Examples of Aligner

align.aligner.Aligner
net.sourceforge.align.filter.aligner.Aligner
Represents aligner - for each alignment on input list aligns source segments with target segments and appends obtained list of alignments to the result. This implies that resulting list can have more alignments than input list but cannot have less. Does not change alignment contents. @author Jarek Lipski (loomchild)
org.broadinstitute.gatk.engine.alignment.Aligner
Create perfect alignments from the read to the genome represented by the given BWT / suffix array. @author mhanna @version 0.1

Examples of net.sourceforge.align.filter.aligner.Aligner

    SplitAlgorithm splitAlgorithm = new SplitAlgorithmMock(1);
    AlignAlgorithm alignAlgorithm = new AlignAlgorithmMock(2);
    MergeAlgorithm mergeAlgorithm = new SeparatorMergeAlgorithm();
    List<Filter> filterList = new ArrayList<Filter>();
    filterList.add(new Modifier(splitAlgorithm, splitAlgorithm));
    filterList.add(new Aligner(alignAlgorithm));
    filterList.add(new Modifier(mergeAlgorithm, mergeAlgorithm));
    CompositeFilter composite = new CompositeFilter(filterList);
    List<Alignment> alignmentList = createAlignmentList(
        SOURCE_SEGMENT_ARRAY, TARGET_SEGMENT_ARRAY);
    List<Alignment> resultAlignmentList = composite.apply(alignmentList);

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Examples of net.sourceforge.align.filter.aligner.Aligner

   * Tests whether alignments with infinite score are ignored and
   * the ones without are not by using {@link OneToOneAlgorithm} aligner.
   */
  @Test
  public void testIgnoreInfiniteProbability() {
    Filter oneToOneAligner = new Aligner(new OneToOneAlgorithm());
    Filter filter = 
      new IgnoreInfiniteProbabilityAlignmentsFilterDecorator(oneToOneAligner);


    List<Alignment> alignmentList = createAlignmentList(
        SOURCE_SEGMENT_ARRAY, TARGET_SEGMENT_ARRAY);

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Examples of net.sourceforge.align.filter.aligner.Aligner

        loadAlignmentList(unificationCorpus);
      filter = new UnifyAligner(unificationAlignmentList);
    } else {
      alignmentList = parser.parse();
      AlignAlgorithm algorithm = createAlgorithm(commandLine, alignmentList);
      filter = new Aligner(algorithm);
    }
    filter = FilterDecorators.decorate(filter);
    Formatter formatter = new AlFormatter(getOut());
    if (alignmentList == null) {
      alignmentList = parser.parse();

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Examples of org.broadinstitute.gatk.engine.alignment.Aligner


        align(referenceFile,bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile,bamFile);
    }


    private static void align(File referenceFile, File bwtFile, File rbwtFile, File suffixArrayFile, File reverseSuffixArrayFile, File bamFile) throws FileNotFoundException {
        Aligner aligner = new BWAJavaAligner(bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile);
        int count = 0;


        SAMFileReader reader = new SAMFileReader(bamFile);
        reader.setValidationStringency(ValidationStringency.SILENT);


        int mismatches = 0;
        int failures = 0;


        for(SAMRecord read: reader) {
            count++;
            if( count > 200000 ) break;
            //if( count < 366000 ) continue;
            //if( count > 2 ) break;
            //if( !read.getReadName().endsWith("SL-XBC:1:82:506:404#0") )
            //    continue;
            //if( !read.getReadName().endsWith("SL-XBC:1:36:30:1926#0") )
            //    continue;
            //if( !read.getReadName().endsWith("SL-XBC:1:60:1342:1340#0") )
            //    continue;


            SAMRecord alignmentCleaned = null;
            try {
                alignmentCleaned = (SAMRecord)read.clone();
            }
            catch( CloneNotSupportedException ex ) {
                throw new ReviewedGATKException("SAMRecord clone not supported", ex);
            }


            if( alignmentCleaned.getReadNegativeStrandFlag() )
                alignmentCleaned.setReadBases(BaseUtils.simpleReverseComplement(alignmentCleaned.getReadBases()));


            alignmentCleaned.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
            alignmentCleaned.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
            alignmentCleaned.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
            alignmentCleaned.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);


            // Clear everything except flags pertaining to pairing and set 'unmapped' status to true.
            alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C);


            Iterable<Alignment[]> alignments = aligner.getAllAlignments(alignmentCleaned.getReadBases());
            if(!alignments.iterator().hasNext() ) {
                //throw new GATKException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
                System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count);
                failures++;
            }

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