src/toolkit/bamtools_filter.cpp

   1 // ***************************************************************************
   2 // bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // ---------------------------------------------------------------------------
   5 // Last modified: 10 December 2012
   6 // ---------------------------------------------------------------------------
   7 // Filters BAM file(s) according to some user-specified criteria
   8 // ***************************************************************************
   9
  10 #include "bamtools_filter.h"
  11
  12 #include <api/BamMultiReader.h>
  13 #include <api/BamWriter.h>
  14 #include <utils/bamtools_filter_engine.h>
  15 #include <utils/bamtools_options.h>
  16 #include <utils/bamtools_utilities.h>
  17 using namespace BamTools;
  18
  19 #include <jsoncpp/json.h>
  20 using namespace Json;
  21
  22 #include <cstdio>
  23 #include <fstream>
  24 #include <iostream>
  25 #include <sstream>
  26 #include <string>
  27 #include <vector>
  28 using namespace std;
  29
  30 namespace BamTools {
  31
  32 // -------------------------------
  33 // string literal constants
  34
  35 // property names
  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";
  59
  60 // boolalpha
  61 const string TRUE_STR  = "true";
  62 const string FALSE_STR = "false";
  63
  64 RefVector filterToolReferences;
  65
  66 struct BamAlignmentChecker {
  67     bool check(const PropertyFilter& filter, const BamAlignment& al) {
  68
  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 ) {
  74
  75             // check alignment data field depending on propertyName
  76             const string& propertyName = (*propertyIter).first;
  77             const PropertyFilterValue& valueFilter = (*propertyIter).second;
  78
  79             if      ( propertyName == ALIGNMENTFLAG_PROPERTY )  keepAlignment &= valueFilter.check(al.AlignmentFlag);
  80             else if ( propertyName == CIGAR_PROPERTY ) {
  81                 stringstream cigarSs;
  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;
  90                     }
  91                     keepAlignment &= valueFilter.check(cigarSs.str());
  92                 }
  93             }
  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);
 109             }
 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);
 117             }
 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);
 125             }
 126             else if ( propertyName == TAG_PROPERTY ) keepAlignment &= checkAlignmentTag(valueFilter, al);
 127             else BAMTOOLS_ASSERT_UNREACHABLE;
 128
 129             // if alignment fails at ANY point, just quit and return false
 130             if ( !keepAlignment ) return false;
 131         }
 132
 133         BAMTOOLS_ASSERT_MESSAGE( keepAlignment, "Error in BamAlignmentChecker... keepAlignment should be true here");
 134         return keepAlignment;
 135     }
 136
 137     bool checkAlignmentTag(const PropertyFilterValue& valueFilter, const BamAlignment& al) {
 138
 139         // ensure filter contains string data
 140         Variant entireTagFilter = valueFilter.Value;
 141         if ( !entireTagFilter.is_type<string>() ) return false;
 142
 143         // localize string from variant
 144         const string& entireTagFilterString = entireTagFilter.get<string>();
 145
 146         // ensure we have at least "XX:x"
 147         if ( entireTagFilterString.length() < 4 ) return false;
 148
 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);
 153         char tagType = '\0';
 154         if ( !al.GetTagType(tagName, tagType) ) return false;
 155
 156         // remove tagName & ":" from beginning tagFilter
 157         string tagFilterString = entireTagFilterString.substr(3);
 158
 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;
 164
 165         PropertyFilterValue tagFilter;
 166         PropertyFilterValue::ValueCompareType compareType;
 167         bool keepAlignment = false;
 168         switch (tagType) {
 169
 170             // signed int tag type
 171             case 'c' :
 172             case 's' :
 173             case 'i' :
 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);
 179                     }
 180                 }
 181                 break;
 182
 183             // unsigned int tag type
 184             case 'C' :
 185             case 'S' :
 186             case 'I' :
 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);
 192                     }
 193                 }
 194                 break;
 195
 196             // 'real' tag type
 197             case 'f' :
 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);
 203                     }
 204                 }
 205                 break;
 206
 207             // string tag type
 208             case 'A':
 209             case 'Z':
 210             case 'H':
 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);
 216                     }
 217                 }
 218                 break;
 219
 220             // unknown tag type
 221             default :
 222                 keepAlignment = false;
 223         }
 224
 225         return keepAlignment;
 226     }
 227 };
 228
 229 } // namespace BamTools
 230
 231 // ---------------------------------------------
 232 // FilterSettings implementation
 233
 234 struct FilterTool::FilterSettings {
 235
 236     // ----------------------------------
 237     // IO opts
 238
 239     // flags
 240     bool HasInput;
 241     bool HasInputFilelist;
 242     bool HasOutput;
 243     bool HasRegion;
 244     bool HasScript;
 245     bool IsForceCompression;
 246
 247     // filenames
 248     vector<string> InputFiles;
 249     string InputFilelist;
 250     string OutputFilename;
 251     string Region;
 252     string ScriptFilename;
 253
 254     // -----------------------------------
 255     // General filter opts
 256
 257     // flags
 258     bool HasAlignmentFlagFilter;
 259     bool HasInsertSizeFilter;
 260     bool HasMapQualityFilter;
 261     bool HasNameFilter;
 262     bool HasQueryBasesFilter;
 263     bool HasTagFilter; //(s)
 264
 265     // filters
 266     string AlignmentFlagFilter;
 267     string InsertSizeFilter;
 268     string NameFilter;
 269     string MapQualityFilter;
 270     string QueryBasesFilter;
 271     string TagFilter;  // support multiple ?
