1 // ***************************************************************************
2 // bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 7 April 2011
7 // ---------------------------------------------------------------------------
8 // Filters BAM file(s) according to some user-specified criteria
9 // ***************************************************************************
11 #include "bamtools_filter.h"
13 #include <api/BamMultiReader.h>
14 #include <api/BamWriter.h>
15 #include <utils/bamtools_filter_engine.h>
16 #include <utils/bamtools_options.h>
17 #include <utils/bamtools_utilities.h>
18 using namespace BamTools;
20 #include <jsoncpp/json.h>
32 // -------------------------------
33 // string literal constants
36 const string ALIGNMENTFLAG_PROPERTY = "alignmentFlag";
37 const string CIGAR_PROPERTY = "cigar";
38 const string INSERTSIZE_PROPERTY = "insertSize";
39 const string ISDUPLICATE_PROPERTY = "isDuplicate";
40 const string ISFAILEDQC_PROPERTY = "isFailedQC";
41 const string ISFIRSTMATE_PROPERTY = "isFirstMate";
42 const string ISMAPPED_PROPERTY = "isMapped";
43 const string ISMATEMAPPED_PROPERTY = "isMateMapped";
44 const string ISMATEREVERSESTRAND_PROPERTY = "isMateReverseStrand";
45 const string ISPAIRED_PROPERTY = "isPaired";
46 const string ISPRIMARYALIGNMENT_PROPERTY = "isPrimaryAlignment";
47 const string ISPROPERPAIR_PROPERTY = "isProperPair";
48 const string ISREVERSESTRAND_PROPERTY = "isReverseStrand";
49 const string ISSECONDMATE_PROPERTY = "isSecondMate";
50 const string ISSINGLETON_PROPERTY = "isSingleton";
51 const string MAPQUALITY_PROPERTY = "mapQuality";
52 const string MATEPOSITION_PROPERTY = "matePosition";
53 const string MATEREFERENCE_PROPERTY = "mateReference";
54 const string NAME_PROPERTY = "name";
55 const string POSITION_PROPERTY = "position";
56 const string QUERYBASES_PROPERTY = "queryBases";
57 const string REFERENCE_PROPERTY = "reference";
58 const string TAG_PROPERTY = "tag";
61 const string TRUE_STR = "true";
62 const string FALSE_STR = "false";
64 RefVector filterToolReferences;
66 struct BamAlignmentChecker {
67 bool check(const PropertyFilter& filter, const BamAlignment& al) {
69 bool keepAlignment = true;
70 const PropertyMap& properties = filter.Properties;
71 PropertyMap::const_iterator propertyIter = properties.begin();
72 PropertyMap::const_iterator propertyEnd = properties.end();
73 for ( ; propertyIter != propertyEnd; ++propertyIter ) {
75 // check alignment data field depending on propertyName
76 const string& propertyName = (*propertyIter).first;
77 const PropertyFilterValue& valueFilter = (*propertyIter).second;
79 if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= valueFilter.check(al.AlignmentFlag);
80 else if ( propertyName == CIGAR_PROPERTY ) {
82 const vector<CigarOp>& cigarData = al.CigarData;
83 if ( !cigarData.empty() ) {
84 vector<CigarOp>::const_iterator cigarBegin = cigarData.begin();
85 vector<CigarOp>::const_iterator cigarIter = cigarBegin;
86 vector<CigarOp>::const_iterator cigarEnd = cigarData.end();
87 for ( ; cigarIter != cigarEnd; ++cigarIter ) {
88 const CigarOp& op = (*cigarIter);
89 cigarSs << op.Length << op.Type;
91 keepAlignment &= valueFilter.check(cigarSs.str());
94 else if ( propertyName == INSERTSIZE_PROPERTY ) keepAlignment &= valueFilter.check(al.InsertSize);
95 else if ( propertyName == ISDUPLICATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsDuplicate());
96 else if ( propertyName == ISFAILEDQC_PROPERTY ) keepAlignment &= valueFilter.check(al.IsFailedQC());
97 else if ( propertyName == ISFIRSTMATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsFirstMate());
98 else if ( propertyName == ISMAPPED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMapped());
99 else if ( propertyName == ISMATEMAPPED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMateMapped());
100 else if ( propertyName == ISMATEREVERSESTRAND_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMateReverseStrand());
101 else if ( propertyName == ISPAIRED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsPaired());
