedFilter) );
+ if ( m_settings->HasIsMateReverseStrandFilter ) propertyTokens.insert( make_pair(ISMATEREVERSESTRAND_PROPERTY, m_settings->IsMateReverseStrandFilter) );
+ if ( m_settings->HasIsPairedFilter ) propertyTokens.insert( make_pair(ISPAIRED_PROPERTY, m_settings->IsPairedFilter) );
+ if ( m_settings->HasIsPrimaryAlignmentFilter ) propertyTokens.insert( make_pair(ISPRIMARYALIGNMENT_PROPERTY, m_settings->IsPrimaryAlignmentFilter) );
+ 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->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) );
+
+ // send add these properties to filter set "COMMAND_LINE"
+ return AddPropertyTokensToFilter(CMD, propertyTokens);
+}
+
+bool FilterTool::FilterToolPrivate::ParseFilterObject(const string& filterName, const Json::Value& filterObject) {
+
+ // filter object parsing variables
+ Json::Value null(Json::nullValue);
+ Json::Value propertyValue;
+
+ // store results
+ map<string, string> propertyTokens;
+
+ // iterate over known properties
+ vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
+ vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
+ for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter ) {
+ const string& propertyName = (*propertyNameIter);
+
+ // if property defined in filter, add to token list
+ propertyValue = filterObject.get(propertyName, null);
+ if ( propertyValue != null )
+ propertyTokens.insert( make_pair(propertyName, propertyValue.asString()) );
+ }
+
+ // add this filter to engin
+ FilterEngine::addFilter(filterName);
+ // add token list to this filter
+ return AddPropertyTokensToFilter(filterName, propertyTokens);
+}
+
+bool FilterTool::FilterToolPrivate::ParseScript(void) {
+
+ // read in script contents from file
+ const string document = GetScriptContents();
+
+ // set up JsonCPP reader and attempt to parse script
+ Json::Value root;
+ 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();
+ return false;
+ }
+
+ // see if root object contains multiple filters
+ const Json::Value filters = root["filters"];
+ if ( !filters.isNull() ) {
+
+ bool success = true;
+
+ // iterate over any filters found
+ int filterIndex = 0;
+ Json::Value::const_iterator filtersIter = filters.begin();
+ Json::Value::const_iterator filtersEnd = filters.end();
+ for ( ; filtersIter != filtersEnd; ++filtersIter, ++filterIndex ) {
+ Json::Value filter = (*filtersIter);
+
+ // convert filter index to string
+ stringstream convert;
+ convert << filterIndex;
+ const string filterName = convert.str();
+
+ // create & parse filter
+ success &= ParseFilterObject(filterName, filter);
+
+ }
+ return success;
+ }
+
+ // otherwise, root is the only filter (just contains properties)
+ // create & parse filter named "ROOT"
+ else return ParseFilterObject("ROOT", root);
+}
+
+
+bool FilterTool::FilterToolPrivate::Run(void) {
+
// set to default input if none provided
if ( !m_settings->HasInputBamFilename )
m_settings->InputFiles.push_back(Options::StandardIn());
- // open files
+ // initialize defined properties & user-specified filters
+ // quit if failed
+ if ( !SetupFilters() ) return 1;
+
+ // open reader without index
BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false);
-
- // do filtering
+ reader.Open(m_settings->InputFiles, false, true);
+ const string headerText = reader.GetHeaderText();
+ m_references = reader.GetReferenceData();
+
+ // open writer
+ BamWriter writer;
+ writer.Open(m_settings->OutputFilename, headerText, m_references);
+
+ // set up error handling
+ ostringstream errorStream("");
+ bool foundError(false);
+ // if no REGION specified, run filter on entire file contents
+ if ( !m_settings->HasRegion ) {
+ BamAlignment al;
+ while ( reader.GetNextAlignment(al) ) {
+ // perform main filter check
+ if ( CheckAlignment(al) )
+ writer.SaveAlignment(al);
+ }
+ }
+
+ // REGION specified
+ else {
+
+ // attempt to parse string into BamRegion struct
+ BamRegion region;
+ if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+
+ // check if there are index files *.bai/*.bti corresponding to the input files
+ bool hasDefaultIndex = false;
+ bool hasBamtoolsIndex = false;
+ bool hasNoIndex = false;
+ int defaultIndexCount = 0;
+ int bamtoolsIndexCount = 0;
+ for (vector<string>::const_iterator f = m_settings->InputFiles.begin(); f != m_settings->InputFiles.end(); ++f) {
+
+ if ( Utilities::FileExists(*f + ".bai") ) {
+ hasDefaultIndex = true;
+ ++defaultIndexCount;
+ }
+
+ if ( Utilities::FileExists(*f + ".bti") ) {
+ hasBamtoolsIndex = true;
+ ++bamtoolsIndexCount;
+ }
+
+ if ( !hasDefaultIndex && !hasBamtoolsIndex ) {
+ hasNoIndex = true;
+ cerr << "*WARNING - could not find index file for " << *f
+ << ", parsing whole file(s) to get alignment counts for target region"
+ << " (could be slow)" << endl;
+ break;
+ }
+ }
+
+ // determine if index file types are heterogeneous
+ bool hasDifferentIndexTypes = false;
+ if ( defaultIndexCount > 0 && bamtoolsIndexCount > 0 ) {
+ hasDifferentIndexTypes = true;
+ cerr << "*WARNING - different index file formats found"
+ << ", parsing whole file(s) to get alignment counts for target region"
+ << " (could be slow)" << endl;
+ }
+
+ // if any input file has no index, or if input files use different index formats
+ // can't use BamMultiReader to jump directly (**for now**)
+ if ( hasNoIndex || hasDifferentIndexTypes ) {
+
+ // read through sequentially, but onlt perform filter on reads overlapping REGION
+ BamAlignment al;
+ while( reader.GetNextAlignment(al) ) {
+ if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ {
+ // perform main filter check
+ if ( CheckAlignment(al) )
+ writer.SaveAlignment(al);
+ }
+ }
+ }
+
+ // has index file for each input file (and same format)
+ else {
+
+ // this is kind of a hack...?
+ BamMultiReader reader;
+ reader.Open(m_settings->InputFiles, true, true, hasDefaultIndex );
+
+ if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+ foundError = true;
+ errorStream << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
+ } else {
+
+ // filter only alignments from specified region
+ BamAlignment al;
+ while ( reader.GetNextAlignment(al) ) {
+ // perform main filter check
+ if ( CheckAlignment(al) )
+ writer.SaveAlignment(al);
+ }
+ }
+ }
+
+ } else {
+ foundError = true;
+ errorStream << "Could not parse REGION: " << m_settings->Region << endl;
+ errorStream << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ }
+ }
+
// clean up & exit
reader.Close();
+ writer.Close();
return 0;
-}
\ No newline at end of file
+}
+
+bool FilterTool::FilterToolPrivate::SetupFilters(void) {
+
+ // add known properties to FilterEngine
+ InitProperties();
+
+ // parse script for filter rules, if given
+ if ( m_settings->HasScriptFilename ) return ParseScript();
+
+ // otherwise check command line for filters
+ else return ParseCommandLine();
+}
projects / bamtools.git / commitdiff