 272
 273     // -----------------------------------
 274     // AlignmentFlag filter opts
 275
 276     // flags
 277     bool HasIsDuplicateFilter;
 278     bool HasIsFailedQCFilter;
 279     bool HasIsFirstMateFilter;
 280     bool HasIsMappedFilter;
 281     bool HasIsMateMappedFilter;
 282     bool HasIsMateReverseStrandFilter;
 283     bool HasIsPairedFilter;
 284     bool HasIsPrimaryAlignmentFilter;
 285     bool HasIsProperPairFilter;
 286     bool HasIsReverseStrandFilter;
 287     bool HasIsSecondMateFilter;
 288     bool HasIsSingletonFilter;
 289
 290     // filters
 291     string IsDuplicateFilter;
 292     string IsFailedQCFilter;
 293     string IsFirstMateFilter;
 294     string IsMappedFilter;
 295     string IsMateMappedFilter;
 296     string IsMateReverseStrandFilter;
 297     string IsPairedFilter;
 298     string IsPrimaryAlignmentFilter;
 299     string IsProperPairFilter;
 300     string IsReverseStrandFilter;
 301     string IsSecondMateFilter;
 302     string IsSingletonFilter;
 303
 304     // ---------------------------------
 305     // constructor
 306
 307     FilterSettings(void)
 308         : HasInput(false)
 309         , HasInputFilelist(false)
 310         , HasOutput(false)
 311         , HasRegion(false)
 312         , HasScript(false)
 313         , IsForceCompression(false)
 314         , OutputFilename(Options::StandardOut())
 315         , HasAlignmentFlagFilter(false)
 316         , HasInsertSizeFilter(false)
 317         , HasMapQualityFilter(false)
 318         , HasNameFilter(false)
 319         , HasQueryBasesFilter(false)
 320         , HasTagFilter(false)
 321         , HasIsDuplicateFilter(false)
 322         , HasIsFailedQCFilter(false)
 323         , HasIsFirstMateFilter(false)
 324         , HasIsMappedFilter(false)
 325         , HasIsMateMappedFilter(false)
 326         , HasIsMateReverseStrandFilter(false)
 327         , HasIsPairedFilter(false)
 328         , HasIsPrimaryAlignmentFilter(false)
 329         , HasIsProperPairFilter(false)
 330         , HasIsReverseStrandFilter(false)
 331         , HasIsSecondMateFilter(false)
 332         , HasIsSingletonFilter(false)
 333         , IsDuplicateFilter(TRUE_STR)
 334         , IsFailedQCFilter(TRUE_STR)
 335         , IsFirstMateFilter(TRUE_STR)
 336         , IsMappedFilter(TRUE_STR)
 337         , IsMateMappedFilter(TRUE_STR)
 338         , IsMateReverseStrandFilter(TRUE_STR)
 339         , IsPairedFilter(TRUE_STR)
 340         , IsPrimaryAlignmentFilter(TRUE_STR)
 341         , IsProperPairFilter(TRUE_STR)
 342         , IsReverseStrandFilter(TRUE_STR)
 343         , IsSecondMateFilter(TRUE_STR)
 344         , IsSingletonFilter(TRUE_STR)
 345     { }
 346 };
 347
 348 // ---------------------------------------------
 349 // FilterToolPrivate declaration
 350
 351 class FilterTool::FilterToolPrivate {
 352
 353     // ctor & dtor
 354     public:
 355         FilterToolPrivate(FilterTool::FilterSettings* settings);
 356         ~FilterToolPrivate(void);
 357
 358     // 'public' interface
 359     public:
 360         bool Run(void);
 361
 362     // internal methods
 363     private:
 364         bool AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens);
 365         bool CheckAlignment(const BamAlignment& al);
 366         const string GetScriptContents(void);
 367         void InitProperties(void);
 368         bool ParseCommandLine(void);
 369         bool ParseFilterObject(const string& filterName, const Json::Value& filterObject);
 370         bool ParseScript(void);
 371         bool SetupFilters(void);
 372
 373     // data members
 374     private:
 375         vector<string> m_propertyNames;
 376         FilterTool::FilterSettings* m_settings;
 377         FilterEngine<BamAlignmentChecker> m_filterEngine;
 378 };
 379
 380 // ---------------------------------------------
 381 // FilterToolPrivate implementation
 382
 383 // constructor
 384 FilterTool::FilterToolPrivate::FilterToolPrivate(FilterTool::FilterSettings* settings)
 385     : m_settings(settings)
 386 { }
 387
 388 // destructor
 389 FilterTool::FilterToolPrivate::~FilterToolPrivate(void) { }
 390
 391 bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName,
 392                                                               const map<string,
 393                                                               string>& propertyTokens)
 394 {
 395     // dummy temp values for token parsing
 396     bool boolValue;
 397     int32_t int32Value;
 398     uint16_t uint16Value;
