1 /** 2 * UGENE - Integrated Bioinformatics Tools. 3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru> 4 * http://ugene.net 5 * 6 * This program is free software; you can redistribute it and/or 7 * modify it under the terms of the GNU General Public License 8 * as published by the Free Software Foundation; either version 2 9 * of the License, or (at your option) any later version. 10 * 11 * This program is distributed in the hope that it will be useful, 12 * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 * GNU General Public License for more details. 15 * 16 * You should have received a copy of the GNU General Public License 17 * along with this program; if not, write to the Free Software 18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, 19 * MA 02110-1301, USA. 20 */ 21 22 #ifndef _U2_GENOME_ALIGNER_TASK_H_ 23 #define _U2_GENOME_ALIGNER_TASK_H_ 24 25 #include <QMutex> 26 #include <QSharedPointer> 27 #include <QTemporaryFile> 28 29 #include <U2Algorithm/DnaAssemblyTask.h> 30 31 #include <U2Formats/StreamSequenceReader.h> 32 #include <U2Formats/StreamSequenceWriter.h> 33 34 #include "GenomeAlignerFindTask.h" 35 #include "GenomeAlignerIO.h" 36 #include "GenomeAlignerIndexPart.h" 37 #include "GenomeAlignerWriteTask.h" 38 39 namespace U2 { 40 41 class U2SequenceObject; 42 class DNATranslation; 43 class LoadDocumentTask; 44 class GenomeAlignerIndexTask; 45 class GenomeAlignerIndex; 46 class ReadShortReadsSubTask; 47 class WriteAlignedReadsSubTask; 48 class DbiConnection; 49 50 class GenomeAlignerTask : public DnaAssemblyToReferenceTask { 51 Q_OBJECT 52 friend class ReadShortReadsSubTask; 53 54 public: 55 GenomeAlignerTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false); 56 ~GenomeAlignerTask(); 57 virtual void prepare(); 58 virtual ReportResult report(); 59 virtual QList<Task *> onSubTaskFinished(Task *subTask); 60 QString getIndexPath(); 61 static const QString OPTION_ALIGN_REVERSED; 62 static const QString OPTION_OPENCL; 63 static const QString OPTION_IF_ABS_MISMATCHES; 64 static const QString OPTION_MISMATCHES; 65 static const QString OPTION_PERCENTAGE_MISMATCHES; 66 static const QString OPTION_INDEX_DIR; 67 static const QString OPTION_QUAL_THRESHOLD; 68 static const QString OPTION_BEST; 69 static const QString OPTION_READS_MEMORY_SIZE; 70 static const QString OPTION_SEQ_PART_SIZE; 71 static const int MIN_SHORT_READ_LENGTH = 30; 72 static int calculateWindowSize(bool absMismatches, int nMismatches, int ptMismatches, int minReadLength, int maxReadLength); 73 74 DNA_ASSEMBLEY_TO_REF_TASK_FACTORY(GenomeAlignerTask) 75 private: 76 LoadDocumentTask *loadDbiTask; 77 GenomeAlignerIndexTask *createIndexTask; 78 ReadShortReadsSubTask *readTask; 79 GenomeAlignerFindTask *findTask; 80 WriteAlignedReadsSubTask *writeTask; 81 GenomeAlignerWriteTask *pWriteTask; 82 Task *unzipTask; 83 84 GenomeAlignerReader *seqReader; 85 GenomeAlignerWriter *seqWriter; 86 AlignContext alignContext; 87 88 QTemporaryFile temp; 89 90 bool justBuildIndex; 91 92 bool alignReversed; 93 bool dbiIO; 94 QString indexFileName; 95 bool prebuiltIndex; 96 GenomeAlignerIndex *index; 97 int qualityThreshold; 98 qint64 readMemSize; 99 int seqPartSize; 100 SearchQuery *lastQuery; 101 bool noDataToAlign; 102 103 // statistics 104 qint64 readsCount; 105 qint64 readsAligned; 106 qint64 shortreadLoadTime; 107 qint64 resultWriteTime; 108 qint64 indexLoadTime; 109 qint64 shortreadIOTime; 110 float currentProgress; 111 112 QMutex writeLock; 113 114 void setupCreateIndexTask(); 115 void createGenomeAlignerWriteTask(); 116 }; 117 118 } // namespace U2 119 120 #endif // _U2_GENOME_ALIGNER_TASK_H_ 121