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: 27 April 2013
   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         int8_t   asciiFilterValue,   asciiQueryValue;
 161         int32_t  intFilterValue,    intQueryValue;
 162         uint32_t uintFilterValue,   uintQueryValue;
 163         float    realFilterValue,   realQueryValue;
 164         string   stringFilterValue, stringQueryValue;
 165
 166         PropertyFilterValue tagFilter;
 167         PropertyFilterValue::ValueCompareType compareType;
 168         bool keepAlignment = false;
 169         switch (tagType) {
 170
 171             // ASCII tag type
 172             case 'A':
 173                 if ( al.GetTag(tagName, asciiQueryValue) ) {
 174                     if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, asciiFilterValue, compareType) ) {
 175                         tagFilter.Value = asciiFilterValue;
 176                         tagFilter.Type  = compareType;
 177                         keepAlignment   = tagFilter.check(asciiQueryValue);
 178                     }
 179                 }
 180                 break;
 181
 182             // signed int tag type
 183             case 'c' :
 184             case 's' :
 185             case 'i' :
 186                 if ( al.GetTag(tagName, intQueryValue) ) {
 187                     if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, intFilterValue, compareType) ) {
 188                         tagFilter.Value = intFilterValue;
 189                         tagFilter.Type  = compareType;
 190                         keepAlignment   = tagFilter.check(intQueryValue);
 191                     }
 192                 }
 193                 break;
 194
 195             // unsigned int tag type
 196             case 'C' :
 197             case 'S' :
 198             case 'I' :
 199                 if ( al.GetTag(tagName, uintQueryValue) ) {
 200                     if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, uintFilterValue, compareType) ) {
 201                         tagFilter.Value = uintFilterValue;
 202                         tagFilter.Type  = compareType;
 203                         keepAlignment   = tagFilter.check(uintQueryValue);
 204                     }
 205                 }
 206                 break;
 207
 208             // 'real' tag type
 209             case 'f' :
 210                 if ( al.GetTag(tagName, realQueryValue) ) {
 211                     if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, realFilterValue, compareType) ) {
 212                         tagFilter.Value = realFilterValue;
 213                         tagFilter.Type  = compareType;
 214                         keepAlignment   = tagFilter.check(realQueryValue);
 215                     }
 216                 }
 217                 break;
 218
 219             // string tag type
 220
 221             case 'Z':
 222             case 'H':
 223                 if ( al.GetTag(tagName, stringQueryValue) ) {
 224                     if ( FilterEngine<BamAlignmentChecker>::parseToken(tagFilterString, stringFilterValue, compareType) ) {
 225                         tagFilter.Value = stringFilterValue;
 226                         tagFilter.Type  = compareType;
 227                         keepAlignment   = tagFilter.check(stringQueryValue);
 228                     }
 229                 }
 230                 break;
 231
 232             // unknown tag type
 233             default :
 234                 keepAlignment = false;
 235         }
 236
 237         return keepAlignment;
 238     }
 239 };
 240
 241 } // namespace BamTools
 242
 243 // ---------------------------------------------
 244 // FilterSettings implementation
 245
 246 struct FilterTool::FilterSettings {
 247
 248     // ----------------------------------
 249     // IO opts
 250
 251     // flags
 252     bool HasInput;
 253     bool HasInputFilelist;
 254     bool HasOutput;
 255     bool HasRegion;
 256     bool HasScript;
 257     bool IsForceCompression;
 258
 259     // filenames
 260     vector<string> InputFiles;
 261     string InputFilelist;
 262     string OutputFilename;
 263     string Region;
 264     string ScriptFilename;
 265
 266     // -----------------------------------
 267     // General filter opts
 268
 269     // flags
 270     bool HasAlignmentFlagFilter;
 271     bool HasInsertSizeFilter;
 272     bool HasMapQualityFilter;
 273     bool HasNameFilter;
 274     bool HasQueryBasesFilter;
 275     bool HasTagFilter; //(s)
 276
 277     // filters
 278     string AlignmentFlagFilter;
 279     string InsertSizeFilter;
 280     string NameFilter;
 281     string MapQualityFilter;
 282     string QueryBasesFilter;
 283     string TagFilter;  // support multiple ?
