| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/ |
| H A D | GenomeLocParser.java | 94 public final boolean contigIsInDictionary(final String contig) { in contigIsInDictionary()
105 public final SAMSequenceRecord getContigInfo(final String contig) { in getContigInfo()
118 public final int getContigIndex(final String contig) { in getContigIndex()
122 protected int getContigIndexWithoutException(final String contig) { in getContigIndexWithoutException()
149 public GenomeLoc createGenomeLoc(String contig, final int start, final int stop) { in createGenomeLoc()
201 public GenomeLoc createGenomeLoc(final String contig, final int pos) { in createGenomeLoc()
275 public boolean isValidGenomeLoc(String contig, int start, int stop ) { in isValidGenomeLoc()
312 final String contig = locatable.getContig(); in parseGenomeLoc() local
417 SAMSequenceRecord contig = contigInfo.getSequence(contigName); in createOverEntireContig() local
431 final SAMSequenceRecord contig = contigInfo.getSequence(contigName); in createGenomeLocAtStart() local
[all …]
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| H A D | MRUCachingSAMSequenceDictionary.java | 52 public final boolean hasContig(final String contig) { in hasContig()
63 public final SAMSequenceRecord getSequence(final String contig) { in getSequence()
91 public final int getSequenceIndex(final String contig) { in getSequenceIndex()
104 protected boolean isCached(final String contig) { in isCached()
126 private SAMSequenceRecord updateCache(final String contig, int index ) { in updateCache()
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| H A D | SimpleInterval.java | 26 private final String contig; field in SimpleInterval
34 public SimpleInterval(final String contig, final int start, final int end){ in SimpleInterval()
58 static void validatePositions(final String contig, final int start, final int end) { in validatePositions()
68 public static boolean isValid(final String contig, final int start, final int end) { in isValid()
105 final String contig; in SimpleInterval() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/ |
| H A D | SimpleIntervalUnitTest.java | 28 public void badIntervals(String contig, int start, int end, String name){ in badIntervals()
34 public void badIntervalsFromLocatable(String contig, int start, int end, String name){ in badIntervalsFromLocatable()
59 public void testGoodIntervals(String str, String contig, int start, int end){ in testGoodIntervals()
61 Assert.assertEquals(interval.getContig(), contig, "contig"); in testGoodIntervals() local
69 public void testGoodIntervalsFromLocatable(String ignoreMe, String contig, int start, int end){ in testGoodIntervalsFromLocatable()
73 Assert.assertEquals(interval.getContig(), contig, "contig"); in testGoodIntervalsFromLocatable() local
78 private static Locatable getLocatable(final String contig, final int start, final int end) { in getLocatable()
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| /dports/biology/jalview/jalview/src/jalview/datamodel/ |
| H A D | VisibleContigsIterator.java | 64 int[] contig = new int[] { vstart, hideStart - 1 }; in VisibleContigsIterator() local
70 int[] contig = new int[] { vstart, end - 1 }; in VisibleContigsIterator() local
85 int[] contig = new int[] { vstart, end - 1 }; in VisibleContigsIterator() local
92 int[] contig = new int[] { start, end - 1 }; in VisibleContigsIterator() local
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| /dports/science/py-scipy/scipy-1.7.1/benchmarks/benchmarks/ |
| H A D | linalg.py | 31 def setup(self, size, contig, module): argument
49 def time_solve(self, size, contig, module): argument
55 def time_solve_triangular(self, size, contig, module): argument
63 def time_inv(self, size, contig, module): argument
69 def time_det(self, size, contig, module): argument
75 def time_eigvals(self, size, contig, module): argument
81 def time_svd(self, size, contig, module): argument
103 def setup(self, shape, contig, module): argument
110 def time_1_norm(self, size, contig, module): argument
116 def time_inf_norm(self, size, contig, module): argument
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ArtificialReadQueryIterator.java | 59 public void queryContained( String contig, int start, int stop ) { in queryContained()
71 public void queryOverlapping( String contig, int start, int stop ) { in queryOverlapping()
76 public void query( String contig, int start, int stop, boolean contained ) { in query()
91 private void initialize( String contig, int start, int stop ) { in initialize()
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| /dports/biology/seqan1/seqan-1.3.1/apps/rabema/ |