 399     uint32_t uint32Value;
 400     string stringValue;
 401     PropertyFilterValue::ValueCompareType type;
 402
 403     // iterate over property token map
 404     map<string, string>::const_iterator mapIter = propertyTokens.begin();
 405     map<string, string>::const_iterator mapEnd  = propertyTokens.end();
 406     for ( ; mapIter != mapEnd; ++mapIter ) {
 407
 408         const string& propertyName = (*mapIter).first;
 409         const string& token        = (*mapIter).second;
 410
 411         // ------------------------------
 412         // convert token to value & compare type
 413         // then add to filter engine
 414
 415         // bool conversion
 416         if ( propertyName == ISDUPLICATE_PROPERTY ||
 417              propertyName == ISFAILEDQC_PROPERTY ||
 418              propertyName == ISFIRSTMATE_PROPERTY ||
 419              propertyName == ISMAPPED_PROPERTY ||
 420              propertyName == ISMATEMAPPED_PROPERTY ||
 421              propertyName == ISMATEREVERSESTRAND_PROPERTY ||
 422              propertyName == ISPAIRED_PROPERTY ||
 423              propertyName == ISPRIMARYALIGNMENT_PROPERTY ||
 424              propertyName == ISPROPERPAIR_PROPERTY ||
 425              propertyName == ISREVERSESTRAND_PROPERTY ||
 426              propertyName == ISSECONDMATE_PROPERTY ||
 427              propertyName == ISSINGLETON_PROPERTY
 428            )
 429         {
 430             FilterEngine<BamAlignmentChecker>::parseToken(token, boolValue, type);
 431             m_filterEngine.setProperty(filterName, propertyName, boolValue, type);
 432         }
 433
 434         // int32_t conversion
 435         else if ( propertyName == INSERTSIZE_PROPERTY ||
 436                   propertyName == MATEPOSITION_PROPERTY ||
 437                   propertyName == POSITION_PROPERTY
 438                 )
 439         {
 440             FilterEngine<BamAlignmentChecker>::parseToken(token, int32Value, type);
 441             m_filterEngine.setProperty(filterName, propertyName, int32Value, type);
 442         }
 443
 444         // uint16_t conversion
 445         else if ( propertyName == MAPQUALITY_PROPERTY )
 446         {
 447             FilterEngine<BamAlignmentChecker>::parseToken(token, uint16Value, type);
 448             m_filterEngine.setProperty(filterName, propertyName, uint16Value, type);
 449         }
 450
 451         // uint32_t conversion
 452         else if ( propertyName == ALIGNMENTFLAG_PROPERTY )
 453         {
 454             FilterEngine<BamAlignmentChecker>::parseToken(token, uint32Value, type);
 455             m_filterEngine.setProperty(filterName, propertyName, uint32Value, type);
 456         }
 457
 458         // string conversion
 459         else if ( propertyName == CIGAR_PROPERTY ||
 460                   propertyName == MATEREFERENCE_PROPERTY ||
 461                   propertyName == NAME_PROPERTY ||
 462                   propertyName == QUERYBASES_PROPERTY ||
 463                   propertyName == REFERENCE_PROPERTY
 464                 )
 465         {
 466             FilterEngine<BamAlignmentChecker>::parseToken(token, stringValue, type);
 467             m_filterEngine.setProperty(filterName, propertyName, stringValue, type);
 468         }
 469
 470         else if ( propertyName == TAG_PROPERTY ) {
 471             // this will be stored directly as the TAG:VALUE token
 472             // (VALUE may contain compare ops, will be parsed out later)
 473             m_filterEngine.setProperty(filterName, propertyName, token, PropertyFilterValue::EXACT);
 474         }
 475
 476         // else unknown property
 477         else {
 478             cerr << "bamtools filter ERROR: unknown property - " << propertyName << endl;
 479             return false;
 480         }
 481     }
 482     return true;
 483 }
 484
 485 bool FilterTool::FilterToolPrivate::CheckAlignment(const BamAlignment& al) {
 486     return m_filterEngine.check(al);
 487 }
 488
 489 const string FilterTool::FilterToolPrivate::GetScriptContents(void) {
 490
 491     // open script for reading
 492     FILE* inFile = fopen(m_settings->ScriptFilename.c_str(), "rb");
 493     if ( !inFile ) {
 494         cerr << "bamtools filter ERROR: could not open script: "
 495              << m_settings->ScriptFilename << " for reading" << endl;
 496         return string();
 497     }
 498
 499     // read in entire script contents
 500     char buffer[1024];
 501     ostringstream docStream("");
 502     while ( true ) {