 284
 285     // -----------------------------------
 286     // AlignmentFlag filter opts
 287
 288     // flags
 289     bool HasIsDuplicateFilter;
 290     bool HasIsFailedQCFilter;
 291     bool HasIsFirstMateFilter;
 292     bool HasIsMappedFilter;
 293     bool HasIsMateMappedFilter;
 294     bool HasIsMateReverseStrandFilter;
 295     bool HasIsPairedFilter;
 296     bool HasIsPrimaryAlignmentFilter;
 297     bool HasIsProperPairFilter;
 298     bool HasIsReverseStrandFilter;
 299     bool HasIsSecondMateFilter;
 300     bool HasIsSingletonFilter;
 301
 302     // filters
 303     string IsDuplicateFilter;
 304     string IsFailedQCFilter;
 305     string IsFirstMateFilter;
 306     string IsMappedFilter;
 307     string IsMateMappedFilter;
 308     string IsMateReverseStrandFilter;
 309     string IsPairedFilter;
 310     string IsPrimaryAlignmentFilter;
 311     string IsProperPairFilter;
 312     string IsReverseStrandFilter;
 313     string IsSecondMateFilter;
 314     string IsSingletonFilter;
 315
 316     // ---------------------------------
 317     // constructor
 318
 319     FilterSettings(void)
 320         : HasInput(false)
 321         , HasInputFilelist(false)
 322         , HasOutput(false)
 323         , HasRegion(false)
 324         , HasScript(false)
 325         , IsForceCompression(false)
 326         , OutputFilename(Options::StandardOut())
 327         , HasAlignmentFlagFilter(false)
 328         , HasInsertSizeFilter(false)
 329         , HasMapQualityFilter(false)
 330         , HasNameFilter(false)
 331         , HasQueryBasesFilter(false)
 332         , HasTagFilter(false)
 333         , HasIsDuplicateFilter(false)
 334         , HasIsFailedQCFilter(false)
 335         , HasIsFirstMateFilter(false)
 336         , HasIsMappedFilter(false)
 337         , HasIsMateMappedFilter(false)
 338         , HasIsMateReverseStrandFilter(false)
 339         , HasIsPairedFilter(false)
 340         , HasIsPrimaryAlignmentFilter(false)
 341         , HasIsProperPairFilter(false)
 342         , HasIsReverseStrandFilter(false)
 343         , HasIsSecondMateFilter(false)
 344         , HasIsSingletonFilter(false)
 345         , IsDuplicateFilter(TRUE_STR)
 346         , IsFailedQCFilter(TRUE_STR)
 347         , IsFirstMateFilter(TRUE_STR)
 348         , IsMappedFilter(TRUE_STR)
 349         , IsMateMappedFilter(TRUE_STR)
 350         , IsMateReverseStrandFilter(TRUE_STR)
 351         , IsPairedFilter(TRUE_STR)
 352         , IsPrimaryAlignmentFilter(TRUE_STR)
 353         , IsProperPairFilter(TRUE_STR)
 354         , IsReverseStrandFilter(TRUE_STR)
 355         , IsSecondMateFilter(TRUE_STR)
 356         , IsSingletonFilter(TRUE_STR)
 357     { }
 358 };
 359
 360 // ---------------------------------------------
 361 // FilterToolPrivate declaration
 362
 363 class FilterTool::FilterToolPrivate {
 364
 365     // ctor & dtor
 366     public:
 367         FilterToolPrivate(FilterTool::FilterSettings* settings);
 368         ~FilterToolPrivate(void);
 369
 370     // 'public' interface
 371     public:
 372         bool Run(void);
 373
 374     // internal methods
 375     private:
 376         bool AddPropertyTokensToFilter(const string& filterName, const map<string, string>& propertyTokens);
 377         bool CheckAlignment(const BamAlignment& al);
 378         const string GetScriptContents(void);
 379         void InitProperties(void);
 380         bool ParseCommandLine(void);
 381         bool ParseFilterObject(const string& filterName, const Json::Value& filterObject);
 382         bool ParseScript(void);
 383         bool SetupFilters(void);
 384
 385     // data members
 386     private:
 387         vector<string> m_propertyNames;
 388         FilterTool::FilterSettings* m_settings;
 389         FilterEngine<BamAlignmentChecker> m_filterEngine;
 390 };
 391
 392 // ---------------------------------------------
 393 // FilterToolPrivate implementation
 394
 395 // constructor
 396 FilterTool::FilterToolPrivate::FilterToolPrivate(FilterTool::FilterSettings* settings)
 397     : m_settings(settings)
 398 { }
 399
 400 // destructor
 401 FilterTool::FilterToolPrivate::~FilterToolPrivate(void) { }
 402
 403 bool FilterTool::FilterToolPrivate::AddPropertyTokensToFilter(const string& filterName,
 404                                                               const map<string,
 405                                                               string>& propertyTokens)
 406 {
 407     // dummy temp values for token parsing
 408     bool boolValue;
