// ***************************************************************************
// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 1 June 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
// ***************************************************************************
+#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>
+using namespace std;
+
+namespace BamTools {
+
+// -------------------------------
+// string literal constants
-#include "bamtools_filter.h"
-#include "bamtools_options.h"
-#include "BamReader.h"
-#include "BamMultiReader.h"
+// 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 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 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 NAME_PROPERTY = "name";
+const string POSITION_PROPERTY = "position";
+const string QUERYBASES_PROPERTY = "queryBases";
+const string REFERENCE_PROPERTY = "reference";
+const string TAG_PROPERTY = "tag";
-using namespace std;
-using namespace BamTools;
+// boolalpha
+const string TRUE_STR = "true";
+const string FALSE_STR = "false";
+
+RefVector filterToolReferences;
+
+struct BamAlignmentChecker {
+ bool check(const PropertyFilter& filter, const BamAlignment& al) {
+
+ 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
struct FilterTool::FilterSettings {
+ // ----------------------------------
+ // IO opts
+
// flags
- bool HasInputBamFilename;
- bool HasOutputBamFilename;
+ bool HasInput;
+ bool HasInputFilelist;
+ bool HasOutput;
+ bool HasRegion;
+ 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 HasTagFilter; //(s)
+
+ // filters
+ string AlignmentFlagFilter;
+ string InsertSizeFilter;
+ string LengthFilter;
+ string MapQualityFilter;
+ string NameFilter;
+ string QueryBasesFilter;
+ string TagFilter; // support multiple ?
+
+ // -----------------------------------
+ // 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;
+ bool HasIsSingletonFilter;
+
+ // filters
+ string IsDuplicateFilter;
+ string IsFailedQCFilter;
+ string IsFirstMateFilter;
+ string IsMappedFilter;
+ string IsMateMappedFilter;
+ string IsMateReverseStrandFilter;
+ string IsPairedFilter;
+ string IsPrimaryAlignmentFilter;
+ string IsProperPairFilter;
+ string IsReverseStrandFilter;
+ string IsSecondMateFilter;
+ string IsSingletonFilter;
+
+ // ---------------------------------
// constructor
+
FilterSettings(void)
- : HasInputBamFilename(false)
- , HasOutputBamFilename(false)
+ : HasInput(false)
+ , HasInputFilelist(false)
+ , HasOutput(false)
+ , HasRegion(false)
+ , HasScript(false)
+ , IsForceCompression(false)
, OutputFilename(Options::StandardOut())
+ , HasAlignmentFlagFilter(false)
+ , HasInsertSizeFilter(false)
+ , HasLengthFilter(false)
+ , HasMapQualityFilter(false)
+ , HasNameFilter(false)
+ , HasQueryBasesFilter(false)
+ , HasTagFilter(false)
+ , HasIsDuplicateFilter(false)
+ , HasIsFailedQCFilter(false)
+ , HasIsFirstMateFilter(false)
+ , HasIsMappedFilter(false)
+ , HasIsMateMappedFilter(false)
+ , HasIsMateReverseStrandFilter(false)
+ , HasIsPairedFilter(false)
+ , HasIsPrimaryAlignmentFilter(false)
+ , HasIsProperPairFilter(false)
+ , HasIsReverseStrandFilter(false)
+ , HasIsSecondMateFilter(false)
+ , HasIsSingletonFilter(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)
+ , IsSingletonFilter(TRUE_STR)
{ }
-};
+};
+
+// ---------------------------------------------
+// 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;
+};
+
+// ---------------------------------------------
+// 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 ||
+ propertyName == ISSINGLETON_PROPERTY
+ )
+ {
+ 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<BamAlignmentChecker>::parseToken(token, int32Value, type);
+ m_filterEngine.setProperty(filterName, propertyName, int32Value, type);
+ }
+
+ // uint16_t conversion
+ else if ( propertyName == MAPQUALITY_PROPERTY )
+ {
+ FilterEngine<BamAlignmentChecker>::parseToken(token, uint16Value, type);
+ m_filterEngine.setProperty(filterName, propertyName, uint16Value, type);
+ }
+
+ // uint32_t conversion
+ else if ( propertyName == ALIGNMENTFLAG_PROPERTY )
+ {
+ FilterEngine<BamAlignmentChecker>::parseToken(token, uint32Value, type);
+ m_filterEngine.setProperty(filterName, propertyName, uint32Value, type);
+ }
+
+ // string conversion
+ else if ( propertyName == CIGAR_PROPERTY ||
+ propertyName == MATEREFERENCE_PROPERTY ||
+ propertyName == NAME_PROPERTY ||
+ propertyName == QUERYBASES_PROPERTY ||
+ propertyName == REFERENCE_PROPERTY
+ )
+ {
+ 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 << "bamtools filter ERROR: unknown property - " << propertyName << endl;
+ return false;
+ }
+ }
+ return true;
+}
+
+bool FilterTool::FilterToolPrivate::CheckAlignment(const BamAlignment& al) {