 503
 504         // peek ahead, make sure there is data available
 505         char ch = fgetc(inFile);
 506         ungetc(ch, inFile);
 507         if( feof(inFile) )
 508             break;
 509
 510         // read next block of data
 511         if ( fgets(buffer, 1024, inFile) == 0 ) {
 512             cerr << "bamtools filter ERROR: could not read script contents" << endl;
 513             return string();
 514         }
 515
 516         docStream << buffer;
 517     }
 518
 519     // close script file
 520     fclose(inFile);
 521
 522     // import buffer contents to document, return
 523     return docStream.str();
 524 }
 525
 526 void FilterTool::FilterToolPrivate::InitProperties(void) {
 527
 528     // store property names in vector
 529     m_propertyNames.push_back(ALIGNMENTFLAG_PROPERTY);
 530     m_propertyNames.push_back(CIGAR_PROPERTY);
 531     m_propertyNames.push_back(INSERTSIZE_PROPERTY);
 532     m_propertyNames.push_back(ISDUPLICATE_PROPERTY);
 533     m_propertyNames.push_back(ISFAILEDQC_PROPERTY);
 534     m_propertyNames.push_back(ISFIRSTMATE_PROPERTY);
 535     m_propertyNames.push_back(ISMAPPED_PROPERTY);
 536     m_propertyNames.push_back(ISMATEMAPPED_PROPERTY);
 537     m_propertyNames.push_back(ISMATEREVERSESTRAND_PROPERTY);
 538     m_propertyNames.push_back(ISPAIRED_PROPERTY);
 539     m_propertyNames.push_back(ISPRIMARYALIGNMENT_PROPERTY);
 540     m_propertyNames.push_back(ISPROPERPAIR_PROPERTY);
 541     m_propertyNames.push_back(ISREVERSESTRAND_PROPERTY);
 542     m_propertyNames.push_back(ISSECONDMATE_PROPERTY);
 543     m_propertyNames.push_back(ISSINGLETON_PROPERTY);
 544     m_propertyNames.push_back(MAPQUALITY_PROPERTY);
 545     m_propertyNames.push_back(MATEPOSITION_PROPERTY);
 546     m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
 547     m_propertyNames.push_back(NAME_PROPERTY);
 548     m_propertyNames.push_back(POSITION_PROPERTY);
 549     m_propertyNames.push_back(QUERYBASES_PROPERTY);
 550     m_propertyNames.push_back(REFERENCE_PROPERTY);
 551     m_propertyNames.push_back(TAG_PROPERTY);
 552
 553     // add vector contents to FilterEngine<BamAlignmentChecker>
 554     vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
 555     vector<string>::const_iterator propertyNameEnd  = m_propertyNames.end();
 556     for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter )
 557         m_filterEngine.addProperty((*propertyNameIter));
 558 }
 559
 560 bool FilterTool::FilterToolPrivate::ParseCommandLine(void) {
 561
 562     // add a rule set to filter engine
 563     const string CMD = "COMMAND_LINE";
 564     m_filterEngine.addFilter(CMD);
 565
 566     // map property names to command line args
 567     map<string, string> propertyTokens;
 568     if ( m_settings->HasAlignmentFlagFilter )       propertyTokens.insert( make_pair(ALIGNMENTFLAG_PROPERTY,       m_settings->AlignmentFlagFilter) );
 569     if ( m_settings->HasInsertSizeFilter )          propertyTokens.insert( make_pair(INSERTSIZE_PROPERTY,          m_settings->InsertSizeFilter) );
 570     if ( m_settings->HasIsDuplicateFilter )         propertyTokens.insert( make_pair(ISDUPLICATE_PROPERTY,         m_settings->IsDuplicateFilter) );
 571     if ( m_settings->HasIsFailedQCFilter )          propertyTokens.insert( make_pair(ISFAILEDQC_PROPERTY,          m_settings->IsFailedQCFilter) );
 572     if ( m_settings->HasIsFirstMateFilter )         propertyTokens.insert( make_pair(ISFIRSTMATE_PROPERTY,         m_settings->IsFirstMateFilter) );
 573     if ( m_settings->HasIsMappedFilter )            propertyTokens.insert( make_pair(ISMAPPED_PROPERTY,            m_settings->IsMappedFilter) );
 574     if ( m_settings->HasIsMateMappedFilter )        propertyTokens.insert( make_pair(ISMATEMAPPED_PROPERTY,        m_settings->IsMateMappedFilter) );
 575     if ( m_settings->HasIsMateReverseStrandFilter ) propertyTokens.insert( make_pair(ISMATEREVERSESTRAND_PROPERTY, m_settings->IsMateReverseStrandFilter) );
 576     if ( m_settings->HasIsPairedFilter )            propertyTokens.insert( make_pair(ISPAIRED_PROPERTY,            m_settings->IsPairedFilter) );
 577     if ( m_settings->HasIsPrimaryAlignmentFilter )  propertyTokens.insert( make_pair(ISPRIMARYALIGNMENT_PROPERTY,  m_settings->IsPrimaryAlignmentFilter) );
 578     if ( m_settings->HasIsProperPairFilter )        propertyTokens.insert( make_pair(ISPROPERPAIR_PROPERTY,        m_settings->IsProperPairFilter) );
