X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Ftoolkit%2Fbamtools_filter.cpp;h=023fbc99d053f15ef217d9903cba7714255b340f;hb=8c80d760637f8df39262683cd2570f0589423d36;hp=59e89dd9e59d7c1f7bf3d3d8c94d9b8fa85763bf;hpb=8807d4776b73d173b10cf6fb77ccbf485d270597;p=bamtools.git diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp index 59e89dd..023fbc9 100644 --- a/src/toolkit/bamtools_filter.cpp +++ b/src/toolkit/bamtools_filter.cpp @@ -3,27 +3,29 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 21 September 2010 +// Last modified: 21 March 2011 // --------------------------------------------------------------------------- // Filters BAM file(s) according to some user-specified criteria. // *************************************************************************** +#include "bamtools_filter.h" + +#include +#include +#include +#include +#include +using namespace BamTools; + +#include +using namespace Json; + #include #include #include #include #include -#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" -#include "jsoncpp/json.h" using namespace std; -using namespace BamTools; -using namespace Json; namespace BamTools { @@ -32,6 +34,7 @@ namespace BamTools { // property names const string ALIGNMENTFLAG_PROPERTY = "alignmentFlag"; +const string CIGAR_PROPERTY = "cigar"; const string INSERTSIZE_PROPERTY = "insertSize"; const string ISDUPLICATE_PROPERTY = "isDuplicate"; const string ISFAILEDQC_PROPERTY = "isFailedQC"; @@ -51,7 +54,7 @@ const string NAME_PROPERTY = "name"; const string POSITION_PROPERTY = "position"; const string QUERYBASES_PROPERTY = "queryBases"; const string REFERENCE_PROPERTY = "reference"; -const string CIGAR_PROPERTY = "cigar"; +const string TAG_PROPERTY = "tag"; // boolalpha const string TRUE_STR = "true"; @@ -72,7 +75,21 @@ struct BamAlignmentChecker { const string& propertyName = (*propertyIter).first; const PropertyFilterValue& valueFilter = (*propertyIter).second; - if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= valueFilter.check(al.AlignmentFlag); + if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= valueFilter.check(al.AlignmentFlag); + else if ( propertyName == CIGAR_PROPERTY ) { + stringstream cigarSs; + const vector& cigarData = al.CigarData; + if ( !cigarData.empty() ) { + vector::const_iterator cigarBegin = cigarData.begin(); + vector::const_iterator cigarIter = cigarBegin; + vector::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()); @@ -101,31 +118,108 @@ struct BamAlignmentChecker { const string& refName = filterToolReferences.at(al.RefID).RefName; keepAlignment &= valueFilter.check(refName); } - else if ( propertyName == CIGAR_PROPERTY ) { - stringstream cigarSs; - const vector& cigarData = al.CigarData; - if ( !cigarData.empty() ) { - vector::const_iterator cigarBegin = cigarData.begin(); - vector::const_iterator cigarIter = cigarBegin; - vector::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 == 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; + 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() ) return false; + + // localize string from variant + const string& entireTagFilterString = entireTagFilter.get(); + + // 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 + int32_t intFilterValue, intQueryValue; + uint32_t uintFilterValue, uintQueryValue; + float realFilterValue, realQueryValue; + string stringFilterValue, stringQueryValue; + + PropertyFilterValue tagFilter; + PropertyFilterValue::ValueCompareType compareType; + bool keepAlignment = false; + switch (tagType) { + + // signed int tag type + case 'c' : + case 's' : + case 'i' : + if ( al.GetTag(tagName, intQueryValue) ) { + if ( FilterEngine::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::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::parseToken(tagFilterString, realFilterValue, compareType) ) { + tagFilter.Value = realFilterValue; + tagFilter.Type = compareType; + keepAlignment = tagFilter.check(realQueryValue); + } + } + break; + + // string tag type + case 'A': + case 'Z': + case 'H': + if ( al.GetTag(tagName, stringQueryValue) ) { + if ( FilterEngine::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 @@ -191,8 +285,7 @@ struct FilterTool::FilterSettings { bool