 409     int32_t int32Value;
 410     uint16_t uint16Value;
 411     uint32_t uint32Value;
 412     string stringValue;
 413     PropertyFilterValue::ValueCompareType type;
 414
 415     // iterate over property token map
 416     map<string, string>::const_iterator mapIter = propertyTokens.begin();
 417     map<string, string>::const_iterator mapEnd  = propertyTokens.end();
 418     for ( ; mapIter != mapEnd; ++mapIter ) {
 419
 420         const string& propertyName = (*mapIter).first;
 421         const string& token        = (*mapIter).second;
 422
 423         // ------------------------------
 424         // convert token to value & compare type
 425         // then add to filter engine
 426
 427         // bool conversion
 428         if ( propertyName == ISDUPLICATE_PROPERTY ||
 429              propertyName == ISFAILEDQC_PROPERTY ||
 430              propertyName == ISFIRSTMATE_PROPERTY ||
 431              propertyName == ISMAPPED_PROPERTY ||
 432              propertyName == ISMATEMAPPED_PROPERTY ||
 433              propertyName == ISMATEREVERSESTRAND_PROPERTY ||
 434              propertyName == ISPAIRED_PROPERTY ||
 435              propertyName == ISPRIMARYALIGNMENT_PROPERTY ||
 436              propertyName == ISPROPERPAIR_PROPERTY ||
 437              propertyName == ISREVERSESTRAND_PROPERTY ||
 438              propertyName == ISSECONDMATE_PROPERTY ||
 439              propertyName == ISSINGLETON_PROPERTY
 440            )
 441         {
 442             FilterEngine<BamAlignmentChecker>::parseToken(token, boolValue, type);
 443             m_filterEngine.setProperty(filterName, propertyName, boolValue, type);
 444         }
 445
 446         // int32_t conversion
 447         else if ( propertyName == INSERTSIZE_PROPERTY ||
 448                   propertyName == MATEPOSITION_PROPERTY ||
 449                   propertyName == POSITION_PROPERTY
 450                 )
 451         {
 452             FilterEngine<BamAlignmentChecker>::parseToken(token, int32Value, type);
 453             m_filterEngine.setProperty(filterName, propertyName, int32Value, type);
 454         }
 455
 456         // uint16_t conversion
 457         else if ( propertyName == MAPQUALITY_PROPERTY )
 458         {
 459             FilterEngine<BamAlignmentChecker>::parseToken(token, uint16Value, type);
 460             m_filterEngine.setProperty(filterName, propertyName, uint16Value, type);
 461         }
 462
 463         // uint32_t conversion
 464         else if ( propertyName == ALIGNMENTFLAG_PROPERTY )
 465         {
 466             FilterEngine<BamAlignmentChecker>::parseToken(token, uint32Value, type);
 467             m_filterEngine.setProperty(filterName, propertyName, uint32Value, type);
 468         }
 469
 470         // string conversion
 471         else if ( propertyName == CIGAR_PROPERTY ||
 472                   propertyName == MATEREFERENCE_PROPERTY ||
 473                   propertyName == NAME_PROPERTY ||
 474                   propertyName == QUERYBASES_PROPERTY ||
 475                   propertyName == REFERENCE_PROPERTY
 476                 )
 477         {
 478             FilterEngine<BamAlignmentChecker>::parseToken(token, stringValue, type);
 479             m_filterEngine.setProperty(filterName, propertyName, stringValue, type);
 480         }
 481
 482         else if ( propertyName == TAG_PROPERTY ) {
 483             // this will be stored directly as the TAG:VALUE token
 484             // (VALUE may contain compare ops, will be parsed out later)
 485             m_filterEngine.setProperty(filterName, propertyName, token, PropertyFilterValue::EXACT);
 486         }
 487
 488         // else unknown property
 489         else {
 490             cerr << "bamtools filter ERROR: unknown property - " << propertyName << endl;
 491             return false;
 492         }
 493     }
 494     return true;
 495 }
 496
 497 bool FilterTool::FilterToolPrivate::CheckAlignment(const BamAlignment& al) {
 498     return m_filterEngine.check(al);
 499 }
 500
 501 const string FilterTool::FilterToolPrivate::GetScriptContents(void) {
 502
 503     // open script for reading
 504     FILE* inFile = fopen(m_settings->ScriptFilename.c_str(), "rb");
 505     if ( !inFile ) {
 506         cerr << "bamtools filter ERROR: could not open script: "
 507              << m_settings->ScriptFilename << " for reading" << endl;
 508         return string();
 509     }
 510
 511     // read in entire script contents
 512     char buffer[1024];
 513     ostringstream docStream("");