 579     if ( m_settings->HasIsReverseStrandFilter )     propertyTokens.insert( make_pair(ISREVERSESTRAND_PROPERTY,     m_settings->IsReverseStrandFilter) );
 580     if ( m_settings->HasIsSecondMateFilter )        propertyTokens.insert( make_pair(ISSECONDMATE_PROPERTY,        m_settings->IsSecondMateFilter) );
 581     if ( m_settings->HasIsSingletonFilter )         propertyTokens.insert( make_pair(ISSINGLETON_PROPERTY,         m_settings->IsSingletonFilter) );
 582     if ( m_settings->HasMapQualityFilter )          propertyTokens.insert( make_pair(MAPQUALITY_PROPERTY,          m_settings->MapQualityFilter) );
 583     if ( m_settings->HasNameFilter )                propertyTokens.insert( make_pair(NAME_PROPERTY,                m_settings->NameFilter) );
 584     if ( m_settings->HasQueryBasesFilter )          propertyTokens.insert( make_pair(QUERYBASES_PROPERTY,          m_settings->QueryBasesFilter) );
 585     if ( m_settings->HasTagFilter )                 propertyTokens.insert( make_pair(TAG_PROPERTY,                 m_settings->TagFilter) );
 586
 587     // send add these properties to filter set "COMMAND_LINE"
 588     return AddPropertyTokensToFilter(CMD, propertyTokens);
 589 }
 590
 591 bool FilterTool::FilterToolPrivate::ParseFilterObject(const string& filterName, const Json::Value& filterObject) {
 592
 593     // filter object parsing variables
 594     Json::Value null(Json::nullValue);
 595     Json::Value propertyValue;
 596
 597     // store results
 598     map<string, string> propertyTokens;
 599
 600     // iterate over known properties
 601     vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
 602     vector<string>::const_iterator propertyNameEnd  = m_propertyNames.end();
 603     for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter ) {
 604         const string& propertyName = (*propertyNameIter);
 605
 606         // if property defined in filter, add to token list
 607         propertyValue = filterObject.get(propertyName, null);
 608         if ( propertyValue != null )
 609             propertyTokens.insert( make_pair(propertyName, propertyValue.asString()) );
 610     }
 611
 612     // add this filter to engin
 613     m_filterEngine.addFilter(filterName);
 614
 615     // add token list to this filter
 616     return AddPropertyTokensToFilter(filterName, propertyTokens);
 617 }
 618
 619 bool FilterTool::FilterToolPrivate::ParseScript(void) {
 620
 621     // read in script contents from file
 622     const string document = GetScriptContents();
 623
 624     // set up JsonCPP reader and attempt to parse script
 625     Json::Value root;
 626     Json::Reader reader;
 627     if ( !reader.parse(document, root) ) {
 628         // use built-in error reporting mechanism to alert user what was wrong with the script
 629         cerr  << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl
 630               << reader.getFormatedErrorMessages();
 631         return false;
 632     }
 633
 634     // initialize return status
 635     bool success = true;
 636
 637     // see if root object contains multiple filters
 638     const Json::Value filters = root["filters"];
 639     if ( !filters.isNull() ) {
 640
 641         // iterate over any filters found
 642         int filterIndex = 0;
 643         Json::Value::const_iterator filtersIter = filters.begin();
 644         Json::Value::const_iterator filtersEnd  = filters.end();
 645         for ( ; filtersIter != filtersEnd; ++filtersIter, ++filterIndex ) {
 646             Json::Value filter = (*filtersIter);
 647
 648             // convert filter index to string
 649             string filterName;
 650
 651             // if id tag supplied
 652             const Json::Value id = filter["id"];
 653             if ( !id.isNull() )
 654                 filterName = id.asString();
 655
 656             // use array index
 657             else {
 658                 stringstream convert;
 659                 convert << filterIndex;
 660                 filterName = convert.str();
 661             }
 662
 663             // create & parse filter
 664             success &= ParseFilterObject(filterName, filter);
 665         }
 666
 667         // see if user defined a "rule" for these filters
 668         // otherwise, use filter engine's default rule behavior
 669         string ruleString("");
 670         const Json::Value rule = root["rule"];
 671         if ( rule.isString() )
 672             ruleString = rule.asString();
 673         m_filterEngine.setRule(ruleString);
 674
 675         // return success/fail