HasMapQualityFilter; bool HasNameFilter; bool HasQueryBasesFilter; - -// bool HasTagFilters; + bool HasTagFilter; //(s) // filters string AlignmentFlagFilter; @@ -200,8 +293,7 @@ struct FilterTool::FilterSettings { string NameFilter; string MapQualityFilter; string QueryBasesFilter; - -// vector TagFilters; + string TagFilter; // support multiple ? // ----------------------------------- // AlignmentFlag filter opts @@ -247,7 +339,7 @@ struct FilterTool::FilterSettings { , HasMapQualityFilter(false) , HasNameFilter(false) , HasQueryBasesFilter(false) -// , HasTagFilters(false) + , HasTagFilter(false) , HasIsDuplicateFilter(false) , HasIsFailedQCFilter(false) , HasIsFirstMateFilter(false) @@ -282,23 +374,22 @@ FilterTool::FilterTool(void) , m_impl(0) { // set program details - Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", "-in [-in ... ] -out -region [ [-script -in ...] [-out | [-forceCompression]] [-region ] [ [-script HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn()); Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut()); - Options::AddValueOption("-region", "REGION", "only read data from this genomic region (see README for more details)", "", m_settings->HasRegion, m_settings->Region, IO_Opts); - Options::AddValueOption("-script", "filename", "the filter script file (see README for more details)", "", m_settings->HasScriptFilename, m_settings->ScriptFilename, IO_Opts); + Options::AddValueOption("-region", "REGION", "only read data from this genomic region (see documentation for more details)", "", m_settings->HasRegion, m_settings->Region, IO_Opts); + Options::AddValueOption("-script", "filename", "the filter script file (see documentation for more details)", "", m_settings->HasScriptFilename, m_settings->ScriptFilename, IO_Opts); Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts); OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters"); - Options::AddValueOption("-alignmentFlag", "int", "keep reads with this *exact* alignment flag (for more detailed queries, see below)", "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts); - Options::AddValueOption("-insertSize", "int", "keep reads with insert size that mathces pattern", "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts); - Options::AddValueOption("-mapQuality", "[0-255]", "keep reads with map quality that matches pattern", "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts); - Options::AddValueOption("-name", "string", "keep reads with name that matches pattern", "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts); - Options::AddValueOption("-queryBases", "string", "keep reads with motif that mathces pattern", "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts); - -// Options::AddValueOption("-tag", "TAG:VALUE", "keep reads with this key=>value pair. If multiple tags are given, reads must match all", "", m_settings->HasTagFilters, m_settings->TagFilters, FilterOpts); + Options::AddValueOption("-alignmentFlag", "int", "keep reads with this *exact* alignment flag (for more detailed queries, see below)", "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts); + Options::AddValueOption("-insertSize", "int", "keep reads with insert size that mathces pattern", "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts); + Options::AddValueOption("-mapQuality", "[0-255]", "keep reads with map quality that matches pattern", "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts); + Options::AddValueOption("-name", "string", "keep reads with name that matches pattern", "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts); + Options::AddValueOption("-queryBases", "string", "keep reads with motif that mathces pattern", "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts); + Options::AddValueOption("-tag", "TAG:VALUE", "keep reads with this key=>value pair", "", m_settings->HasTagFilter, m_settings->TagFilter, FilterOpts); OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters"); Options::AddValueOption("-isDuplicate", "true/false", "keep only alignments that are marked as duplicate?", "", m_settings->HasIsDuplicateFilter, m_settings->IsDuplicateFilter, AlignmentFlagOpts, TRUE_STR); @@ -350,8 +441,10 @@ FilterTool::FilterToolPrivate::FilterToolPrivate(FilterTool::FilterSettings* set // destructor FilterTool::FilterToolPrivate::~FilterToolPrivate(void) { } -bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName, const map& propertyTokens) { - +bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName, + const map& propertyTokens) +{ // dummy temp values for token parsing bool boolValue; int32_t int32Value; @@ -386,7 +479,7 @@ bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filt propertyName == ISSECONDMATE_PROPERTY ) { - m_filterEngine.parseToken(token, boolValue, type); + FilterEngine::parseToken(token, boolValue, type); m_filterEngine.setProperty(filterName, propertyName, boolValue, type); } @@ -396,39 +489,45 @@ bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filt propertyName == POSITION_PROPERTY ) { - m_filterEngine.parseToken(token, int32Value, type); + FilterEngine::parseToken(token, int32Value, type); m_filterEngine.setProperty(filterName, propertyName, int32Value, type); } // uint16_t conversion else if ( propertyName == MAPQUALITY_PROPERTY ) { - m_filterEngine.parseToken(token, uint16Value, type); + FilterEngine::parseToken(token, uint16Value, type); m_filterEngine.setProperty(filterName, propertyName, uint16Value, type); } // uint32_t conversion else if ( propertyName == ALIGNMENTFLAG_PROPERTY ) { - m_filterEngine.parseToken(token, uint32Value, type); + FilterEngine::parseToken(token, uint32Value, type); m_filterEngine.setProperty(filterName, propertyName, uint32Value, type); } // string conversion - else if ( propertyName == MATEREFERENCE_PROPERTY || + else if ( propertyName == CIGAR_PROPERTY || + propertyName == MATEREFERENCE_PROPERTY || propertyName == NAME_PROPERTY || propertyName == QUERYBASES_PROPERTY || - propertyName == REFERENCE_PROPERTY || - propertyName == CIGAR_PROPERTY + propertyName == REFERENCE_PROPERTY ) { - m_filterEngine.parseToken(token, stringValue, type); + FilterEngine::parseToken(token, stringValue, type); m_filterEngine.setProperty(filterName, propertyName, stringValue, type); } + else if ( propertyName == TAG_PROPERTY ) { + // this will be stored directly as the TAG:VALUE token + // (VALUE may contain compare ops, will be parsed out later) + m_filterEngine.setProperty(filterName, propertyName, token, PropertyFilterValue::EXACT); + } + // else unknown property else { - cerr << "Unknown property: " << propertyName << "!" << endl; + cerr << "bamtools filter ERROR: unknown property - " << propertyName << endl; return false; } } @@ -444,7 +543,8 @@ 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; + cerr << "bamtools filter ERROR: could not open script: " + << m_settings->ScriptFilename << " for reading" << endl; return false; } @@ -460,7 +560,7 @@ const string FilterTool::FilterToolPrivate::GetScriptContents(void) { // read next block of data if ( fgets(buffer, 1024, inFile) == 0 ) { - cerr << "FilterTool error : could not read from script" << endl; + cerr << "bamtools filter ERROR: could not read script contents" << endl; return false; } @@ -479,6 +579,7 @@ 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); @@ -498,7 +599,7 @@ void FilterTool::FilterToolPrivate::InitProperties(void) { m_propertyNames.push_back(POSITION_PROPERTY); m_propertyNames.push_back(QUERYBASES_PROPERTY); m_propertyNames.push_back(REFERENCE_PROPERTY); - m_propertyNames.push_back(CIGAR_PROPERTY); + m_propertyNames.push_back(TAG_PROPERTY); // add vector contents to FilterEngine vector::const_iterator propertyNameIter = m_propertyNames.begin(); @@ -531,7 +632,8 @@ bool FilterTool::FilterToolPrivate::ParseCommandLine(void) { 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); } @@ -574,7 +676,8 @@ bool FilterTool::FilterToolPrivate::ParseScript(void) { Json::Reader reader; if ( !reader.parse(document, root) ) { // use built-in error reporting mechanism to alert user what was wrong with the script - cerr << "Failed to parse configuration\n" << reader.getFormatedErrorMessages(); + cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl + << reader.getFormatedErrorMessages(); return false; } @@ -597,9 +700,8 @@ bool FilterTool::FilterToolPrivate::ParseScript(void) { // if id tag supplied const Json::Value id = filter["id"]; - if ( !id.isNull() ) { + if ( !id.isNull() ) filterName = id.asString(); - } // use array index else { @@ -632,37 +734,44 @@ bool FilterTool::FilterToolPrivate::ParseScript(void) { return success; } - bool FilterTool::FilterToolPrivate::Run(void) { // set to default input if none provided if ( !m_settings->HasInputBamFilename ) m_settings->InputFiles.push_back(Options::StandardIn()); - + // initialize defined properties & user-specified filters // quit if failed - if ( !SetupFilters() ) return 1; + if ( !SetupFilters() ) return false; // open reader without index BamMultiReader reader; - if (!reader.Open(m_settings->InputFiles, false, true)) { - cerr << "Could not open input files for reading." << endl; + 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(); - // open writer + // determine compression mode for BamWriter + bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && + !m_settings->IsForceCompression ); + BamWriter::CompressionMode compressionMode = BamWriter::Compressed; + if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed; + + // open BamWriter BamWriter writer; - bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression ); - if (!writer.Open(m_settings->OutputFilename, headerText, filterToolReferences, writeUncompressed)) { - cerr << "Could not open " << m_settings->OutputFilename << " for writing." << endl; + 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; } - - BamAlignment al; - + // if no region specified, filter entire file + BamAlignment al; if ( !m_settings->HasRegion ) { while ( reader.GetNextAlignment(al) ) { if ( CheckAlignment(al) ) @@ -677,38 +786,31 @@ bool FilterTool::FilterToolPrivate::Run(void) { BamRegion region; if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) { - // attempt to re-open reader with index files - reader.Close(); - bool openedOK = reader.Open(m_settings->InputFiles, true, true ); - - // if error - if ( !openedOK ) { - cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl; - return 1; - } - - // if index data available, we can use SetRegion - if ( reader.IsIndexLoaded() ) { - + // attempt to find index files + reader.LocateIndexes(); + + // if index data available for all BAM files, we can use SetRegion + if ( reader.HasIndexes() ) { + // attempt to use SetRegion(), if failed report error if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) { - cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl; + cerr << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl; reader.Close(); - return 1; + return false; } // everything checks out, just iterate through specified region, filtering alignments - while ( reader.GetNextAlignmentCore(al) ) + while ( reader.GetNextAlignment(al) ) if ( CheckAlignment(al) ) writer.SaveAlignment(al); - } + } // no index data available, we have to iterate through until we // find overlapping alignments else { - while( reader.GetNextAlignmentCore(al) ) { - if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) && - (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) ) + while ( reader.GetNextAlignment(al) ) { + if ( (al.RefID >= region.LeftRefID) && ((al.Position + al.Length) >= region.LeftPosition) && + (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) ) { if ( CheckAlignment(al) ) writer.SaveAlignment(al); @@ -719,26 +821,28 @@ bool FilterTool::FilterToolPrivate::Run(void) { // error parsing REGION string else { - cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl; - cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl; + cerr << "bamtools filter ERROR: could not parse REGION: " << m_settings->Region << endl; + cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid" + << endl; reader.Close(); - return 1; + return false; } } // clean up & exit reader.Close(); writer.Close(); - return 0; + return true; } bool FilterTool::FilterToolPrivate::SetupFilters(void) { - // add known properties to FilterEngine + // set up filter engine with supported properties InitProperties(); // parse script for filter rules, if given - if ( m_settings->HasScriptFilename ) return ParseScript(); + if ( m_settings->HasScriptFilename ) + return ParseScript(); // otherwise check command line for filters else return ParseCommandLine();