+ 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 << "bamtools filter ERROR: could not open script: "
+ << m_settings->ScriptFilename << " for reading" << endl;
+ return string();
+ }
+
+ // 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 << "bamtools filter ERROR: could not read script contents" << endl;
+ return string();
+ }
+
+ docStream << buffer;
+ }
+
+ // close script file
+ fclose(inFile);
+
+ // import buffer contents to document, return
+ 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(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(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(NAME_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<BamAlignmentChecker>
+ vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
+ vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
+ for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter )
+ m_filterEngine.addProperty((*propertyNameIter));
+}
+
+bool FilterTool::FilterToolPrivate::ParseCommandLine(void) {
+
+ // add a rule set to filter engine
+ const string CMD = "COMMAND_LINE";
+ m_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->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);
+}
+
+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
+ m_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 << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl
+ << reader.getFormatedErrorMessages();
+ return false;
+ }
+
+ // initialize return status
+ bool success = true;
+
+ // see if root object contains multiple filters
+ const Json::Value filters = root["filters"];
+ if ( !filters.isNull() ) {
+
+ // 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
+ string filterName;
+
+ // if id tag supplied
+ const Json::Value id = filter["id"];
+ if ( !id.isNull() )
+ filterName = id.asString();
+
+ // use array index
+ else {
+ stringstream convert;
+ convert << filterIndex;
+ filterName = convert.str();
+ }
+
+ // create & parse filter
+ success &= ParseFilterObject(filterName, filter);
+ }
+
+ // 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.isString() )
+ ruleString = rule.asString();
+ m_filterEngine.setRule(ruleString);
+
+ // return success/fail
+ return success;
+ }
+
+ // otherwise, root is the only filter (just contains properties)
+ // create & parse filter named "ROOT"
+ else success = ParseFilterObject("ROOT", root);
+
+ // return success/failure
+ return success;
+}
+
+bool FilterTool::FilterToolPrivate::Run(void) {
+
+ // set to default input if none provided
+ 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 false;
+
+ // open reader without index
+ BamMultiReader reader;
+ 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();
+ filterToolReferences = reader.GetReferenceData();
+
+ // 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;
+ 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) )
+ writer.SaveAlignment(al);
+ }
+ }
+
+ // otherwise attempt to use region as constraint
+ else {
+
+ // if region string parses OK
+ BamRegion region;
+ if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+
+ // 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 << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl;
+ reader.Close();
+ return false;
+ }
+
+ // everything checks out, just iterate through specified region, filtering alignments
+ 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.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 << "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 false;
+ }
+ }
+
+ // clean up & exit
+ reader.Close();
+ writer.Close();
+ return true;
+}
+
+bool FilterTool::FilterToolPrivate::SetupFilters(void) {
+
+ // set up filter engine with supported properties
+ InitProperties();
+
+ // parse script for filter rules, if given
+ 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
- Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", "-in <filename> [-in <filename> ... ] -out <filename> ");
-
- // set up options
+
+ 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");
- 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());
+
+ 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) {
}
int FilterTool::Run(int argc, char* argv[]) {
-
+
// parse command line arguments
Options::Parse(argc, argv, 1);
-
- // set to default input if none provided
- if ( !m_settings->HasInputBamFilename )
- m_settings->InputFiles.push_back(Options::StandardIn());
-
- // open files
- BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false);
-
- // do filtering
-
- // clean up & exit
- reader.Close();
- return 0;
-}
\ No newline at end of file
+
+ // 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