 676         return success;
 677     }
 678
 679     // otherwise, root is the only filter (just contains properties)
 680     // create & parse filter named "ROOT"
 681     else success = ParseFilterObject("ROOT", root);
 682
 683     // return success/failure
 684     return success;
 685 }
 686
 687 bool FilterTool::FilterToolPrivate::Run(void) {
 688
 689     // set to default input if none provided
 690     if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
 691         m_settings->InputFiles.push_back(Options::StandardIn());
 692
 693     // add files in the filelist to the input file list
 694     if ( m_settings->HasInputFilelist ) {
 695
 696         ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
 697         if ( !filelist.is_open() ) {
 698             cerr << "bamtools filter ERROR: could not open input BAM file list... Aborting." << endl;
 699             return false;
 700         }
 701
 702         string line;
 703         while ( getline(filelist, line) )
 704             m_settings->InputFiles.push_back(line);
 705     }
 706
 707     // initialize defined properties & user-specified filters
 708     // quit if failed
 709     if ( !SetupFilters() )
 710         return false;
 711
 712     // open reader without index
 713     BamMultiReader reader;
 714     if ( !reader.Open(m_settings->InputFiles) ) {
 715         cerr << "bamtools filter ERROR: could not open input files for reading." << endl;
 716         return false;
 717     }
 718
 719     // retrieve reader header & reference data
 720     const string headerText = reader.GetHeaderText();
 721     filterToolReferences = reader.GetReferenceData();
 722
 723     // determine compression mode for BamWriter
 724     bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
 725                               !m_settings->IsForceCompression );
 726     BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
 727     if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
 728
 729     // open BamWriter
 730     BamWriter writer;
 731     writer.SetCompressionMode(compressionMode);
 732     if ( !writer.Open(m_settings->OutputFilename, headerText, filterToolReferences) ) {
 733         cerr << "bamtools filter ERROR: could not open " << m_settings->OutputFilename << " for writing." << endl;
 734         reader.Close();
 735         return false;
 736     }
 737
 738     // if no region specified, filter entire file
 739     BamAlignment al;
 740     if ( !m_settings->HasRegion ) {
 741         while ( reader.GetNextAlignment(al) ) {
 742             if ( CheckAlignment(al) )
 743                 writer.SaveAlignment(al);
 744         }
 745     }
 746
 747     // otherwise attempt to use region as constraint
 748     else {
 749
 750         // if region string parses OK
 751         BamRegion region;
 752         if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
 753
 754             // attempt to find index files
 755             reader.LocateIndexes();
 756
 757             // if index data available for all BAM files, we can use SetRegion
 758             if ( reader.HasIndexes() ) {
 759
 760                 // attempt to use SetRegion(), if failed report error
 761                 if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
 762                     cerr << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl;
 763                     reader.Close();
 764                     return false;
 765                 }
 766
 767                 // everything checks out, just iterate through specified region, filtering alignments
 768                 while ( reader.GetNextAlignment(al) )
 769                     if ( CheckAlignment(al) )
 770                         writer.SaveAlignment(al);
 771                 }
 772
 773             // no index data available, we have to iterate through until we
 774             // find overlapping alignments
 775             else {
 776                 while ( reader.GetNextAlignment(al) ) {
 777                     if ( (al.RefID >= region.LeftRefID)  && ((al.Position + al.Length) >= region.LeftPosition) &&
 778                          (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
 779                     {
 780                         if ( CheckAlignment(al) )
 781                             writer.SaveAlignment(al);
 782                     }
 783                 }
 784             }
 785         }
 786
 787         // error parsing REGION string
 788         else {