102 else if ( propertyName == ISPRIMARYALIGNMENT_PROPERTY ) keepAlignment &= valueFilter.check(al.IsPrimaryAlignment());
103 else if ( propertyName == ISPROPERPAIR_PROPERTY ) keepAlignment &= valueFilter.check(al.IsProperPair());
104 else if ( propertyName == ISREVERSESTRAND_PROPERTY ) keepAlignment &= valueFilter.check(al.IsReverseStrand());
105 else if ( propertyName == ISSECONDMATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsSecondMate());
106 else if ( propertyName == ISSINGLETON_PROPERTY ) {
107 const bool isSingleton = al.IsPaired() && al.IsMapped() && !al.IsMateMapped();
108 keepAlignment &= valueFilter.check(isSingleton);
110 else if ( propertyName == MAPQUALITY_PROPERTY ) keepAlignment &= valueFilter.check(al.MapQuality);
111 else if ( propertyName == MATEPOSITION_PROPERTY ) keepAlignment &= ( al.IsPaired() && al.IsMateMapped() && valueFilter.check(al.MateRefID) );
112 else if ( propertyName == MATEREFERENCE_PROPERTY ) {
113 if ( !al.IsPaired() || !al.IsMateMapped() ) return false;
114 BAMTOOLS_ASSERT_MESSAGE( (al.MateRefID>=0 && (al.MateRefID<(int)filterToolReferences.size())), "Invalid MateRefID");
115 const string& refName = filterToolReferences.at(al.MateRefID).RefName;
116 keepAlignment &= valueFilter.check(refName);
118 else if ( propertyName == NAME_PROPERTY ) keepAlignment &= valueFilter.check(al.Name);
119 else if ( propertyName == POSITION_PROPERTY ) keepAlignment &= valueFilter.check(al.Position);
120 else if ( propertyName == QUERYBASES_PROPERTY ) keepAlignment &= valueFilter.check(al.QueryBases);
121 else if ( propertyName == REFERENCE_PROPERTY ) {
122 BAMTOOLS_ASSERT_MESSAGE( (al.RefID>=0 && (al.RefID<(int)filterToolReferences.size())), "Invalid RefID");
123 const string& refName = filterToolReferences.at(al.RefID).RefName;
124 keepAlignment &= valueFilter.check(refName);
126 else if ( propertyName == TAG_PROPERTY ) keepAlignment &= checkAlignmentTag(valueFilter, al);
127 else BAMTOOLS_ASSERT_UNREACHABLE;
129 // if alignment fails at ANY point, just quit and return false
130 if ( !keepAlignment ) return false;
133 BAMTOOLS_ASSERT_MESSAGE( keepAlignment, "Error in BamAlignmentChecker... keepAlignment should be true here");
134 return keepAlignment;
137 bool checkAlignmentTag(const PropertyFilterValue& valueFilter, const BamAlignment& al) {
139 // ensure filter contains string data
140 Variant entireTagFilter = valueFilter.Value;
141 if ( !entireTagFilter.is_type<string>() ) return false;
143 // localize string from variant
144 const string& entireTagFilterString = entireTagFilter.get<string>();
146 // ensure we have at least "XX:x"
147 if ( entireTagFilterString.length() < 4 ) return false;
149 // get tagName & lookup in alignment
150 // if found, set tagType to tag type character
151 // if not found, return false
152 const string& tagName = entireTagFilterString.substr(0,2);
154 if ( !al.GetTagType(tagName, tagType) ) return false;
156 // remove tagName & ":" from beginning tagFilter
157 string tagFilterString = entireTagFilterString.substr(3);
159 // switch on tag type to set tag query value & parse filter token
160 int32_t intFilterValue, intQueryValue;
161 uint32_t uintFilterValue, uintQueryValue;
162 float realFilterValue, realQueryValue;
163 string stringFilterValue, stringQueryValue;
165 PropertyFilterValue tagFilter;
166 PropertyFilterValue::ValueCompareType compareType;
167 bool keepAlignment = false;
170 // signed int tag type
174 if ( al.GetTag(tagName, intQueryValue) ) {
175 if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, intFilterValue, compareType) ) {
176 tagFilter.Value = intFilterValue;
177 tagFilter.Type = compareType;
178 keepAlignment = tagFilter.check(intQueryValue);
183 // unsigned int tag type
187 if ( al.GetTag(tagName, uintQueryValue) ) {
188 if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, uintFilterValue, compareType) ) {
189 tagFilter.Value = uintFilterValue;
190 tagFilter.Type = compareType;
191 keepAlignment = tagFilter.check(uintQueryValue);
198 if ( al.GetTag(tagName, realQueryValue) ) {
199 if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, realFilterValue, compareType) ) {