 514     while ( true ) {
 515
 516         // peek ahead, make sure there is data available
 517         char ch = fgetc(inFile);
 518         ungetc(ch, inFile);
 519         if( feof(inFile) )
 520             break;
 521
 522         // read next block of data
 523         if ( fgets(buffer, 1024, inFile) == 0 ) {
 524             cerr << "bamtools filter ERROR: could not read script contents" << endl;
 525             return string();
 526         }
 527
 528         docStream << buffer;
 529     }
 530
 531     // close script file
 532     fclose(inFile);
 533
 534     // import buffer contents to document, return
 535     return docStream.str();
 536 }
 537
 538 void FilterTool::FilterToolPrivate::InitProperties(void) {
 539
 540     // store property names in vector
 541     m_propertyNames.push_back(ALIGNMENTFLAG_PROPERTY);
 542     m_propertyNames.push_back(CIGAR_PROPERTY);
 543     m_propertyNames.push_back(INSERTSIZE_PROPERTY);
 544     m_propertyNames.push_back(ISDUPLICATE_PROPERTY);
 545     m_propertyNames.push_back(ISFAILEDQC_PROPERTY);
 546     m_propertyNames.push_back(ISFIRSTMATE_PROPERTY);
 547     m_propertyNames.push_back(ISMAPPED_PROPERTY);
 548     m_propertyNames.push_back(ISMATEMAPPED_PROPERTY);
 549     m_propertyNames.push_back(ISMATEREVERSESTRAND_PROPERTY);
 550     m_propertyNames.push_back(ISPAIRED_PROPERTY);
 551     m_propertyNames.push_back(ISPRIMARYALIGNMENT_PROPERTY);
 552     m_propertyNames.push_back(ISPROPERPAIR_PROPERTY);
 553     m_propertyNames.push_back(ISREVERSESTRAND_PROPERTY);
 554     m_propertyNames.push_back(ISSECONDMATE_PROPERTY);
 555     m_propertyNames.push_back(ISSINGLETON_PROPERTY);
 556     m_propertyNames.push_back(MAPQUALITY_PROPERTY);
 557     m_propertyNames.push_back(MATEPOSITION_PROPERTY);
 558     m_propertyNames.push_back(MATEREFERENCE_PROPERTY);
 559     m_propertyNames.push_back(NAME_PROPERTY);
 560     m_propertyNames.push_back(POSITION_PROPERTY);
 561     m_propertyNames.push_back(QUERYBASES_PROPERTY);
 562     m_propertyNames.push_back(REFERENCE_PROPERTY);
 563     m_propertyNames.push_back(TAG_PROPERTY);
 564
 565     // add vector contents to FilterEngine<BamAlignmentChecker>
 566     vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
 567     vector<string>::const_iterator propertyNameEnd  = m_propertyNames.end();
 568     for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter )
 569         m_filterEngine.addProperty((*propertyNameIter));
 570 }
 571
 572 bool FilterTool::FilterToolPrivate::ParseCommandLine(void) {
 573
 574     // add a rule set to filter engine
 575     const string CMD = "COMMAND_LINE";
 576     m_filterEngine.addFilter(CMD);
 577
 578     // map property names to command line args
 579     map<string, string> propertyTokens;
 580     if ( m_settings->HasAlignmentFlagFilter )       propertyTokens.insert( make_pair(ALIGNMENTFLAG_PROPERTY,       m_settings->AlignmentFlagFilter) );
 581     if ( m_settings->HasInsertSizeFilter )          propertyTokens.insert( make_pair(INSERTSIZE_PROPERTY,          m_settings->InsertSizeFilter) );
 582     if ( m_settings->HasIsDuplicateFilter )         propertyTokens.insert( make_pair(ISDUPLICATE_PROPERTY,         m_settings->IsDuplicateFilter) );
 583     if ( m_settings->HasIsFailedQCFilter )          propertyTokens.insert( make_pair(ISFAILEDQC_PROPERTY,          m_settings->IsFailedQCFilter) );
 584     if ( m_settings->HasIsFirstMateFilter )         propertyTokens.insert( make_pair(ISFIRSTMATE_PROPERTY,         m_settings->IsFirstMateFilter) );
 585     if ( m_settings->HasIsMappedFilter )            propertyTokens.insert( make_pair(ISMAPPED_PROPERTY,            m_settings->IsMappedFilter) );
 586     if ( m_settings->HasIsMateMappedFilter )        propertyTokens.insert( make_pair(ISMATEMAPPED_PROPERTY,        m_settings->IsMateMappedFilter) );
 587     if ( m_settings->HasIsMateReverseStrandFilter ) propertyTokens.insert( make_pair(ISMATEREVERSESTRAND_PROPERTY, m_settings->IsMateReverseStrandFilter) );
 588     if ( m_settings->HasIsPairedFilter )            propertyTokens.insert( make_pair(ISPAIRED_PROPERTY,            m_settings->IsPairedFilter) );
 589     if ( m_settings->HasIsPrimaryAlignmentFilter )  propertyTokens.insert( make_pair(ISPRIMARYALIGNMENT_PROPERTY,  m_settings->IsPrimaryAlignmentFilter) );
 590     if ( m_settings->HasIsProperPairFilter )        propertyTokens.insert( make_pair(ISPROPERPAIR_PROPERTY,        m_settings->IsProperPairFilter) );
