| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/bwa/ |
| H A D | BwaMemAlignmentUtils.java | 27 final List<String> refNames, final SAMFileHeader header, in applyAlignment()
100 final List<String> refNames ) { in createSATags()
131 public static String asTag( final BwaMemAlignment alignment, final List<String> refNames ) { in asTag()
139 … final SAMFileHeader header, final List<String> refNames, in toSAMStreamForRead()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/ |
| H A D | PSBwaAligner.java | 33 … final List<String> refNames, final SAMFileHeader header) { in applyAlignments()
85 final List<String> refNames = bwaIndex.getReferenceContigNames(); in apply() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/ |
| H A D | StructuralVariationDiscoveryPipelineSpark.java | 307 …final List<String> refNames = SequenceDictionaryUtils.getContigNamesList(referenceSequenceDictiona… in getContigRawAlignments() local
393 …final List<String> refNames = SequenceDictionaryUtils.getContigNamesList(header.getSequenceDiction… in filterAndConvertToAlignedContigViaSAM() local
433 … final List<String> refNames, final SAMFileHeader header) { in filterAndConvertToAlignedContigDirect()
448 … final List<String> refNames, in getAlignedContigsInOneAssembly()
473 … final List<String> refNames, in getAlignmentsForOneContig()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/bwa/ |
| H A D | BwaMemAlignmentUtilsTest.java | 13 final List<String> refNames = new ArrayList<>(5); in testSATags() local
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | AlignedContigGeneratorUnitTest.java | 33 private static final List<String> refNames = Collections.singletonList(dummyRefName); field in AlignedContigGeneratorUnitTest
120 …ilterAndConvertToAlignedContigDirect(Collections.singletonList(excuse), refNames, null).isEmpty()); in testConvertAlignedAssemblyOrExcuseToAlignedContigsDirectAndConcordanceWithSAMRoute() local
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| H A D | AlignedAssemblyUnitTest.java | 27 private static final List<String> refNames = Collections.singletonList(dummyRefName); field in AlignedAssemblyUnitTest
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| H A D | AlignmentIntervalUnitTest.java | 22 private static final List<String> refNames = Collections.singletonList(dummyRefName); field in AlignmentIntervalUnitTest
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/ |
| H A D | roi_builder.h | 92 seqan::StringSet<seqan::CharString> refNames; variable
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | AlignedAssemblyOrExcuse.java | 251 …rd> toSAMStreamForAlignmentsOfThisAssembly(final SAMFileHeader header, final List<String> refNames, in toSAMStreamForAlignmentsOfThisAssembly()
331 …final List<String> refNames = SequenceDictionaryUtils.getContigNamesList(cleanHeader.getSequenceDi… in writeAssemblySAMFile() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/ |
| H A D | BwaSparkEngine.java | 162 final List<String> refNames = bwaMemIndex.getReferenceContigNames(); in apply() local
|
| /dports/www/libwww/w3c-libwww-5.4.2/Library/src/ |
| H A D | HTNDir.c | 52 HTList* refNames; /* referee names list */ member
105 int refs, HTList * refNames) in HTNewsNode_new()
515 int refs, HTList * refNames) in HTNewsDir_addElement()
|
| /dports/lang/go-devel/go-becaeea1199b875bc24800fa88f2f4fea119bf78/src/cmd/internal/obj/ |
| H A D | objfile.go | 620 func (w *writer) refNames() { func
|
| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | SealRefInfo.java | 253 final ArrayList<String> refNames=new ArrayList<String>(); field in SealRefInfo
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| H A D | DecontaminateByNormalization.java | 682 private final ArrayList<String> refNames=new ArrayList<String>(); field in DecontaminateByNormalization
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| H A D | Seal.java | 2826 private final ArrayList<String> refNames=new ArrayList<String>(); local
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | SingleSequenceReferenceAligner.java | 36 private final List<String> refNames; field in SingleSequenceReferenceAligner
|
| /dports/cad/kicad-devel/kicad-a17a58203b33e08b966075833b177dad5740c236/eeschema/netlist_exporters/ |
| H A D | netlist_exporter_pspice.cpp | 274 std::set<wxString> refNames; // Set of reference names, to check for duplication in ProcessNetlist() local
|
| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | SendSketch.java | 728 private String refNames=null; field in SendSketch
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| /dports/biology/bamtools/bamtools-2.5.2/src/api/internal/bam/ |
| H A D | BamReader_p.cpp | 230 std::vector<std::string> refNames; in GetReferenceID() local
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | AlignmentInterval.java | 279 …public AlignmentInterval(final BwaMemAlignment alignment, final List<String> refNames, final int u… in AlignmentInterval()
|
| /dports/biology/bbmap/bbmap/current/kmer/ |
| H A D | TableLoaderLockFree.java | 724 public ArrayList<String> refNames; field in TableLoaderLockFree
|
| /dports/multimedia/projectx/Project-X_0.91.0/src/net/sourceforge/dvb/projectx/subtitle/ |
| H A D | ColorAreas.java | 566 …private final String[] refNames = { "null", "transp", "dark" , "lite", "white" //fixed //S9 … field in ColorAreas
|
| /dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/ |
| H A D | readSet.c | 1083 char ** refNames; in readBAMFile() local
|
| /dports/biology/velvet/velvet_1.2.10/src/ |
| H A D | readSet.c | 971 char ** refNames; in readBAMFile() local
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | clusterfitcommand.cpp | 382 set<string> refNames; vector<string> refLabels; vector< vector<string> > otus; in execute() local
|