200 tagFilter.Value = realFilterValue;
201 tagFilter.Type = compareType;
202 keepAlignment = tagFilter.check(realQueryValue);
211 if ( al.GetTag(tagName, stringQueryValue) ) {
212 if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, stringFilterValue, compareType) ) {
213 tagFilter.Value = stringFilterValue;
214 tagFilter.Type = compareType;
215 keepAlignment = tagFilter.check(stringQueryValue);
222 keepAlignment = false;
225 return keepAlignment;
229 } // namespace BamTools
231 // ---------------------------------------------
232 // FilterSettings implementation
234 struct FilterTool::FilterSettings {
236 // ----------------------------------
240 bool HasInputBamFilename;
241 bool HasOutputBamFilename;
243 bool HasScriptFilename;
244 bool IsForceCompression;
247 vector<string> InputFiles;
248 string OutputFilename;
250 string ScriptFilename;
252 // -----------------------------------
253 // General filter opts
256 bool HasAlignmentFlagFilter;
257 bool HasInsertSizeFilter;
258 bool HasMapQualityFilter;
260 bool HasQueryBasesFilter;
261 bool HasTagFilter; //(s)
264 string AlignmentFlagFilter;
265 string InsertSizeFilter;
267 string MapQualityFilter;
268 string QueryBasesFilter;
269 string TagFilter; // support multiple ?
271 // -----------------------------------
272 // AlignmentFlag filter opts
275 bool HasIsDuplicateFilter;
276 bool HasIsFailedQCFilter;
277 bool HasIsFirstMateFilter;
278 bool HasIsMappedFilter;
279 bool HasIsMateMappedFilter;
280 bool HasIsMateReverseStrandFilter;
281 bool HasIsPairedFilter;
282 bool HasIsPrimaryAlignmentFilter;
283 bool HasIsProperPairFilter;
284 bool HasIsReverseStrandFilter;
285 bool HasIsSecondMateFilter;
286 bool HasIsSingletonFilter;
289 string IsDuplicateFilter;
290 string IsFailedQCFilter;
291 string IsFirstMateFilter;
292 string IsMappedFilter;
293 string IsMateMappedFilter;
294 string IsMateReverseStrandFilter;
295 string IsPairedFilter;
296 string IsPrimaryAlignmentFilter;
297 string IsProperPairFilter;
298 string IsReverseStrandFilter;
299 string IsSecondMateFilter;
300 string IsSingletonFilter;
302 // ---------------------------------
306 : HasInputBamFilename(false)
307 , HasOutputBamFilename(false)
309 , HasScriptFilename(false)
310 , IsForceCompression(false)
311 , OutputFilename(Options::StandardOut())
312 , HasAlignmentFlagFilter(false)
313 , HasInsertSizeFilter(false)
314 , HasMapQualityFilter(false)
315 , HasNameFilter(false)
316 , HasQueryBasesFilter(false)
317 , HasTagFilter(false)
318 , HasIsDuplicateFilter(false)
319 , HasIsFailedQCFilter(false)
320 , HasIsFirstMateFilter(false)
321 , HasIsMappedFilter(false)
322 , HasIsMateMappedFilter(false)
323 , HasIsMateReverseStrandFilter(false)
324 , HasIsPairedFilter(false)
325 , HasIsPrimaryAlignmentFilter(false)
326 , HasIsProperPairFilter(false)
327 , HasIsReverseStrandFilter(false)
328 , HasIsSecondMateFilter(false)
329 , HasIsSingletonFilter(false)
330 , IsDuplicateFilter(TRUE_STR)
331 , IsFailedQCFilter(TRUE_STR)
332 , IsFirstMateFilter(TRUE_STR)
333 , IsMappedFilter(TRUE_STR)
334 , IsMateMappedFilter(TRUE_STR)
335 , IsMateReverseStrandFilter(TRUE_STR)
336 , IsPairedFilter(TRUE_STR)
337 , IsPrimaryAlignmentFilter(TRUE_STR)
338 , IsProperPairFilter(TRUE_STR)
339 , IsReverseStrandFilter(TRUE_STR)
340 , IsSecondMateFilter(TRUE_STR)
341 , IsSingletonFilter(TRUE_STR)
345 // ---------------------------------------------
346 // FilterToolPrivate declaration
348 class FilterTool::FilterToolPrivate {
352 FilterToolPrivate(FilterTool::FilterSettings* settings);
353 ~FilterToolPrivate(void);
355 // 'public' interface
361 bool AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens);
362 bool CheckAlignment(const BamAlignment& al);
363 const string GetScriptContents(void);
364 void InitProperties(void);
365 bool ParseCommandLine(void);
366 bool ParseFilterObject(const string& filterName, const Json::Value& filterObject);
367 bool ParseScript(void);
368 bool SetupFilters(void);
372 vector<string> m_propertyNames;
373 FilterTool::FilterSettings* m_settings;
374 FilterEngine<BamAlignmentChecker> m_filterEngine;