 591     if ( m_settings->HasIsReverseStrandFilter )     propertyTokens.insert( make_pair(ISREVERSESTRAND_PROPERTY,     m_settings->IsReverseStrandFilter) );
 592     if ( m_settings->HasIsSecondMateFilter )        propertyTokens.insert( make_pair(ISSECONDMATE_PROPERTY,        m_settings->IsSecondMateFilter) );
 593     if ( m_settings->HasIsSingletonFilter )         propertyTokens.insert( make_pair(ISSINGLETON_PROPERTY,         m_settings->IsSingletonFilter) );
 594     if ( m_settings->HasMapQualityFilter )          propertyTokens.insert( make_pair(MAPQUALITY_PROPERTY,          m_settings->MapQualityFilter) );
 595     if ( m_settings->HasNameFilter )                propertyTokens.insert( make_pair(NAME_PROPERTY,                m_settings->NameFilter) );
 596     if ( m_settings->HasQueryBasesFilter )          propertyTokens.insert( make_pair(QUERYBASES_PROPERTY,          m_settings->QueryBasesFilter) );
 597     if ( m_settings->HasTagFilter )                 propertyTokens.insert( make_pair(TAG_PROPERTY,                 m_settings->TagFilter) );
 598
 599     // send add these properties to filter set "COMMAND_LINE"
 600     return AddPropertyTokensToFilter(CMD, propertyTokens);
 601 }
 602
 603 bool FilterTool::FilterToolPrivate::ParseFilterObject(const string& filterName, const Json::Value& filterObject) {
 604
 605     // filter object parsing variables
 606     Json::Value null(Json::nullValue);
 607     Json::Value propertyValue;
 608
 609     // store results
 610     map<string, string> propertyTokens;
 611
 612     // iterate over known properties
 613     vector<string>::const_iterator propertyNameIter = m_propertyNames.begin();
 614     vector<string>::const_iterator propertyNameEnd  = m_propertyNames.end();
 615     for ( ; propertyNameIter != propertyNameEnd; ++propertyNameIter ) {
 616         const string& propertyName = (*propertyNameIter);
 617
 618         // if property defined in filter, add to token list
 619         propertyValue = filterObject.get(propertyName, null);
 620         if ( propertyValue != null )
 621             propertyTokens.insert( make_pair(propertyName, propertyValue.asString()) );
 622     }
 623
 624     // add this filter to engin
 625     m_filterEngine.addFilter(filterName);
 626
 627     // add token list to this filter
 628     return AddPropertyTokensToFilter(filterName, propertyTokens);
 629 }
 630
 631 bool FilterTool::FilterToolPrivate::ParseScript(void) {
 632
 633     // read in script contents from file
 634     const string document = GetScriptContents();
 635
 636     // set up JsonCPP reader and attempt to parse script
 637     Json::Value root;
 638     Json::Reader reader;
 639     if ( !reader.parse(document, root) ) {
 640         // use built-in error reporting mechanism to alert user what was wrong with the script
 641         cerr  << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl
 642               << reader.getFormatedErrorMessages();
 643         return false;
 644     }
 645
 646     // initialize return status
 647     bool success = true;
 648
 649     // see if root object contains multiple filters
 650     const Json::Value filters = root["filters"];
 651     if ( !filters.isNull() ) {
 652
 653         // iterate over any filters found
 654         int filterIndex = 0;
 655         Json::Value::const_iterator filtersIter = filters.begin();
 656         Json::Value::const_iterator filtersEnd  = filters.end();
 657         for ( ; filtersIter != filtersEnd; ++filtersIter, ++filterIndex ) {
 658             Json::Value filter = (*filtersIter);
 659
 660             // convert filter index to string
 661             string filterName;
 662
 663             // if id tag supplied
 664             const Json::Value id = filter["id"];
 665             if ( !id.isNull() )
 666                 filterName = id.asString();
 667
 668             // use array index
 669             else {
 670                 stringstream convert;
 671                 convert << filterIndex;
 672                 filterName = convert.str();
 673             }
 674
 675             // create & parse filter
 676             success &= ParseFilterObject(filterName, filter);
 677         }
 678
 679         // see if user defined a "rule" for these filters
 680         // otherwise, use filter engine's default rule behavior
 681         string ruleString("");
 682         const Json::Value rule = root["rule"];
 683         if ( rule.isString() )
 684             ruleString = rule.asString();
 685         m_filterEngine.setRule(ruleString);
 686