| H A D | verification.h | 78 void verifyMatchestoErrorFunctionResults_FindReads( in verifyMatchestoErrorFunctionResults_FindReads()
117 void verifyMatchestoErrorFunctionResults_FindReads( in verifyMatchestoErrorFunctionResults_FindReads()
148 void verifyMatchestoErrorFunctionResults_FindReads( in verifyMatchestoErrorFunctionResults_FindReads()
177 void verifyMatchestoErrorFunctionResults_FindReads( in verifyMatchestoErrorFunctionResults_FindReads()
207 void verifyMatchestoErrorFunctionResults_FindReads( in verifyMatchestoErrorFunctionResults_FindReads()
275 TContigSeq /*const*/ & contig = contigs[contigId].seq; in verifyMatchesToErrorFunctionResults() local
336 TContigSeq const & contig = contigs[it->contigId].seq; in verifyMatchesToErrorFunctionResults() local
355 TContigSeq const & contig = contigs[it->contigId].seq; in verifyMatchesToErrorFunctionResults() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | AssemblyContigWithFineTunedAlignmentsUnitTest.java | 87 … public void testGetAlignmentSignatureBasicType(final AssemblyContigWithFineTunedAlignments contig, in testGetAlignmentSignatureBasicType()
106 …public void testGetAlignmentSignatureBasicType(final AssemblyContigWithFineTunedAlignments contig)… in testGetAlignmentSignatureBasicType()
124 …oid testGetReasonForAlignmentClassificationFailure(final AssemblyContigWithFineTunedAlignments con… in testGetReasonForAlignmentClassificationFailure()
143 …void testHasIncompletePicture(final AssemblyContigWithFineTunedAlignments contig, final boolean ex… in testHasIncompletePicture()
154 …lic void testHasIncompletePictureFromTwoAlignments(final AssemblyContigWithFineTunedAlignments con… in testHasIncompletePictureFromTwoAlignments()
165 …oid testHasIncompletePictureFromMultipleAlignments(final AssemblyContigWithFineTunedAlignments con… in testHasIncompletePictureFromMultipleAlignments()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align_split/ |
| H A D | test_align_split.h | 48 seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT"; in SEQAN_DEFINE_TEST() local
97 …seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCT" "AGTAGGCA… in SEQAN_DEFINE_TEST() local
176 seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT"; in SEQAN_DEFINE_TEST() local
205 …seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCT" "AGTAGGCA… in SEQAN_DEFINE_TEST() local
274 seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT"; in SEQAN_DEFINE_TEST() local
316 …seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCT" "AGTAGGCA… in SEQAN_DEFINE_TEST() local
395 seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT"; in SEQAN_DEFINE_TEST() local
424 …seqan::DnaString contig = "AGCATGTTAGATAAGATAGCTGTGCT" "AGTAGGCA… in SEQAN_DEFINE_TEST() local
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/cramtools/ref/ |
| H A D | ReferenceSequenceFromSeekable.java | 51 public byte[] getSubsequenceAt(String contig, long start, long stop) { in getSubsequenceAt()
149 String contig = tokens.group(1); in buildIndex() local
165 private String contig; field in ReferenceSequenceFromSeekable.FastaSequenceIndexEntry
172 …public FastaSequenceIndexEntry(String contig, long location, long size, int basesPerLine, int byte… in FastaSequenceIndexEntry()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | SVLocation.java | 4 private int contig; field in SVLocation
7 public SVLocation( final int contig, final int position ) { in SVLocation()
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| H A D | SVInterval.java | 43 private final int contig; field in SVInterval
50 public SVInterval( final int contig, final int start, final int end ) { in SVInterval()
56 void accept(final int contig, final int start, final int end); in accept()
85 …public SVInterval( final int contig, final int start, final int end, final SVIntervalConstructorAr… in SVInterval()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | SVFastqUtilsUnitTest.java | 58 public void testMappingToString(final String str, final String[] contig, final int[] start, in testMappingToString()
72 public void testMappingFromString(final String str, final String[] contig, final int[] start, in testMappingFromString()
232 … public void testMappingFromGATKRead(final GATKRead read, final String[] contig, final int[] start, in testMappingFromGATKRead()
241 …public void testMappingFromFastqRead(final SVFastqUtils.FastqRead read, final String[] contig, fin… in testMappingFromFastqRead()
250 … public void testMappingToStringRead(final GATKRead read, final String[] contig, final int[] start, in testMappingToStringRead()
259 …oid assertMappingIsAsExpected(final SVFastqUtils.Mapping mapping, final String[] contig, final int… in assertMappingIsAsExpected()
