Examples of org.broadinstitute.gatk.utils.commandline.ParsingEngine

    private void performBAMListFileUnpackingTest( File tempListFile, List<SAMReaderID> expectedUnpackedFileList ) throws Exception {
        List<String> bamFiles = new ArrayList<String>();
        bamFiles.add(tempListFile.getAbsolutePath());


        CommandLineGATK testInstance = new CommandLineGATK();
        testInstance.setParser(new ParsingEngine(testInstance));


        List<SAMReaderID> unpackedBAMFileList = ListFileUtils.unpackBAMFileList(bamFiles,new ParsingEngine(testInstance));


        Assert.assertEquals(unpackedBAMFileList.size(), expectedUnpackedFileList.size(),
                            "Unpacked BAM file list contains extraneous lines");
        Assert.assertEquals(unpackedBAMFileList, expectedUnpackedFileList,
                            "Unpacked BAM file list does not contain correct BAM file names");

                }
            }


            for (Class<? extends ReadFilter> filter: filterManager.getValues()) {
                String filterName = filterManager.getName(filter);
                writeFilter(filterName, ArgumentDefinitionField.getArgumentFields(new ParsingEngine(null),filter), dependents);
            }


            writeDependencies(dependents);
            
            return 0;

Related Classes of org.broadinstitute.gatk.utils.commandline.ParsingEngine

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