 687         // return success/fail
 688         return success;
 689     }
 690
 691     // otherwise, root is the only filter (just contains properties)
 692     // create & parse filter named "ROOT"
 693     else success = ParseFilterObject("ROOT", root);
 694
 695     // return success/failure
 696     return success;
 697 }
 698
 699 bool FilterTool::FilterToolPrivate::Run(void) {
 700
 701     // set to default input if none provided
 702     if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
 703         m_settings->InputFiles.push_back(Options::StandardIn());
 704
 705     // add files in the filelist to the input file list
 706     if ( m_settings->HasInputFilelist ) {
 707
 708         ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
 709         if ( !filelist.is_open() ) {
 710             cerr << "bamtools filter ERROR: could not open input BAM file list... Aborting." << endl;
 711             return false;
 712         }
 713
 714         string line;
 715         while ( getline(filelist, line) )
 716             m_settings->InputFiles.push_back(line);
 717     }
 718
 719     // initialize defined properties & user-specified filters
 720     // quit if failed
 721     if ( !SetupFilters() )
 722         return false;
 723
 724     // open reader without index
 725     BamMultiReader reader;
 726     if ( !reader.Open(m_settings->InputFiles) ) {
 727         cerr << "bamtools filter ERROR: could not open input files for reading." << endl;
 728         return false;
 729     }
 730
 731     // retrieve reader header & reference data
 732     const string headerText = reader.GetHeaderText();
 733     filterToolReferences = reader.GetReferenceData();
 734
 735     // determine compression mode for BamWriter
 736     bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
 737                               !m_settings->IsForceCompression );
 738     BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
 739     if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
 740
 741     // open BamWriter
 742     BamWriter writer;
 743     writer.SetCompressionMode(compressionMode);
 744     if ( !writer.Open(m_settings->OutputFilename, headerText, filterToolReferences) ) {
 745         cerr << "bamtools filter ERROR: could not open " << m_settings->OutputFilename << " for writing." << endl;
 746         reader.Close();
 747         return false;
 748     }
 749
 750     // if no region specified, filter entire file
 751     BamAlignment al;
 752     if ( !m_settings->HasRegion ) {
 753         while ( reader.GetNextAlignment(al) ) {
 754             if ( CheckAlignment(al) )
 755                 writer.SaveAlignment(al);
 756         }
 757     }
 758
 759     // otherwise attempt to use region as constraint
 760     else {
 761
 762         // if region string parses OK
 763         BamRegion region;
 764         if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
 765
 766             // attempt to find index files
 767             reader.LocateIndexes();
 768
 769             // if index data available for all BAM files, we can use SetRegion
 770             if ( reader.HasIndexes() ) {
 771
 772                 // attempt to use SetRegion(), if failed report error
 773                 if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
 774                     cerr << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl;
 775                     reader.Close();
 776                     return false;
 777                 }
 778
 779                 // everything checks out, just iterate through specified region, filtering alignments
 780                 while ( reader.GetNextAlignment(al) )
 781                     if ( CheckAlignment(al) )
 782                         writer.SaveAlignment(al);
 783                 }
 784
 785             // no index data available, we have to iterate through until we
 786             // find overlapping alignments
 787             else {
 788                 while ( reader.GetNextAlignment(al) ) {
 789                     if ( (al.RefID >= region.LeftRefID)  && ((al.Position + al.Length) >= region.LeftPosition) &&
 790                          (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
 791                     {
 792                         if ( CheckAlignment(al) )
 793                             writer.SaveAlignment(al);
 794                     }
 795                 }
 796             }
 797         }
 798
 799         // error parsing REGION string
 800         else {