 789             cerr << "bamtools filter ERROR: could not parse REGION: " << m_settings->Region << endl;
 790             cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
 791                  << endl;
 792             reader.Close();
 793             return false;
 794         }
 795     }
 796
 797     // clean up & exit
 798     reader.Close();
 799     writer.Close();
 800     return true;
 801 }
 802
 803 bool FilterTool::FilterToolPrivate::SetupFilters(void) {
 804
 805     // set up filter engine with supported properties
 806     InitProperties();
 807
 808     // parse script for filter rules, if given
 809     if ( m_settings->HasScript )
 810         return ParseScript();
 811
 812     // otherwise check command line for filters
 813     else return ParseCommandLine();
 814 }
 815
 816 // ---------------------------------------------
 817 // FilterTool implementation
 818
 819 FilterTool::FilterTool(void)
 820     : AbstractTool()
 821     , m_settings(new FilterSettings)
 822     , m_impl(0)
 823 {
 824     // ----------------------------------
 825     // set program details
 826
 827     const string usage = "[-in <filename> -in <filename> ... | -list <filelist>] "
 828                          "[-out <filename> | [-forceCompression]] [-region <REGION>] "
 829                          "[ [-script <filename] | [filterOptions] ]";
 830
 831     Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", usage );
 832
 833     // ----------------------------------
 834     // I/O options
 835
 836     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
 837
 838     const string inDesc     = "the input BAM file(s)";
 839     const string listDesc   = "the input BAM file list, one line per file";
 840     const string outDesc    = "the output BAM file";
 841     const string regionDesc = "only read data from this genomic region (see documentation for more details)";
 842     const string scriptDesc = "the filter script file (see documentation for more details)";
 843     const string forceDesc  = "if results are sent to stdout (like when piping to another tool), "
 844                               "default behavior is to leave output uncompressed. Use this flag to "
 845                               "override and force compression";
 846
 847     Options::AddValueOption("-in",     "BAM filename", inDesc,     "", m_settings->HasInput,  m_settings->InputFiles,     IO_Opts, Options::StandardIn());
 848     Options::AddValueOption("-list",   "filename",     listDesc,   "", m_settings->HasInputFilelist,  m_settings->InputFilelist, IO_Opts);
 849     Options::AddValueOption("-out",    "BAM filename", outDesc,    "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
 850     Options::AddValueOption("-region", "REGION",       regionDesc, "", m_settings->HasRegion, m_settings->Region,         IO_Opts);
 851     Options::AddValueOption("-script", "filename",     scriptDesc, "", m_settings->HasScript, m_settings->ScriptFilename, IO_Opts);
 852     Options::AddOption("-forceCompression",forceDesc, m_settings->IsForceCompression, IO_Opts);
 853
 854     // ----------------------------------
 855     // general filter options
 856
 857     OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters");
 858
 859     const string flagDesc    = "keep reads with this *exact* alignment flag (for more detailed queries, see below)";
 860     const string insertDesc  = "keep reads with insert size that matches pattern";
 861     const string mapQualDesc = "keep reads with map quality that matches pattern";
 862     const string nameDesc    = "keep reads with name that matches pattern";
 863     const string queryDesc   = "keep reads with motif that matches pattern";
 864     const string tagDesc     = "keep reads with this key=>value pair";
 865
 866     Options::AddValueOption("-alignmentFlag", "int",       flagDesc,    "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
 867     Options::AddValueOption("-insertSize",    "int",       insertDesc,  "", m_settings->HasInsertSizeFilter,    m_settings->InsertSizeFilter,    FilterOpts);
 868     Options::AddValueOption("-mapQuality",    "[0-255]",   mapQualDesc, "", m_settings->HasMapQualityFilter,    m_settings->MapQualityFilter,    FilterOpts);
 869     Options::AddValueOption("-name",          "string",    nameDesc,    "", m_settings->HasNameFilter,          m_settings->NameFilter,          FilterOpts);
 870     Options::AddValueOption("-queryBases",    "string",    queryDesc,   "", m_settings->HasQueryBasesFilter,    m_settings->QueryBasesFilter,    FilterOpts);