277 Assert.assertEquals(ai.referenceSpan.getContig(), contig[i]); in assertMappingIsAsExpected() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | ReferenceShard.java | 17 private final String contig; field in ReferenceShard
21 public ReferenceShard(int shardNumber, String contig) { in ReferenceShard()
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| H A D | VariantShard.java | 17 private final String contig; field in VariantShard
20 public VariantShard(int shardNumber, String contig) { in VariantShard()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/sv/ |
| H A D | BafEvidence.java | 11 final String contig; field in BafEvidence
15 …public BafEvidence(final String sample, final String contig, final int position, final double valu… in BafEvidence()
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| H A D | DepthEvidence.java | 11 final String contig; field in DepthEvidence
16 public DepthEvidence(final String contig, int start, final int end, final int[] counts) { in DepthEvidence()
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| H A D | SplitReadEvidence.java | 11 final String contig; field in SplitReadEvidence
16 …public SplitReadEvidence(final String sample, final String contig, final int position, final int c… in SplitReadEvidence()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/fasta/ |
| H A D | CachingIndexedFastaSequenceFileUnitTest.java | 65 SAMSequenceRecord contig = caching.getSequenceDictionary().getSequence(0); in testCachingIndexedFastaReaderSequential1() local
78 SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0); in testSequential() local
112 SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0); in testCachingIndexedFastaReaderTwoStage() local
164 final String contig, final int start, final int stop ) { in mixedCasesTestHelper()
179 …private String fetchBaseString(final ReferenceSequenceFile reader, final String contig, final int … in fetchBaseString()
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| /dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/ |
| H A D | ReadsPreprocessingPipelineTestData.java | 181 …public static GATKRead makeRead(String contig, KV<Integer, Integer> startLength, int i, Class<?> c… in makeRead()
193 public static GATKRead makeRead(String contig, int start, int length, int i, Class<?> clazz) { in makeRead()
231 private SimpleInterval makeInterval(String contig, KV<Integer, Integer> startLength) { in makeInterval()
235 private ReferenceBases getBases(String contig, int start, int end) { in getBases()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/ |
| H A D | CRAMReferenceSequenceFile.java | 58 public ReferenceSequence getSequence(String contig) in getSequence()
90 public ReferenceSequence getSubsequenceAt(String contig, long start, long stop ) in getSubsequenceAt()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | FermiLiteAssemblyHandler.java | 298 private static void replaceConnection( final Contig contig, in replaceConnection()
392 private static int countPredecessors( final Contig contig ) { in countPredecessors()
398 private static void tracePaths( final Contig contig, in tracePaths()
466 private final Contig contig; field in FermiLiteAssemblyHandler.ContigLocation
470 public ContigLocation(final Contig contig, final int offset, final boolean canonical ) { in ContigLocation()
514 private final Contig contig; field in FermiLiteAssemblyHandler.ContigStrand
517 public ContigStrand( final Contig contig, final boolean isRC ) { in ContigStrand()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/ |
| H A D | DataProviderForExampleGencodeGtfGene.java | 435 …c GencodeGtfGeneFeature dynamicallyCreateTestGencodeGtfGeneFeature(final String contig, final int … in dynamicallyCreateTestGencodeGtfGeneFeature()
524 …tic GencodeGtfExonFeature createStopCodonExon(final int exonStart, final String contig, final int … in createStopCodonExon()
567 …e static GencodeGtfUTRFeature create3pUtr(final AtomicInteger featureOrderNum, final String contig, in create3pUtr()
581 …e static GencodeGtfUTRFeature create5pUtr(final AtomicInteger featureOrderNum, final String contig, in create5pUtr()
597 …ic GencodeGtfExonFeature createStartCodonExon(final int exonStart, final String contig, final int … in createStartCodonExon()
653 …private static GencodeGtfExonFeature createMiddleExon(final int exonStart, final String contig, fi… in createMiddleExon()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/codecs/sampileup/ |
| H A D | SAMPileupFeature.java | 23 private final String contig; field in SAMPileupFeature
31 …SAMPileupFeature(final String contig, final int position, final byte refBase, final List<SAMPileup… in SAMPileupFeature()
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