 801             cerr << "bamtools filter ERROR: could not parse REGION: " << m_settings->Region << endl;
 802             cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
 803                  << endl;
 804             reader.Close();
 805             return false;
 806         }
 807     }
 808
 809     // clean up & exit
 810     reader.Close();
 811     writer.Close();
 812     return true;
 813 }
 814
 815 bool FilterTool::FilterToolPrivate::SetupFilters(void) {
 816
 817     // set up filter engine with supported properties
 818     InitProperties();
 819
 820     // parse script for filter rules, if given
 821     if ( m_settings->HasScript )
 822         return ParseScript();
 823
 824     // otherwise check command line for filters
 825     else return ParseCommandLine();
 826 }
 827
 828 // ---------------------------------------------
 829 // FilterTool implementation
 830
 831 FilterTool::FilterTool(void)
 832     : AbstractTool()
 833     , m_settings(new FilterSettings)
 834     , m_impl(0)
 835 {
 836     // ----------------------------------
 837     // set program details
 838
 839     const string usage = "[-in <filename> -in <filename> ... | -list <filelist>] "
 840                          "[-out <filename> | [-forceCompression]] [-region <REGION>] "
 841                          "[ [-script <filename] | [filterOptions] ]";
 842
 843     Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", usage );
 844
 845     // ----------------------------------
 846     // I/O options
 847
 848     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
 849
 850     const string inDesc     = "the input BAM file(s)";
 851     const string listDesc   = "the input BAM file list, one line per file";
 852     const string outDesc    = "the output BAM file";
 853     const string regionDesc = "only read data from this genomic region (see documentation for more details)";
 854     const string scriptDesc = "the filter script file (see documentation for more details)";
 855     const string forceDesc  = "if results are sent to stdout (like when piping to another tool), "
 856                               "default behavior is to leave output uncompressed. Use this flag to "
 857                               "override and force compression";
 858
 859     Options::AddValueOption("-in",     "BAM filename", inDesc,     "", m_settings->HasInput,  m_settings->InputFiles,     IO_Opts, Options::StandardIn());
 860     Options::AddValueOption("-list",   "filename",     listDesc,   "", m_settings->HasInputFilelist,  m_settings->InputFilelist, IO_Opts);
 861     Options::AddValueOption("-out",    "BAM filename", outDesc,    "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
 862     Options::AddValueOption("-region", "REGION",       regionDesc, "", m_settings->HasRegion, m_settings->Region,         IO_Opts);
 863     Options::AddValueOption("-script", "filename",     scriptDesc, "", m_settings->HasScript, m_settings->ScriptFilename, IO_Opts);
 864     Options::AddOption("-forceCompression",forceDesc, m_settings->IsForceCompression, IO_Opts);
 865
 866     // ----------------------------------
 867     // general filter options
 868
 869     OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters");
 870
 871     const string flagDesc    = "keep reads with this *exact* alignment flag (for more detailed queries, see below)";
 872     const string insertDesc  = "keep reads with insert size that matches pattern";
 873     const string mapQualDesc = "keep reads with map quality that matches pattern";
 874     const string nameDesc    = "keep reads with name that matches pattern";
 875     const string queryDesc   = "keep reads with motif that matches pattern";
 876     const string tagDesc     = "keep reads with this key=>value pair";
 877
 878     Options::AddValueOption("-alignmentFlag", "int",       flagDesc,    "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
 879     Options::AddValueOption("-insertSize",    "int",       insertDesc,  "", m_settings->HasInsertSizeFilter,    m_settings->InsertSizeFilter,    FilterOpts);
 880     Options::AddValueOption("-mapQuality",    "[0-255]",   mapQualDesc, "", m_settings->HasMapQualityFilter,    m_settings->MapQualityFilter,    FilterOpts);
 881     Options::AddValueOption("-name",          "string",    nameDesc,    "", m_settings->HasNameFilter,          m_settings->NameFilter,          FilterOpts);
 882     Options::AddValueOption("-queryBases",    "string",    queryDesc,   "", m_settings->HasQueryBasesFilter,    m_settings->QueryBasesFilter,    FilterOpts);
