/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/ |
H A D | BwaSparkEngine.java | 34 private final String indexFileName; field in BwaSparkEngine 48 final String indexFileName, in BwaSparkEngine() argument 54 if (indexFileName != null) { in BwaSparkEngine() 55 this.indexFileName = indexFileName; in BwaSparkEngine() 60 this.indexFileName = IOUtils.getPath(indexFile).getFileName().toString(); in BwaSparkEngine() 101 final String indexFileName = this.indexFileName; in align() local 104 …new ReadAligner(resolveIndexFileName ? SparkFiles.get(indexFileName) : indexFileName, broadcastHea… in align() 121 …ReadAligner( final String indexFileName, final SAMFileHeader readsHeader, final boolean alignsPair… in ReadAligner() argument 122 this.bwaMemIndex = BwaMemIndexCache.getInstance(indexFileName); in ReadAligner()
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/dports/textproc/jalingo/jalingo-0.6.0-src/src/ja/lingo/engine/dictionaryindex/builder/ |
H A D | DictionaryIndexBuilder.java | 35 private String indexFileName; field in DictionaryIndexBuilder 37 public DictionaryIndexBuilder( String indexFileName ) throws IOException { in DictionaryIndexBuilder() argument 38 Arguments.assertNotNull( "indexFileName", indexFileName ); in DictionaryIndexBuilder() 41 this.indexFileName = indexFileName; in DictionaryIndexBuilder() 43 builderFormat = new BuilderFormat( indexFileName ); in DictionaryIndexBuilder() 94 info.setIndexFileName( indexFileName ); in close()
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H A D | BuilderFormat.java | 43 public BuilderFormat( String indexFileName ) throws IOException { in BuilderFormat() argument 44 Arguments.assertNotNull( "indexFileName", indexFileName ); in BuilderFormat() 46 this.indexFos = new FileOutputStream( indexFileName ); in BuilderFormat()
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/dports/security/rcracki_mt/rcracki_mt_0.7.0_src/rcracki_mt/ |
H A D | RTIReader.cpp | 41 this->indexFileName = fname + ".index"; in RTIReader() 51 if( stat( indexFileName.c_str(), &indexFileStats ) == -1 ) in RTIReader() 53 std::cerr << "ERROR: stat() for file: " << indexFileName << " FAILED! " << std::endl; in RTIReader() 64 indexFileData = fopen( indexFileName.c_str(), "rb"); in RTIReader() 67 …std::cerr << "ERROR: could not open index file: " << indexFileName.c_str() << " EXITING!" << std::… in RTIReader() 89 this->indexFileName = fname + ".index"; in RTIReader() 99 if( stat( indexFileName.c_str(), &indexFileStats ) == -1 ) in RTIReader() 101 std::cerr << "ERROR: stat() for file: " << indexFileName << " FAILED! " << std::endl; in RTIReader() 112 indexFileData = fopen( indexFileName.c_str(), "rb"); in RTIReader() 115 …std::cerr << "ERROR: could not open index file: " << indexFileName.c_str() << " EXITING!" << std::… in RTIReader() [all …]
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/dports/devel/hadoop2/hadoop-2.7.2-src/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-core/src/main/java/org/apache/hadoop/mapred/ |
H A D | SpillRecord.java | 56 public SpillRecord(Path indexFileName, JobConf job) throws IOException { in SpillRecord() argument 57 this(indexFileName, job, null); in SpillRecord() 60 public SpillRecord(Path indexFileName, JobConf job, String expectedIndexOwner) in SpillRecord() argument 62 this(indexFileName, job, new PureJavaCrc32(), expectedIndexOwner); in SpillRecord() 65 public SpillRecord(Path indexFileName, JobConf job, Checksum crc, in SpillRecord() argument 71 SecureIOUtils.openFSDataInputStream(new File(indexFileName.toUri() in SpillRecord() 74 final long length = rfs.getFileStatus(indexFileName).getLen(); in SpillRecord() 85 indexFileName, -1); in SpillRecord()
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/dports/textproc/jalingo/jalingo-0.6.0-src/src/ja/lingo/engine/beans/ |
H A D | Info.java | 33 private String indexFileName; field in Info 84 return indexFileName; in getIndexFileName() 86 public void setIndexFileName( String indexFileName ) { in setIndexFileName() argument 87 this.indexFileName = indexFileName; in setIndexFileName() 140 ", indexFileName='" + indexFileName + '\'' + in toString()
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie/ |
H A D | BowtieTask.cpp | 141 if (settings.indexFileName.isEmpty()) { in prepare() 147 settings.indexFileName = settings.refSeqUrl.dirPath() + "/" + indexName; in prepare() 149 …settings.indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFil… in prepare() 154 QFileInfo file(settings.indexFileName + indexSuffixes[i]); in prepare() 162 QFileInfo file(settings.indexFileName + indexSuffixes[0]); in prepare() 241 arguments.append(settings.indexFileName); in prepare() 377 QString indexFileName = settings.indexFileName; in prepare() local 378 if (indexFileName.isEmpty()) { in prepare() 380 … indexFileName = settings.refSeqUrl.dirPath() + "/" + settings.refSeqUrl.baseFileName(); in prepare() 382 … indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFileName(); in prepare() [all …]