377 // ---------------------------------------------
378 // FilterToolPrivate implementation
381 FilterTool::FilterToolPrivate::FilterToolPrivate(FilterTool::FilterSettings* settings)
382 : m_settings(settings)
386 FilterTool::FilterToolPrivate::~FilterToolPrivate(void) { }
388 bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName,
390 string>& propertyTokens)
392 // dummy temp values for token parsing
395 uint16_t uint16Value;
396 uint32_t uint32Value;
398 PropertyFilterValue::ValueCompareType type;
400 // iterate over property token map
401 map<string, string>::const_iterator mapIter = propertyTokens.begin();
402 map<string, string>::const_iterator mapEnd = propertyTokens.end();
403 for ( ; mapIter != mapEnd; ++mapIter ) {
405 const string& propertyName = (*mapIter).first;
406 const string& token = (*mapIter).second;
408 // ------------------------------
409 // convert token to value & compare type
410 // then add to filter engine
413 if ( propertyName == ISDUPLICATE_PROPERTY ||
414 propertyName == ISFAILEDQC_PROPERTY ||
415 propertyName == ISFIRSTMATE_PROPERTY ||
416 propertyName == ISMAPPED_PROPERTY ||
417 propertyName == ISMATEMAPPED_PROPERTY ||
418 propertyName == ISMATEREVERSESTRAND_PROPERTY ||
419 propertyName == ISPAIRED_PROPERTY ||
420 propertyName == ISPRIMARYALIGNMENT_PROPERTY ||
421 propertyName == ISPROPERPAIR_PROPERTY ||
422 propertyName == ISREVERSESTRAND_PROPERTY ||
423 propertyName == ISSECONDMATE_PROPERTY ||
424 propertyName == ISSINGLETON_PROPERTY
427 FilterEngine<BamAlignmentChecker>::parseToken(token, boolValue, type);
428 m_filterEngine.setProperty(filterName, propertyName, boolValue, type);
431 // int32_t conversion
432 else if ( propertyName == INSERTSIZE_PROPERTY ||
433 propertyName == MATEPOSITION_PROPERTY ||
434 propertyName == POSITION_PROPERTY
437 FilterEngine<BamAlignmentChecker>::parseToken(token, int32Value, type);
438 m_filterEngine.setProperty(filterName, propertyName, int32Value, type);
441 // uint16_t conversion
442 else if ( propertyName == MAPQUALITY_PROPERTY )
444 FilterEngine<BamAlignmentChecker>::parseToken(token, uint16Value, type);
445 m_filterEngine.setProperty(filterName, propertyName, uint16Value, type);
448 // uint32_t conversion
449 else if ( propertyName == ALIGNMENTFLAG_PROPERTY )
451 FilterEngine<BamAlignmentChecker>::parseToken(token, uint32Value, type);
452 m_filterEngine.setProperty(filterName, propertyName, uint32Value, type);
456 else if ( propertyName == CIGAR_PROPERTY ||
457 propertyName == MATEREFERENCE_PROPERTY ||
458 propertyName == NAME_PROPERTY ||
459 propertyName == QUERYBASES_PROPERTY ||
460 propertyName == REFERENCE_PROPERTY
463 FilterEngine<BamAlignmentChecker>::parseToken(token, stringValue, type);
464 m_filterEngine.setProperty(filterName, propertyName, stringValue, type);
467 else if ( propertyName == TAG_PROPERTY ) {
468 // this will be stored directly as the TAG:VALUE token
469 // (VALUE may contain compare ops, will be parsed out later)
470 m_filterEngine.setProperty(filterName, propertyName, token, PropertyFilterValue::EXACT);
473 // else unknown property
475 cerr << "bamtools filter ERROR: unknown property - " << propertyName << endl;
482 bool FilterTool::FilterToolPrivate::CheckAlignment(const BamAlignment& al) {
483 return m_filterEngine.check(al);
486 const string FilterTool::FilterToolPrivate::GetScriptContents(void) {
488 // open script for reading
489 FILE* inFile = fopen(m_settings->ScriptFilename.c_str(), "rb");
491 cerr << "bamtools filter ERROR: could not open script: "
492 << m_settings->ScriptFilename << " for reading" << endl;
496 // read in entire script contents
498 ostringstream docStream("");
501 // peek ahead, make sure there is data available
502 char ch = fgetc(inFile);
504 if( feof(inFile) ) break;
506 // read next block of data
507 if ( fgets(buffer, 1024, inFile) == 0 ) {
508 cerr << "bamtools filter ERROR: could not read script contents" << endl;
518 // import buffer contents to document, return
519 string document = docStream.str();
523 void FilterTool::FilterToolPrivate::InitProperties(void) {
525 // store property names in vector