 871     Options::AddValueOption("-tag",           "TAG:VALUE", tagDesc,     "", m_settings->HasTagFilter,           m_settings->TagFilter,           FilterOpts);
 872
 873     // ----------------------------------
 874     // alignment flag filter options
 875
 876     OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters");
 877
 878     const string boolArg           = "true/false";
 879     const string isDupDesc         = "keep only alignments that are marked as duplicate?";
 880     const string isFailQcDesc      = "keep only alignments that failed QC?";
 881     const string isFirstMateDesc   = "keep only alignments marked as first mate?";
 882     const string isMappedDesc      = "keep only alignments that were mapped?";
 883     const string isMateMappedDesc  = "keep only alignments with mates that mapped";
 884     const string isMateReverseDesc = "keep only alignments with mate on reverese strand?";
 885     const string isPairedDesc      = "keep only alignments that were sequenced as paired?";
 886     const string isPrimaryDesc     = "keep only alignments marked as primary?";
 887     const string isProperPairDesc  = "keep only alignments that passed PE resolution?";
 888     const string isReverseDesc     = "keep only alignments on reverse strand?";
 889     const string isSecondMateDesc  = "keep only alignments marked as second mate?";
 890     const string isSingletonDesc   = "keep only singletons";
 891
 892     Options::AddValueOption("-isDuplicate",         boolArg, isDupDesc,         "", m_settings->HasIsDuplicateFilter,         m_settings->IsDuplicateFilter,         AlignmentFlagOpts, TRUE_STR);
 893     Options::AddValueOption("-isFailedQC",          boolArg, isFailQcDesc,      "", m_settings->HasIsFailedQCFilter,          m_settings->IsFailedQCFilter,          AlignmentFlagOpts, TRUE_STR);
 894     Options::AddValueOption("-isFirstMate",         boolArg, isFirstMateDesc,   "", m_settings->HasIsFirstMateFilter,         m_settings->IsFirstMateFilter,         AlignmentFlagOpts, TRUE_STR);
 895     Options::AddValueOption("-isMapped",            boolArg, isMappedDesc,      "", m_settings->HasIsMappedFilter,            m_settings->IsMappedFilter,            AlignmentFlagOpts, TRUE_STR);
 896     Options::AddValueOption("-isMateMapped",        boolArg, isMateMappedDesc,  "", m_settings->HasIsMateMappedFilter,        m_settings->IsMateMappedFilter,        AlignmentFlagOpts, TRUE_STR);
 897     Options::AddValueOption("-isMateReverseStrand", boolArg, isMateReverseDesc, "", m_settings->HasIsMateReverseStrandFilter, m_settings->IsMateReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
 898     Options::AddValueOption("-isPaired",            boolArg, isPairedDesc,      "", m_settings->HasIsPairedFilter,            m_settings->IsPairedFilter,            AlignmentFlagOpts, TRUE_STR);
 899     Options::AddValueOption("-isPrimaryAlignment",  boolArg, isPrimaryDesc,     "", m_settings->HasIsPrimaryAlignmentFilter,  m_settings->IsPrimaryAlignmentFilter,  AlignmentFlagOpts, TRUE_STR);
 900     Options::AddValueOption("-isProperPair",        boolArg, isProperPairDesc,  "", m_settings->HasIsProperPairFilter,        m_settings->IsProperPairFilter,        AlignmentFlagOpts, TRUE_STR);
 901     Options::AddValueOption("-isReverseStrand",     boolArg, isReverseDesc,     "", m_settings->HasIsReverseStrandFilter,     m_settings->IsReverseStrandFilter,     AlignmentFlagOpts, TRUE_STR);
 902     Options::AddValueOption("-isSecondMate",        boolArg, isSecondMateDesc,  "", m_settings->HasIsSecondMateFilter,        m_settings->IsSecondMateFilter,        AlignmentFlagOpts, TRUE_STR);
 903     Options::AddValueOption("-isSingleton",         boolArg, isSingletonDesc,   "", m_settings->HasIsSingletonFilter,         m_settings->IsSingletonFilter,         AlignmentFlagOpts, TRUE_STR);
 904 }
 905
 906 FilterTool::~FilterTool(void) {
 907
 908     delete m_settings;
 909     m_settings = 0;
 910
 911     delete m_impl;
 912     m_impl = 0;
 913 }
 914
 915 int FilterTool::Help(void) {
 916     Options::DisplayHelp();
 917     return 0;
 918 }
 919
 920 int FilterTool::Run(int argc, char* argv[]) {
 921
 922     // parse command line arguments
 923     Options::Parse(argc, argv, 1);
 924
 925     // initialize FilterTool with settings
 926     m_impl = new FilterToolPrivate(m_settings);
 927
 928     // run FilterTool, return success/fail
 929     if ( m_impl->Run() )
 930         return 0;
 931     else
 932         return 1;
 933 }