Package htsjdk.samtools

Examples of htsjdk.samtools.ValidationStringency

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public class AlignmentDecoder implements FeatureDecoder<PicardAlignment> {

    @Override
    public Iterator<PicardAlignment> decodeAll(InputStream is, boolean strictParsing) throws IOException {
        SAMFileReader reader = new SAMFileReader(is);
        ValidationStringency stringency =
                strictParsing ? ValidationStringency.STRICT : ValidationStringency.SILENT;
        reader.setValidationStringency(stringency);
        return new WrappedIterator(reader.iterator());
    }
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     */
    @Override
    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);
        final ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
        if (VALIDATION_STRINGENCY == ValidationStringency.STRICT) {
            SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
        }
        try {
            final SAMFileReader reader = new SAMFileReader(INPUT);
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        final SAMFileReader headerReader = new SAMFileReader(HEADER);
        final SAMFileHeader replacementHeader = headerReader.getFileHeader();
        headerReader.close();

        final ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
        SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);

        try {
            if (BamFileIoUtils.isBamFile(INPUT)) {
                blockCopyReheader(replacementHeader);
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        final Date startDate = new Date();
        this.defaultHeaders.add(new StringHeader(commandLine));
        this.defaultHeaders.add(new StringHeader("Started on: " + startDate));

        Log.setGlobalLogLevel(VERBOSITY);
        final ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
        SAMFileReader.setDefaultValidationStringency(VALIDATION_STRINGENCY);
        SamReaderFactory.setDefaultValidationStringency(VALIDATION_STRINGENCY);
        BlockCompressedOutputStream.setDefaultCompressionLevel(COMPRESSION_LEVEL);

        if (MAX_RECORDS_IN_RAM != null) {
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        }
        else {
            out = new PrintWriter(System.out);
        }

        final ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
        SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
        boolean result;
        try {
            final SAMFileReader samReader = new SAMFileReader(INPUT);
            if (!samReader.isBinary()) VALIDATE_INDEX=false;
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Related Classes of htsjdk.samtools.ValidationStringency

  • org.broad.igv.cli_plugin.AlignmentDecoder
  • picard.cmdline.CommandLineProgram
  • picard.sam.CleanSam
  • picard.sam.ReplaceSamHeader
  • picard.sam.ValidateSamFile
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