526 m_propertyNames.push_back(ALIGNMENTFLAG_PROPERTY);
527 m_propertyNames.push_back(CIGAR_PROPERTY);
528 m_propertyNames.push_back(INSERTSIZE_PROPERTY);
529 m_propertyNames.push_back(ISDUPLICATE_PROPERTY);
530 m_propertyNames.push_back(ISFAILEDQC_PROPERTY);
531 m_propertyNames.push_back(ISFIRSTMATE_PROPERTY);
532 m_propertyNames.push_back(ISMAPPED_PROPERTY);
533 m_propertyNames.push_back(ISMATEMAPPED_PROPERTY);
534 m_propertyNames.push_back(ISMATEREVERSESTRAND_PROPERTY);
535 m_propertyNames.push_back(ISPAIRED_PROPERTY);
536 m_propertyNames.push_back(ISPRIMARYALIGNMENT_PROPERTY);
537 m_propertyNames.push_back(ISPROPERPAIR_PROPERTY);
538 m_propertyNames.push_back(ISREVERSESTRAND_PROPERTY);
539 m_propertyNames.push_back(ISSECONDMATE_PROPERTY);
540 m_propertyNames.push_back(ISSINGLETON_PROPERTY);
541 m_propertyNames.push_back(MAPQUALITY_PROPERTY);
542 m_propertyNames.push_back(MATEPOSITION_PROPERTY);
543 m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
544 m_propertyNames.push_back(NAME_PROPERTY);
545 m_propertyNames.push_back(POSITION_PROPERTY);
546 m_propertyNames.push_back(QUERYBASES_PROPERTY);
547 m_propertyNames.push_back(REFERENCE_PROPERTY);
548 m_propertyNames.push_back(TAG_PROPERTY);
550 // add vector contents to FilterEngine<BamAlignmentChecker>
551 vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
552 vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
553 for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter )
554 m_filterEngine.addProperty((*propertyNameIter));
557 bool FilterTool::FilterToolPrivate::ParseCommandLine(void) {
559 // add a rule set to filter engine
560 const string CMD = "COMMAND_LINE";
561 m_filterEngine.addFilter(CMD);
563 // map property names to command line args
564 map<string, string> propertyTokens;
565 if ( m_settings->HasAlignmentFlagFilter ) propertyTokens.insert( make_pair(ALIGNMENTFLAG_PROPERTY, m_settings->AlignmentFlagFilter) );
566 if ( m_settings->HasInsertSizeFilter ) propertyTokens.insert( make_pair(INSERTSIZE_PROPERTY, m_settings->InsertSizeFilter) );
567 if ( m_settings->HasIsDuplicateFilter ) propertyTokens.insert( make_pair(ISDUPLICATE_PROPERTY, m_settings->IsDuplicateFilter) );
568 if ( m_settings->HasIsFailedQCFilter ) propertyTokens.insert( make_pair(ISFAILEDQC_PROPERTY, m_settings->IsFailedQCFilter) );
569 if ( m_settings->HasIsFirstMateFilter ) propertyTokens.insert( make_pair(ISFIRSTMATE_PROPERTY, m_settings->IsFirstMateFilter) );
570 if ( m_settings->HasIsMappedFilter ) propertyTokens.insert( make_pair(ISMAPPED_PROPERTY, m_settings->IsMappedFilter) );
571 if ( m_settings->HasIsMateMappedFilter ) propertyTokens.insert( make_pair(ISMATEMAPPED_PROPERTY, m_settings->IsMateMappedFilter) );
572 if ( m_settings->HasIsMateReverseStrandFilter ) propertyTokens.insert( make_pair(ISMATEREVERSESTRAND_PROPERTY, m_settings->IsMateReverseStrandFilter) );
573 if ( m_settings->HasIsPairedFilter ) propertyTokens.insert( make_pair(ISPAIRED_PROPERTY, m_settings->IsPairedFilter) );
574 if ( m_settings->HasIsPrimaryAlignmentFilter ) propertyTokens.insert( make_pair(ISPRIMARYALIGNMENT_PROPERTY, m_settings->IsPrimaryAlignmentFilter) );
575 if ( m_settings->HasIsProperPairFilter ) propertyTokens.insert( make_pair(ISPROPERPAIR_PROPERTY, m_settings->IsProperPairFilter) );
576 if ( m_settings->HasIsReverseStrandFilter ) propertyTokens.insert( make_pair(ISREVERSESTRAND_PROPERTY, m_settings->IsReverseStrandFilter) );
577 if ( m_settings->HasIsSecondMateFilter ) propertyTokens.insert( make_pair(ISSECONDMATE_PROPERTY, m_settings->IsSecondMateFilter) );
578 if ( m_settings->HasIsSingletonFilter ) propertyTokens.insert( make_pair(ISSINGLETON_PROPERTY, m_settings->IsSingletonFilter) );
579 if ( m_settings->HasMapQualityFilter ) propertyTokens.insert( make_pair(MAPQUALITY_PROPERTY, m_settings->MapQualityFilter) );
580 if ( m_settings->HasNameFilter ) propertyTokens.insert( make_pair(NAME_PROPERTY, m_settings->NameFilter) );
581 if ( m_settings->HasQueryBasesFilter ) propertyTokens.insert( make_pair(QUERYBASES_PROPERTY, m_settings->QueryBasesFilter) );