 883     Options::AddValueOption("-tag",           "TAG:VALUE", tagDesc,     "", m_settings->HasTagFilter,           m_settings->TagFilter,           FilterOpts);
 884
 885     // ----------------------------------
 886     // alignment flag filter options
 887
 888     OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters");
 889
 890     const string boolArg           = "true/false";
 891     const string isDupDesc         = "keep only alignments that are marked as duplicate?";
 892     const string isFailQcDesc      = "keep only alignments that failed QC?";
 893     const string isFirstMateDesc   = "keep only alignments marked as first mate?";
 894     const string isMappedDesc      = "keep only alignments that were mapped?";
 895     const string isMateMappedDesc  = "keep only alignments with mates that mapped";
 896     const string isMateReverseDesc = "keep only alignments with mate on reverese strand?";
 897     const string isPairedDesc      = "keep only alignments that were sequenced as paired?";
 898     const string isPrimaryDesc     = "keep only alignments marked as primary?";
 899     const string isProperPairDesc  = "keep only alignments that passed PE resolution?";
 900     const string isReverseDesc     = "keep only alignments on reverse strand?";
 901     const string isSecondMateDesc  = "keep only alignments marked as second mate?";
 902     const string isSingletonDesc   = "keep only singletons";
 903
 904     Options::AddValueOption("-isDuplicate",         boolArg, isDupDesc,         "", m_settings->HasIsDuplicateFilter,         m_settings->IsDuplicateFilter,         AlignmentFlagOpts, TRUE_STR);
 905     Options::AddValueOption("-isFailedQC",          boolArg, isFailQcDesc,      "", m_settings->HasIsFailedQCFilter,          m_settings->IsFailedQCFilter,          AlignmentFlagOpts, TRUE_STR);
 906     Options::AddValueOption("-isFirstMate",         boolArg, isFirstMateDesc,   "", m_settings->HasIsFirstMateFilter,         m_settings->IsFirstMateFilter,         AlignmentFlagOpts, TRUE_STR);
 907     Options::AddValueOption("-isMapped",            boolArg, isMappedDesc,      "", m_settings->HasIsMappedFilter,            m_settings->IsMappedFilter,            AlignmentFlagOpts, TRUE_STR);
 908     Options::AddValueOption("-isMateMapped",        boolArg, isMateMappedDesc,  "", m_settings->HasIsMateMappedFilter,        m_settings->IsMateMappedFilter,        AlignmentFlagOpts, TRUE_STR);
 909     Options::AddValueOption("-isMateReverseStrand", boolArg, isMateReverseDesc, "", m_settings->HasIsMateReverseStrandFilter, m_settings->IsMateReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
 910     Options::AddValueOption("-isPaired",            boolArg, isPairedDesc,      "", m_settings->HasIsPairedFilter,            m_settings->IsPairedFilter,            AlignmentFlagOpts, TRUE_STR);
 911     Options::AddValueOption("-isPrimaryAlignment",  boolArg, isPrimaryDesc,     "", m_settings->HasIsPrimaryAlignmentFilter,  m_settings->IsPrimaryAlignmentFilter,  AlignmentFlagOpts, TRUE_STR);
 912     Options::AddValueOption("-isProperPair",        boolArg, isProperPairDesc,  "", m_settings->HasIsProperPairFilter,        m_settings->IsProperPairFilter,        AlignmentFlagOpts, TRUE_STR);
 913     Options::AddValueOption("-isReverseStrand",     boolArg, isReverseDesc,     "", m_settings->HasIsReverseStrandFilter,     m_settings->IsReverseStrandFilter,     AlignmentFlagOpts, TRUE_STR);
 914     Options::AddValueOption("-isSecondMate",        boolArg, isSecondMateDesc,  "", m_settings->HasIsSecondMateFilter,        m_settings->IsSecondMateFilter,        AlignmentFlagOpts, TRUE_STR);
 915     Options::AddValueOption("-isSingleton",         boolArg, isSingletonDesc,   "", m_settings->HasIsSingletonFilter,         m_settings->IsSingletonFilter,         AlignmentFlagOpts, TRUE_STR);
 916 }
 917
 918 FilterTool::~FilterTool(void) {
 919
 920     delete m_settings;
 921     m_settings = 0;
 922
 923     delete m_impl;
 924     m_impl = 0;
 925 }
 926
 927 int FilterTool::Help(void) {
 928     Options::DisplayHelp();
 929     return 0;
 930 }
 931
 932 int FilterTool::Run(int argc, char* argv[]) {
 933
 934     // parse command line arguments
 935     Options::Parse(argc, argv, 1);
 936
 937     // initialize FilterTool with settings
 938     m_impl = new FilterToolPrivate(m_settings);
 939
 940     // run FilterTool, return success/fail
 941     if ( m_impl->Run() )
 942         return 0;
 943     else
 944         return 1;
 945 }