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie2/ |
H A D | Bowtie2Task.cpp | 78 if (settings.indexFileName.isEmpty()) { in prepare() 84 settings.indexFileName = settings.refSeqUrl.dirPath() + "/" + indexName; in prepare() 86 …settings.indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFil… in prepare() 161 arguments.append(settings.indexFileName); in prepare() 263 QString indexFileName = settings.indexFileName; in prepare() local 264 if (indexFileName.isEmpty()) { in prepare() 266 … indexFileName = settings.refSeqUrl.dirPath() + "/" + settings.refSeqUrl.baseFileName(); in prepare() 268 … indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFileName(); in prepare() 271 … buildIndexTask = new Bowtie2BuildIndexTask(settings.refSeqUrl.getURLString(), indexFileName); in prepare()
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/dports/biology/ugene/ugene-40.1/src/plugins/CoreTests/src/ |
H A D | DnaAssemblyTests.cpp | 62 indexFileName = el.attribute(INDEX_FILE_ATTR); in init() 63 if (!indexFileName.isEmpty()) { in init() 64 indexFileName.prepend(env->getVar("COMMON_DATA_DIR") + "/"); in init() 127 if (indexFileName.isEmpty()) { in prepare() 128 …indexFileName = GUrlUtils::rollFileName(dir + "/" + GUrl(refSeqUrl).baseFileName() + "_index_" + i… in prepare() 137 settings.indexFileName = indexFileName; in prepare()
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/dports/devel/hadoop/hadoop-1.2.1/src/mapred/org/apache/hadoop/mapred/ |
H A D | SpillRecord.java | 52 public SpillRecord(Path indexFileName, JobConf job, String expectedIndexOwner) in SpillRecord() argument 54 this(indexFileName, job, new PureJavaCrc32(), expectedIndexOwner); in SpillRecord() 57 public SpillRecord(Path indexFileName, JobConf job, Checksum crc, in SpillRecord() argument 63 new File(indexFileName.toUri().getPath()), expectedIndexOwner)); in SpillRecord() 65 final long length = rfs.getFileStatus(indexFileName).getLen(); in SpillRecord() 76 indexFileName, -1); in SpillRecord()
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/dports/net/liveMedia/live/liveMedia/ |
H A D | MPEG2TransportStreamIndexFile.cpp | 28 ::MPEG2TransportStreamIndexFile(UsageEnvironment& env, char const* indexFileName) in MPEG2TransportStreamIndexFile() argument 30 fFileName(strDup(indexFileName)), fFid(NULL), fMPEGVersion(0), fCurrentIndexRecordNum(0), in MPEG2TransportStreamIndexFile() 33 u_int64_t indexFileSize = GetFileSize(indexFileName, NULL); in MPEG2TransportStreamIndexFile() 35 env << "Warning: Size of the index file \"" << indexFileName in MPEG2TransportStreamIndexFile() 44 ::createNew(UsageEnvironment& env, char const* indexFileName) { in createNew() argument 45 if (indexFileName == NULL) return NULL; in createNew() 47 = new MPEG2TransportStreamIndexFile(env, indexFileName); in createNew()
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/dports/net/liveMedia/live/testProgs/ |
H A D | testMPEG2TransportStreamTrickPlay.cpp | 76 char* indexFileName = new char[len+2]; // allow for trailing x\0 in main() local 77 sprintf(indexFileName, "%sx", inputFileName); in main() 79 = MPEG2TransportStreamIndexFile::createNew(*env, indexFileName); in main() 81 *env << "Failed to open index file \"" << indexFileName << "\" (does it exist?)\n"; in main()
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/dports/biology/ugene/ugene-40.1/src/plugins/genome_aligner/src/ |
H A D | GenomeAlignerTask.cpp | 108 if (settings.indexFileName.isEmpty()) { in GenomeAlignerTask() 110 indexFileName = settings.refSeqUrl.dirPath() + "/" + settings.refSeqUrl.baseFileName(); in GenomeAlignerTask() 117 …indexFileName = indexDir + "/" + settings.refSeqUrl.baseFileName() + "." + GenomeAlignerIndex::HEA… in GenomeAlignerTask() 120 indexFileName = settings.indexFileName; in GenomeAlignerTask() 124 taskLog.details(tr("Index file name: %1").arg(indexFileName)); in GenomeAlignerTask() 308 s.indexFileName = indexFileName; in setupCreateIndexTask() 377 return indexFileName; in getIndexPath()
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/dports/astro/marble/marble-21.12.3/src/lib/marble/ |
H A D | DiscCache.cpp | 18 static QString indexFileName( const QString &cacheDirectory ) in indexFileName() function 30 QFile file( indexFileName( m_CacheDirectory ) ); in DiscCache() 49 QFile file( indexFileName( m_CacheDirectory ) ); in ~DiscCache() 76 if ( it.fileName() == indexFileName( m_CacheDirectory ) ) // skip index file in clear()