582 if ( m_settings->HasTagFilter ) propertyTokens.insert( make_pair(TAG_PROPERTY, m_settings->TagFilter) );
584 // send add these properties to filter set "COMMAND_LINE"
585 return AddPropertyTokensToFilter(CMD, propertyTokens);
588 bool FilterTool::FilterToolPrivate::ParseFilterObject(const string& filterName, const Json::Value& filterObject) {
590 // filter object parsing variables
591 Json::Value null(Json::nullValue);
592 Json::Value propertyValue;
595 map<string, string> propertyTokens;
597 // iterate over known properties
598 vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
599 vector<string>::const_iterator propertyNameEnd = m_propertyNames.end();
600 for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter ) {
601 const string& propertyName = (*propertyNameIter);
603 // if property defined in filter, add to token list
604 propertyValue = filterObject.get(propertyName, null);
605 if ( propertyValue != null )
606 propertyTokens.insert( make_pair(propertyName, propertyValue.asString()) );
609 // add this filter to engin
610 m_filterEngine.addFilter(filterName);
612 // add token list to this filter
613 return AddPropertyTokensToFilter(filterName, propertyTokens);
616 bool FilterTool::FilterToolPrivate::ParseScript(void) {
618 // read in script contents from file
619 const string document = GetScriptContents();
621 // set up JsonCPP reader and attempt to parse script
624 if ( !reader.parse(document, root) ) {
625 // use built-in error reporting mechanism to alert user what was wrong with the script
626 cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl
627 << reader.getFormatedErrorMessages();
631 // initialize return status
634 // see if root object contains multiple filters
635 const Json::Value filters = root["filters"];
636 if ( !filters.isNull() ) {
638 // iterate over any filters found
640 Json::Value::const_iterator filtersIter = filters.begin();
641 Json::Value::const_iterator filtersEnd = filters.end();
642 for ( ; filtersIter != filtersEnd; ++filtersIter, ++filterIndex ) {
643 Json::Value filter = (*filtersIter);
645 // convert filter index to string
648 // if id tag supplied
649 const Json::Value id = filter["id"];
651 filterName = id.asString();
655 stringstream convert;
656 convert << filterIndex;
657 filterName = convert.str();
660 // create & parse filter
661 success &= ParseFilterObject(filterName, filter);
664 // see if user defined a "rule" for these filters
665 // otherwise, use filter engine's default rule behavior
666 string ruleString("");
667 const Json::Value rule = root["rule"];
668 if ( rule.isString() )
669 ruleString = rule.asString();
670 m_filterEngine.setRule(ruleString);
672 // return success/fail
676 // otherwise, root is the only filter (just contains properties)
677 // create & parse filter named "ROOT"
678 else success = ParseFilterObject("ROOT", root);
680 // return success/failure
684 bool FilterTool::FilterToolPrivate::Run(void) {
686 // set to default input if none provided
687 if ( !m_settings->HasInputBamFilename )
688 m_settings->InputFiles.push_back(Options::StandardIn());
690 // initialize defined properties & user-specified filters
692 if ( !SetupFilters() ) return false;
694 // open reader without index
695 BamMultiReader reader;
696 if ( !reader.Open(m_settings->InputFiles) ) {
697 cerr << "bamtools filter ERROR: could not open input files for reading." << endl;
701 // retrieve reader header & reference data
702 const string headerText = reader.GetHeaderText();
703 filterToolReferences = reader.GetReferenceData();
705 // determine compression mode for BamWriter
706 bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
707 !m_settings->IsForceCompression );
708 BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
709 if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
713 writer.SetCompressionMode(compressionMode);
714 if ( !writer.Open(m_settings->OutputFilename, headerText, filterToolReferences) ) {
715 cerr << "bamtools filter ERROR: could not open " << m_settings->OutputFilename << " for writing." << endl;
720 // if no region specified, filter entire file
722 if ( !m_settings->HasRegion ) {
