Examples with MalformedFeatureFile htsjdk.tribble.TribbleException.MalformedFeatureFile used on opensource projects

Example 1 with MalformedFeatureFile

use of htsjdk.tribble.TribbleException.MalformedFeatureFile in project ASCIIGenome by dariober.

the class MakeTabixIndex method blockCompressAndIndex.

/**
 * Block compress input file and create associated tabix index.
 * @throws IOException
 * @throws InvalidRecordException
 */
private void blockCompressAndIndex(String intab, File bgzfOut, TabixFormat fmt) throws IOException, InvalidRecordException {
    LineIterator lin = utils.IOUtils.openURIForLineIterator(intab);
    BlockCompressedOutputStream writer = new BlockCompressedOutputStream(bgzfOut);
    long filePosition = writer.getFilePointer();
    TabixIndexCreator indexCreator = new TabixIndexCreator(fmt);
    boolean first = true;
    // This is relevant to vcf files only: Prepare header and codec
    // ------------------------------------------------------------
    VCFHeader vcfHeader = null;
    VCFCodec vcfCodec = null;
    if (fmt.equals(TabixFormat.VCF)) {
        try {
            VCFFileReader vcfr = new VCFFileReader(new File(intab), false);
            // new VCFHeader();
            vcfHeader = vcfr.getFileHeader();
            vcfr.close();
        } catch (MalformedFeatureFile e) {
            vcfHeader = new VCFHeader();
        }
        vcfCodec = new VCFCodec();
        vcfCodec.setVCFHeader(vcfHeader, Utils.getVCFHeaderVersion(vcfHeader));
    }
    // ------------------------------------------------------------
    int nWarnings = 10;
    while (lin.hasNext()) {
        String line = lin.next().trim();
        try {
            if (line.isEmpty() || line.startsWith("track ")) {
                continue;
            }
            if (line.startsWith("#")) {
                writer.write((line + "\n").getBytes());
                filePosition = writer.getFilePointer();
                continue;
            }
            if (line.startsWith("##FASTA")) {
                break;
            }
            if (first && !fmt.equals(TabixFormat.VCF)) {
                String dummy = this.makeDummyLine(line, fmt);
                addLineToIndex(dummy, indexCreator, filePosition, fmt, null, null);
                writer.write(dummy.getBytes());
                writer.write('\n');
                filePosition = writer.getFilePointer();
                first = false;
            }
            addLineToIndex(line, indexCreator, filePosition, fmt, vcfHeader, vcfCodec);
            writer.write(line.getBytes());
            writer.write('\n');
            filePosition = writer.getFilePointer();
        } catch (Exception e) {
            if (e.getMessage().contains("added out sequence of order") || e.getMessage().contains("Features added out of order")) {
                // Get a string marker for out-of-order from htsjdk/tribble/index/tabix/TabixIndexCreator.java
                throw new InvalidRecordException();
            }
            if (nWarnings >= 0) {
                System.err.println("Warning: " + e.getMessage() + ". Skipping:\n" + line);
            }
            if (nWarnings == 0) {
                System.err.println("Additional warnings will not be show.");
            }
            nWarnings--;
        }
    }
    writer.flush();
    Index index = indexCreator.finalizeIndex(writer.getFilePointer());
    index.writeBasedOnFeatureFile(bgzfOut);
    writer.close();
    CloserUtil.close(lin);
}