+
+// ---------------------------------------------
+// FilterTool implementation
+
+FilterTool::FilterTool(void)
+ : AbstractTool()
+ , m_settings(new FilterSettings)
+ , m_impl(0)
+{
+ // ----------------------------------
+ // set program details
+
+ const string usage = "[-in <filename> -in <filename> ... | -list <filelist>] "
+ "[-out <filename> | [-forceCompression]] [-region <REGION>] "
+ "[ [-script <filename] | [filterOptions] ]";
+
+ Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", usage );
+
+ // ----------------------------------
+ // I/O options
+
+ OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
+
+ const string inDesc = "the input BAM file(s)";
+ const string listDesc = "the input BAM file list, one line per file";
+ const string outDesc = "the output BAM file";
+ const string regionDesc = "only read data from this genomic region (see documentation for more details)";
+ const string scriptDesc = "the filter script file (see documentation for more details)";
+ const string forceDesc = "if results are sent to stdout (like when piping to another tool), "
+ "default behavior is to leave output uncompressed. Use this flag to "
+ "override and force compression";
+
+ Options::AddValueOption("-in", "BAM filename", inDesc, "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", listDesc, "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
+ Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-region", "REGION", regionDesc, "", m_settings->HasRegion, m_settings->Region, IO_Opts);
+ Options::AddValueOption("-script", "filename", scriptDesc, "", m_settings->HasScript, m_settings->ScriptFilename, IO_Opts);
+ Options::AddOption("-forceCompression",forceDesc, m_settings->IsForceCompression, IO_Opts);
+
+ // ----------------------------------
+ // general filter options
+
+ OptionGroup* FilterOpts = Options::CreateOptionGroup("General Filters");
+
+ const string flagDesc = "keep reads with this *exact* alignment flag (for more detailed queries, see below)";
+ const string insertDesc = "keep reads with insert size that matches pattern";
+ const string lengthDesc = "keep reads with length that matches pattern";
+ const string mapQualDesc = "keep reads with map quality that matches pattern";
+ const string nameDesc = "keep reads with name that matches pattern";
+ const string queryDesc = "keep reads with motif that matches pattern";
+ const string tagDesc = "keep reads with this key=>value pair";
+
+ Options::AddValueOption("-alignmentFlag", "int", flagDesc, "", m_settings->HasAlignmentFlagFilter, m_settings->AlignmentFlagFilter, FilterOpts);
+ Options::AddValueOption("-insertSize", "int", insertDesc, "", m_settings->HasInsertSizeFilter, m_settings->InsertSizeFilter, FilterOpts);
+ Options::AddValueOption("-length", "int", lengthDesc, "", m_settings->HasLengthFilter, m_settings->LengthFilter, FilterOpts);
+ Options::AddValueOption("-mapQuality", "[0-255]", mapQualDesc, "", m_settings->HasMapQualityFilter, m_settings->MapQualityFilter, FilterOpts);
+ Options::AddValueOption("-name", "string", nameDesc, "", m_settings->HasNameFilter, m_settings->NameFilter, FilterOpts);
+ Options::AddValueOption("-queryBases", "string", queryDesc, "", m_settings->HasQueryBasesFilter, m_settings->QueryBasesFilter, FilterOpts);
+ Options::AddValueOption("-tag", "TAG:VALUE", tagDesc, "", m_settings->HasTagFilter, m_settings->TagFilter, FilterOpts);
+
+ // ----------------------------------
+ // alignment flag filter options
+
+ OptionGroup* AlignmentFlagOpts = Options::CreateOptionGroup("Alignment Flag Filters");
+
+ const string boolArg = "true/false";
+ const string isDupDesc = "keep only alignments that are marked as duplicate?";
+ const string isFailQcDesc = "keep only alignments that failed QC?";
+ const string isFirstMateDesc = "keep only alignments marked as first mate?";
+ const string isMappedDesc = "keep only alignments that were mapped?";
+ const string isMateMappedDesc = "keep only alignments with mates that mapped";
+ const string isMateReverseDesc = "keep only alignments with mate on reverese strand?";
+ const string isPairedDesc = "keep only alignments that were sequenced as paired?";
+ const string isPrimaryDesc = "keep only alignments marked as primary?";
+ const string isProperPairDesc = "keep only alignments that passed PE resolution?";
+ const string isReverseDesc = "keep only alignments on reverse strand?";
+ const string isSecondMateDesc = "keep only alignments marked as second mate?";
+ const string isSingletonDesc = "keep only singletons";
+
+ Options::AddValueOption("-isDuplicate", boolArg, isDupDesc, "", m_settings->HasIsDuplicateFilter, m_settings->IsDuplicateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isFailedQC", boolArg, isFailQcDesc, "", m_settings->HasIsFailedQCFilter, m_settings->IsFailedQCFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isFirstMate", boolArg, isFirstMateDesc, "", m_settings->HasIsFirstMateFilter, m_settings->IsFirstMateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMapped", boolArg, isMappedDesc, "", m_settings->HasIsMappedFilter, m_settings->IsMappedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMateMapped", boolArg, isMateMappedDesc, "", m_settings->HasIsMateMappedFilter, m_settings->IsMateMappedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isMateReverseStrand", boolArg, isMateReverseDesc, "", m_settings->HasIsMateReverseStrandFilter, m_settings->IsMateReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isPaired", boolArg, isPairedDesc, "", m_settings->HasIsPairedFilter, m_settings->IsPairedFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isPrimaryAlignment", boolArg, isPrimaryDesc, "", m_settings->HasIsPrimaryAlignmentFilter, m_settings->IsPrimaryAlignmentFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isProperPair", boolArg, isProperPairDesc, "", m_settings->HasIsProperPairFilter, m_settings->IsProperPairFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isReverseStrand", boolArg, isReverseDesc, "", m_settings->HasIsReverseStrandFilter, m_settings->IsReverseStrandFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isSecondMate", boolArg, isSecondMateDesc, "", m_settings->HasIsSecondMateFilter, m_settings->IsSecondMateFilter, AlignmentFlagOpts, TRUE_STR);
+ Options::AddValueOption("-isSingleton", boolArg, isSingletonDesc, "", m_settings->HasIsSingletonFilter, m_settings->IsSingletonFilter, AlignmentFlagOpts, TRUE_STR);
+}
+
+FilterTool::~FilterTool(void) {
+
+ delete m_settings;
+ m_settings = 0;
+
+ delete m_impl;
+ m_impl = 0;
+}
+
+int FilterTool::Help(void) {
+ Options::DisplayHelp();
+ return 0;
+}
+
+int FilterTool::Run(int argc, char* argv[]) {
+
+ // parse command line arguments
+ Options::Parse(argc, argv, 1);
+
+ // initialize FilterTool with settings
+ m_impl = new FilterToolPrivate(m_settings);
+
+ // run FilterTool, return success/fail
+ if ( m_impl->Run() )
+ return 0;
+ else
+ return 1;
+}