723 while ( reader.GetNextAlignment(al) ) {
724 if ( CheckAlignment(al) )
725 writer.SaveAlignment(al);
729 // otherwise attempt to use region as constraint
732 // if region string parses OK
734 if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
736 // attempt to find index files
737 reader.LocateIndexes();
739 // if index data available for all BAM files, we can use SetRegion
740 if ( reader.HasIndexes() ) {
742 // attempt to use SetRegion(), if failed report error
743 if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
744 cerr << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl;
749 // everything checks out, just iterate through specified region, filtering alignments
750 while ( reader.GetNextAlignment(al) )
751 if ( CheckAlignment(al) )
752 writer.SaveAlignment(al);
755 // no index data available, we have to iterate through until we
756 // find overlapping alignments
758 while ( reader.GetNextAlignment(al) ) {
759 if ( (al.RefID >= region.LeftRefID) && ((al.Position + al.Length) >= region.LeftPosition) &&
760 (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
762 if ( CheckAlignment(al) )
763 writer.SaveAlignment(al);
769 // error parsing REGION string
771 cerr << "bamtools filter ERROR: could not parse REGION: " << m_settings->Region << endl;
772 cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
785 bool FilterTool::FilterToolPrivate::SetupFilters(void) {
787 // set up filter engine with supported properties
790 // parse script for filter rules, if given
791 if ( m_settings->HasScriptFilename )
792 return ParseScript();
794 // otherwise check command line for filters
795 else return ParseCommandLine();
798 // ---------------------------------------------
799 // FilterTool implementation
801 FilterTool::FilterTool(void)
803 , m_settings(new FilterSettings)
806 // ----------------------------------
807 // set program details
809 const string usage = "[-in <filename> -in <filename> ...] "
810 "[-out <filename> | [-forceCompression]] [-region <REGION>] "
811 "[ [-script <filename] | [filterOptions] ]";
812 Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", usage );
814 // ----------------------------------
817 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
819 const string inDesc = "the input BAM file(s)";
820 const string outDesc = "the output BAM file";
821 const string regionDesc = "only read data from this genomic region (see documentation for more details)";
822 const string scriptDesc = "the filter script file (see documentation for more details)";
823 const string forceDesc = "if results are sent to stdout (like when piping to another tool), "
824 "default behavior is to leave output uncompressed. Use this flag to "
825 "override and force compression";
827 Options::AddValueOption("-in", "BAM filename", inDesc, "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
828 Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
829 Options::AddValueOption("-region", "REGION", regionDesc, "", m_settings->HasRegion, m_settings->Region, IO_Opts);
830 Options::AddValueOption("-script", "filename", scriptDesc, "", m_settings->HasScriptFilename, m_settings->ScriptFilename, IO_Opts);
831 Options::AddOption("-forceCompression",forceDesc, m_settings->IsForceCompression, IO_Opts);
833 // ----------------------------------
834 // general filter options
836 OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters");
838 const string flagDesc = "keep reads with this *exact* alignment flag (for more detailed queries, see below)";
839 const string insertDesc = "keep reads with insert size that matches pattern";
840 const string mapQualDesc = "keep reads with map quality that matches pattern";
841 const string nameDesc = "keep reads with name that matches pattern";
842 const string queryDesc = "keep reads with motif that matches pattern";
843 const string tagDesc = "keep reads with this key=>value pair";
845 Options::AddValueOption("-alignmentFlag", "int", flagDesc, "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
846 Options::AddValueOption("-insertSize", "int", insertDesc, "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts);
