| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/ |
| H A D | vcf_materialization.h | 80 seqan::CharString vcfFileName; variable
123 char const * vcfFileName,
126 … rng(rng), methOptions(methOptions), fastaFileName(fastaFileName), vcfFileName(vcfFileName), in rng()
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| H A D | mason_splicing.cpp | 135 …vcfMat(rng, toCString(options.matOptions.fastaFileName), toCString(options.matOptions.vcfFileName)) in MasonSplicingApp()
329 if (!empty(options.matOptions.vcfFileName)) in _performSplicing()
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| H A D | vcf_materialization.cpp | 164 if (!empty(vcfFileName)) in init()
167 if (!open(vcfFileIn, toCString(vcfFileName))) in init()
276 if (empty(vcfFileName)) in _materializeNext()
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| H A D | mason_materializer.cpp | 87 toCString(options.matOptions.vcfFileName), in MasonMaterializerApp()
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| H A D | mason_options.h | 183 seqan::CharString vcfFileName; member
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| H A D | mason_options.cpp | 373 getOptionValue(vcfFileName, parser, "input-vcf"); in getOptionValues()
385 << " VARIANTS VCF \t" << vcfFileName << "\n"; in print()
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| H A D | mason_simulator.cpp | 868 toCString(options.matOptions.vcfFileName), in MasonSimulatorApp()
1098 if (!empty(options.matOptions.vcfFileName)) in _initAlignmentSplitter()
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | vcfintersect.cpp | 62 string vcfFileName; in main() local
128 vcfFileName = string(optarg); in main()
133 vcfFileName = string(optarg); in main()
239 if (!vcfFileName.empty()) { in main()
240 if (vcfFileName == "-") { in main()
248 otherVariantFile.open(vcfFileName); in main()
251 cerr << "could not open VCF file " << vcfFileName << endl; in main()
258 …scription=\"" + tagValue + " if this allele intersects with one in " + vcfFileName + ", '.' if n… in main()
276 …" + s.str() + ",Description=\"The value of " + mergeFromTag + " in " + vcfFileName + " '.' if th… in main()
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| H A D | vcf2dag.cpp | 39 string vcfFileName; in main() local
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| H A D | vcfremap.cpp | 47 string vcfFileName; in main() local
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| H A D | vcfgeno2haplo.cpp | 56 string vcfFileName; in main() local
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | vcfintersect.cpp | 52 string vcfFileName; in main() local
118 vcfFileName = string(optarg); in main()
123 vcfFileName = string(optarg); in main()
229 if (!vcfFileName.empty()) { in main()
230 if (vcfFileName == "-") { in main()
238 otherVariantFile.open(vcfFileName); in main()
241 cerr << "could not open VCF file " << vcfFileName << endl; in main()
248 …scription=\"" + tagValue + " if this allele intersects with one in " + vcfFileName + ", '.' if n… in main()
266 …" + s.str() + ",Description=\"The value of " + mergeFromTag + " in " + vcfFileName + " '.' if th… in main()
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| H A D | vcf2dag.cpp | 28 string vcfFileName; in main() local
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| H A D | vcfremap.cpp | 36 string vcfFileName; in main() local
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| H A D | vcfgeno2haplo.cpp | 46 string vcfFileName; in main() local
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | vcfintersect.cpp | 52 string vcfFileName; in main() local
118 vcfFileName = string(optarg); in main()
123 vcfFileName = string(optarg); in main()
229 if (!vcfFileName.empty()) { in main()
230 if (vcfFileName == "-") { in main()
238 otherVariantFile.open(vcfFileName); in main()
241 cerr << "could not open VCF file " << vcfFileName << endl; in main()
248 …scription=\"" + tagValue + " if this allele intersects with one in " + vcfFileName + ", '.' if n… in main()
266 …" + s.str() + ",Description=\"The value of " + mergeFromTag + " in " + vcfFileName + " '.' if th… in main()
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| H A D | vcf2dag.cpp | 28 string vcfFileName; in main() local
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| H A D | vcfremap.cpp | 36 string vcfFileName; in main() local
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| H A D | vcfgeno2haplo.cpp | 46 string vcfFileName; in main() local
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/variant/ |
| H A D | AbstractVCFReader.java | 144 final String vcfFileName, in write() argument
151 if(IOUtils.isBCF(vcfFileName)) in write()
153 BCFReader reader = new BCFReader(vcfFileName); in write()
158 if(readers[i].getFileName().equals(vcfFileName)) in write()
181 final TabixReader tr = new TabixReader(vcfFileName); in write()
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| H A D | IOUtils.java | 97 final String vcfFileName, in writeVCF() argument
105 File filterFile = getFile(vcfFileName, nfiles, ".filter", null); in writeVCF()
109 AbstractVCFReader.write(manualHash, vcfFileName, vcfIndex, writer, vcfView, features); in writeVCF()
120 private static File getFile(final String vcfFileName, final int nfiles, in getFile() argument
125 if(vcfFileName.startsWith("http")) in getFile()
127 int ind = vcfFileName.lastIndexOf('/')+1; in getFile()
128 return new File(vcfFileName.substring(ind)+suffix); in getFile()
131 return new File(vcfFileName+suffix); in getFile()
135 file_dialog.setSelectedFile(new File(vcfFileName+suffix)); in getFile()
1397 final String vcfFileName, in makeFeature() argument
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/spark/ |
| H A D | GATKSparkTool.java | 713 for (String vcfFileName : vcfFileNames) { in addVCFsForSpark()
715 if (vcfFileName.endsWith(FileExtensions.VCF)) { in addVCFsForSpark()
716 vcfIndexFileName = vcfFileName + FileExtensions.VCF_INDEX; in addVCFsForSpark()
717 } else if (vcfFileName.endsWith(FileExtensions.COMPRESSED_VCF)) { in addVCFsForSpark()
718 vcfIndexFileName = vcfFileName + FileExtensions.COMPRESSED_VCF_INDEX; in addVCFsForSpark()
722 ctx.addFile(vcfFileName); in addVCFsForSpark()
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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 | SVVCFWriter.java | 39 public static void writeVCF(final List<VariantContext> localVariants, final String vcfFileName, in writeVCF() argument
49 …writeVariants(vcfFileName, sortedVariantsList, referenceSequenceDictionary, defaultToolVCFHeaderLi… in writeVCF()
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