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/dports/games/libretro-scummvm/scummvm-7b1e929/engines/tinsel/ |
H A D | handle.cpp | 102 const char *indexFileName = TinselV1PSX ? PSX_INDEX_FILENAME : INDEX_FILENAME; in SetupHandleTable() local 104 if (f.open(indexFileName)) { in SetupHandleTable() 111 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable() 137 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable() 143 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable() 146 error(CANNOT_FIND_FILE, indexFileName); in SetupHandleTable()
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/dports/games/scummvm/scummvm-2.5.1/engines/tinsel/ |
H A D | handle.cpp | 88 const char *indexFileName = TinselV1PSX ? PSX_INDEX_FILENAME : INDEX_FILENAME; in SetupHandleTable() local 90 if (f.open(indexFileName)) { in SetupHandleTable() 97 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable() 123 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable() 129 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable() 132 error(CANNOT_FIND_FILE, indexFileName); in SetupHandleTable()
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/Fasta/ |
H A D | Fasta.cpp | 247 string indexFileName = filename + index->indexFileExtension(); in open() local 249 if(stat(indexFileName.c_str(), &stFileInfo) == 0) { in open() 252 stat(indexFileName.c_str(), &index_attrib); in open() 257 index->readIndexFile(indexFileName); in open() 259 cerr << "index file " << indexFileName << " not found, generating..." << endl; in open() 261 index->writeIndexFile(indexFileName); in open()
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/dports/databases/kexi/kexi-3.2.0/src/migration/xbase/ |
H A D | xbasemigrate.cpp | 343 foreach( const QString& indexFileName, indexFileNames ) { in getConstraints() 352 QString fileExtension = indexFileName.right( 3 ); in getConstraints() 364 if ( index->OpenIndex(qPrintable(indexFileName)) != XB_NO_ERROR ) { in getConstraints() 365 qDebug()<<"Couldn't open index file"<<indexFileName; in getConstraints() 375 qDebug()<<"Expression mismatch in "<<indexFileName; in getConstraints()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/util_sarray/ |
H A D | SArrayIndexSerializer.h | 35 …static void serialize(const SArrayIndex *index, const QString &indexFileName, const QString &refFi… 36 static void deserialize(SArrayIndex *index, const QString &indexFileName, TaskStateInfo &ti);
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H A D | SArrayIndexSerializer.cpp | 31 void SArrayIndexSerializer::serialize(const SArrayIndex *index, const QString &indexFileName, const… in serialize() argument 33 QFile file(indexFileName); in serialize() 34 if (indexFileName.isEmpty() || !file.open(QIODevice::WriteOnly)) { in serialize() 187 void SArrayIndexSerializer::deserialize(SArrayIndex *index, const QString &indexFileName, TaskState… in deserialize() argument 188 QFile file(indexFileName); in deserialize()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/registry/ |
H A D | DnaAssemblyTask.cpp | 47 settings.indexFileName = settings.refSeqUrl.getURLString(); in setUpIndexBuilding() 53 settings.indexFileName = settings.refSeqUrl.getURLString(); in setUpIndexBuilding() 59 settings.indexFileName = baseUrl; in setUpIndexBuilding()
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/commons/ |
H A D | DBWriter.h | 16 …DBWriter(const char* dataFileName, const char* indexFileName, unsigned int threads, size_t mode, i… 26 char* getIndexFileName() { return indexFileName; } in getIndexFileName() 83 char* indexFileName; variable
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/dports/databases/mongodb36/mongodb-src-r3.6.23/src/third_party/timelib-2017.05/zones/ |
H A D | build-idx.php | 2 $indexFileName = 'timezonedb.idx'; variable 49 file_put_contents( $indexFileName, $idx_data );
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/dports/net/liveMedia/live/mediaServer/ |
H A D | DynamicRTSPServer.cpp | 187 char* indexFileName = new char[indexFileNameLen]; in createNewSMS() local 188 sprintf(indexFileName, "%sx", fileName); in createNewSMS() 190 …ion(MPEG2TransportFileServerMediaSubsession::createNew(env, fileName, indexFileName, reuseSource)); in createNewSMS() 191 delete[] indexFileName; in createNewSMS()
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/dports/net/liveMedia/live/liveMedia/include/ |
H A D | MPEG2TransportStreamIndexFile.hh | 36 char const* indexFileName); 67 MPEG2TransportStreamIndexFile(UsageEnvironment& env, char const* indexFileName);
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