847 Options::AddValueOption("-mapQuality", "[0-255]", mapQualDesc, "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts);
848 Options::AddValueOption("-name", "string", nameDesc, "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts);
849 Options::AddValueOption("-queryBases", "string", queryDesc, "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts);
850 Options::AddValueOption("-tag", "TAG:VALUE", tagDesc, "", m_settings->HasTagFilter, m_settings->TagFilter, FilterOpts);
852 // ----------------------------------
853 // alignment flag filter options
855 OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters");
857 const string boolArg = "true/false";
858 const string isDupDesc = "keep only alignments that are marked as duplicate?";
859 const string isFailQcDesc = "keep only alignments that failed QC?";
860 const string isFirstMateDesc = "keep only alignments marked as first mate?";
861 const string isMappedDesc = "keep only alignments that were mapped?";
862 const string isMateMappedDesc = "keep only alignments with mates that mapped";
863 const string isMateReverseDesc = "keep only alignments with mate on reverese strand?";
864 const string isPairedDesc = "keep only alignments that were sequenced as paired?";
865 const string isPrimaryDesc = "keep only alignments marked as primary?";
866 const string isProperPairDesc = "keep only alignments that passed PE resolution?";
867 const string isReverseDesc = "keep only alignments on reverse strand?";
868 const string isSecondMateDesc = "keep only alignments marked as second mate?";
869 const string isSingletonDesc = "keep only singletons";
871 Options::AddValueOption("-isDuplicate", boolArg, isDupDesc, "", m_settings->HasIsDuplicateFilter, m_settings->IsDuplicateFilter, AlignmentFlagOpts, TRUE_STR);
872 Options::AddValueOption("-isFailedQC", boolArg, isFailQcDesc, "", m_settings->HasIsFailedQCFilter, m_settings->IsFailedQCFilter, AlignmentFlagOpts, TRUE_STR);
873 Options::AddValueOption("-isFirstMate", boolArg, isFirstMateDesc, "", m_settings->HasIsFirstMateFilter, m_settings->IsFirstMateFilter, AlignmentFlagOpts, TRUE_STR);
874 Options::AddValueOption("-isMapped", boolArg, isMappedDesc, "", m_settings->HasIsMappedFilter, m_settings->IsMappedFilter, AlignmentFlagOpts, TRUE_STR);
875 Options::AddValueOption("-isMateMapped", boolArg, isMateMappedDesc, "", m_settings->HasIsMateMappedFilter, m_settings->IsMateMappedFilter, AlignmentFlagOpts, TRUE_STR);
876 Options::AddValueOption("-isMateReverseStrand", boolArg, isMateReverseDesc, "", m_settings->HasIsMateReverseStrandFilter, m_settings->IsMateReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
877 Options::AddValueOption("-isPaired", boolArg, isPairedDesc, "", m_settings->HasIsPairedFilter, m_settings->IsPairedFilter, AlignmentFlagOpts, TRUE_STR);
878 Options::AddValueOption("-isPrimaryAlignment", boolArg, isPrimaryDesc, "", m_settings->HasIsPrimaryAlignmentFilter, m_settings->IsPrimaryAlignmentFilter, AlignmentFlagOpts, TRUE_STR);
879 Options::AddValueOption("-isProperPair", boolArg, isProperPairDesc, "", m_settings->HasIsProperPairFilter, m_settings->IsProperPairFilter, AlignmentFlagOpts, TRUE_STR);
880 Options::AddValueOption("-isReverseStrand", boolArg, isReverseDesc, "", m_settings->HasIsReverseStrandFilter, m_settings->IsReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
881 Options::AddValueOption("-isSecondMate", boolArg, isSecondMateDesc, "", m_settings->HasIsSecondMateFilter, m_settings->IsSecondMateFilter, AlignmentFlagOpts, TRUE_STR);
882 Options::AddValueOption("-isSingleton", boolArg, isSingletonDesc, "", m_settings->HasIsSingletonFilter, m_settings->IsSingletonFilter, AlignmentFlagOpts, TRUE_STR);
885 FilterTool::~FilterTool(void) {
894 int FilterTool::Help(void) {
895 Options::DisplayHelp();
899 int FilterTool::Run(int argc, char* argv[]) {
901 // parse command line arguments
902 Options::Parse(argc, argv, 1);
904 // initialize FilterTool with settings
905 m_impl = new FilterToolPrivate(m_settings);
907 // run FilterTool, return success/fail