Searched refs:vcfFiles (Results 1 – 5 of 5) sorted by relevance
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
| H A D | GATKSVVCFUtilsUnitTest.java | 77 … final List<Path> vcfFiles = Files.walk(Paths.get(toolsTestDir + "spark/sv/integration/outputs")) in testDataForSVVCFFiles() local
80 vcfFiles.addAll( Files.walk(Paths.get(toolsTestDir + "spark/sv/utils")) in testDataForSVVCFFiles()
83 vcfFiles.forEach(p -> data.add( new Object[]{p})); in testDataForSVVCFFiles()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/ |
| H A D | MultiComparator.java | 413 List<String> vcfFiles = fileChooser.getFiles(VCFview.VCFFILE_SUFFIX); in loadFromProperty()
414 loadBamAndVcf(listBams, vcfFiles, index); in loadFromProperty()
980 List<String> vcfFiles = fileChooser.getFiles(VCFview.VCFFILE_SUFFIX); in makeFileMenu()
982 loadBamAndVcf(listBams, vcfFiles, index); in makeFileMenu()
1017 List<String> vcfFiles, in loadBamAndVcf() argument
1060 if (vcfFiles.size() > 0) in loadBamAndVcf()
1065 VCFview vcfView = new VCFview(null, thisVCFPanel, vcfFiles, in loadBamAndVcf()
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| H A D | EntryEdit.java | 540 final List<String> vcfFiles = fileChooser.getFiles(VCFview.VCFFILE_SUFFIX); in EntryEdit()
541 loadBamAndVcf(listBams, vcfFiles); in EntryEdit()
1413 List<String> vcfFiles = fileChooser.getFiles(VCFview.VCFFILE_SUFFIX); in makeFileMenu()
1414 loadBamAndVcf(listBams, vcfFiles); in makeFileMenu()
1919 private void loadBamAndVcf(List<String> listBams, List<String> vcfFiles) in loadBamAndVcf() argument
1964 logger4j.debug("No. VCF FILES="+vcfFiles.size()); in loadBamAndVcf()
1965 if (vcfFiles.size() > 0) in loadBamAndVcf()
1968 vcfView = new VCFview(null, vcfPanel, vcfFiles, in loadBamAndVcf()
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/variant/ |
| H A D | VCFview.java | 141 private List<String> vcfFiles; field in VCFview
208 final List<String> vcfFiles, in VCFview() argument
224 this.vcfFiles = vcfFiles; in VCFview()
234 (vcfFiles.size()+1)*(LINE_HEIGHT+5))); in VCFview()
245 vcfReaders = new AbstractVCFReader[vcfFiles.size()]; in VCFview()
247 for(int i=0; i<vcfFiles.size(); i++) in VCFview()
249 readHeader(vcfFiles.get(i), i); in VCFview()
318 vcfFiles.addAll(vcfFileList); in createMenus()
341 for(int i=0; i<vcfFiles.size(); i++) in createMenus()
484 IOUtils.export(manualHash, vcfFiles, VCFview.this); in createMenus()
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| H A D | IOUtils.java | 157 final List<String> vcfFiles, in export() argument
168 for(int i=0; i<vcfFiles.size(); i++) in export()
170 …File filterFile = IOUtils.writeVCF(manualHash, vcfFiles.get(i), i, vcfView, features, vcfFiles.siz… in export()
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