Examples of SAMReaderID

Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID

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    public Collection<SAMFileWriter> getWriters() {
        return writerMap.values();
    }

    public void addAlignment(SAMRecord samRecord) {
        final SAMReaderID id = toolkit.getReaderIDForRead(samRecord);
        String rg = samRecord.getStringAttribute("RG");
        if ( rg != null ) {
            String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg);
            samRecord.setAttribute("RG",rg_orig);
        }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID

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    @Test(expectedExceptions=UserException.class)
    public void testDuplicateSamFileHandlingSingleDuplicate() throws Exception {
        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();

        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));

        testEngine.setSAMFileIDs(samFiles);
        testEngine.checkForDuplicateSamFiles();
    }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID

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    @Test(expectedExceptions=UserException.class)
    public void testDuplicateSamFileHandlingMultipleDuplicates() throws Exception {
        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();

        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleNORG.bam"), new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"),  new Tags()));
        samFiles.add(new SAMReaderID(new File(publicTestDir + "exampleNORG.bam"), new Tags()));

        testEngine.setSAMFileIDs(samFiles);
        testEngine.checkForDuplicateSamFiles();
    }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID

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        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();

        final File relativePathToBAMFile = new File(publicTestDir + "exampleBAM.bam");
        final File absolutePathToBAMFile = new File(relativePathToBAMFile.getAbsolutePath());
        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
        samFiles.add(new SAMReaderID(relativePathToBAMFile, new Tags()));
        samFiles.add(new SAMReaderID(absolutePathToBAMFile, new Tags()));

        testEngine.setSAMFileIDs(samFiles);
        testEngine.checkForDuplicateSamFiles();
    }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID

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                                               publicTestDir + "exampleBAM.bam",
                                               "         "
                                              );

        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));

        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
    }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID

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                                               "#" + publicTestDir + "foo.bam",
                                               "      # " + publicTestDir + "bar.bam"
                                              );

        List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
        expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File(publicTestDir + "exampleBAM.bam"), new Tags()));

        performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
    }
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Examples of org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID

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            Tags inputFileNameTags = parser.getTags(inputFileName);
            inputFileName = expandFileName(inputFileName);
            if (inputFileName.toLowerCase().endsWith(".list") ) {
                try {
                    for ( String fileName : new XReadLines(new File(inputFileName), true, LIST_FILE_COMMENT_START) ) {
                        unpackedReads.add(new SAMReaderID(fileName,parser.getTags(inputFileName)));
                    }
                }
                catch( FileNotFoundException ex ) {
                    throw new UserException.CouldNotReadInputFile(new File(inputFileName), "Unable to find file while unpacking reads", ex);
                }
            }
            else if(inputFileName.toLowerCase().endsWith(".bam")) {
                unpackedReads.add(new SAMReaderID(inputFileName,inputFileNameTags));
            }
            else if(inputFileName.endsWith("stdin")) {
                unpackedReads.add(new SAMReaderID(inputFileName,inputFileNameTags));
            }
            else {
                throw new UserException.CommandLineException(String.format("The GATK reads argument (-I, --input_file) supports only BAM files with the .bam extension and lists of BAM files " +
                        "with the .list extension, but the file %s has neither extension.  Please ensure that your BAM file or list " +
                        "of BAM files is in the correct format, update the extension, and try again.",inputFileName));
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