Exemplo n.º 1
0
  public String getPairOrientation() {
    // LOG.info("getPairOrientation");
    String pairOrientation = "";
    if (EntryFlagHelper.isPaired(entry)
        && !EntryFlagHelper.isMateUnmapped(entry)
        && entry.getTargetIndex() == entry.getPairAlignmentLink().getTargetIndex()) {

      char s1 = EntryFlagHelper.isReadReverseStrand(entry) ? 'R' : 'F';
      char s2 = EntryFlagHelper.isMateReverseStrand(entry) ? 'R' : 'F';
      char o1 = ' ';
      char o2 = ' ';
      char[] tmp = new char[4];
      if (EntryFlagHelper.isFirstInPair(entry)) {
        o1 = '1';
        o2 = '2';
      } else if (EntryFlagHelper.isSecondInPair(entry)) {
        o1 = '2';
        o2 = '1';
      }
      if (getInferredInsertSize() > 0) {
        tmp[0] = s1;
        tmp[1] = o1;
        tmp[2] = s2;
        tmp[3] = o2;

      } else {
        tmp[2] = s1;
        tmp[3] = o1;
        tmp[0] = s2;
        tmp[1] = o2;
      }
      pairOrientation = new String(tmp);
    }
    return pairOrientation;
  }
Exemplo n.º 2
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  public int getMappingQuality() {
    if (entry.hasMappingQuality()) {
      return entry.getMappingQuality();
    } else {

      return 255;
    }
  }
Exemplo n.º 3
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  /**
   * Return the next alignment.
   *
   * @return the next alignment within the window.
   */
  public Alignment next() {
    if (!hasNext()) {
      throw new NoSuchElementException();
    }
    Alignments.AlignmentEntry entry;

    entry = nextEntry;

    nextEntry = null;
    //    LOG.debug(String.format("next targetIndex: %d position: %d", targetIndex,
    // entry.getPosition()));
    currentPosition = entry.getPosition();
    return new GobyAlignment(this, entry);
  }
Exemplo n.º 4
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  /**
   * This method splits blocks whose boundaries contain a read deletion.
   *
   * @param blocks
   * @param alignmentEntry
   * @return
   */
  private ObjectArrayList<AlignmentBlock> introduceDeletions(
      ObjectArrayList<AlignmentBlock> blocks, Alignments.AlignmentEntry alignmentEntry) {

    ObjectArrayList<AlignmentBlock> newBlocks = new ObjectArrayList<AlignmentBlock>();

    for (Alignments.SequenceVariation var : alignmentEntry.getSequenceVariationsList()) {

      for (AlignmentBlock block : blocks) {
        if (!block.isSoftClipped()) {

          final int vrPos = var.getPosition() + entry.getPosition();
          if (hasReadDeletion(var) && vrPos >= block.getStart() && vrPos <= block.getEnd()) {

            ByteList leftBases = new ByteArrayList(block.getBases());
            ByteList leftScores = new ByteArrayList(block.getQualities());
            ByteList rightBases = new ByteArrayList(block.getBases());
            ByteList rightScores = new ByteArrayList(block.getQualities());
            int deletionPosition = var.getPosition() - 1;
            leftBases = leftBases.subList(0, deletionPosition);
            rightBases = rightBases.subList(deletionPosition, rightBases.size());

            leftScores = leftScores.subList(0, deletionPosition);
            rightScores = rightScores.subList(deletionPosition, rightScores.size());

            AlignmentBlock left =
                AlignmentBlock.getInstance(
                    block.getStart(),
                    leftBases.toByteArray(new byte[leftBases.size()]),
                    leftScores.toByteArray(new byte[leftScores.size()]),
                    this);

            AlignmentBlock right =
                AlignmentBlock.getInstance(
                    block.getStart() + leftBases.size() + var.getFrom().length(),
                    rightBases.toByteArray(new byte[rightBases.size()]),
                    rightScores.toByteArray(new byte[rightScores.size()]),
                    this);

            blocks.remove(block);
            newBlocks.add(left);
            newBlocks.add(right);
          }
        }
      }
    }

    newBlocks.addAll(blocks);
    return newBlocks;
  }
Exemplo n.º 5
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  /**
   * Returns the mate for a paired-end read. Please note that this method will return an unmapped
   * mate for any single end read as well. Do check if the read is paired before calling getMate().
   *
   * @return The mate, or a constant unmapped mate (for single end reads, or paired end where the
   *     mate is not found).
   */
  public ReadMate getMate() {
    if (entry.hasPairAlignmentLink()) {
      Alignments.RelatedAlignmentEntry link = entry.getPairAlignmentLink();
      String mateChr = getChromosome(link.getTargetIndex());
      int mateStart = link.getPosition();
      boolean mateNegativeStrand = EntryFlagHelper.isMateReverseStrand(entry);

      boolean isReadUnmappedFlag = EntryFlagHelper.isReadUnmapped(entry);
      final ReadMate mate =
          new ReadMate(mateChr, mateStart, mateNegativeStrand, isReadUnmappedFlag);
      return mate;
    } else {
      return unmappedMate;
    }
  }
Exemplo n.º 6
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  public boolean isPaired() {
    if (entry.hasPairFlags()) {

      return EntryFlagHelper.isPaired(entry);

    } else return false;
  }
Exemplo n.º 7
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  public String getValueString(double position, WindowFunction windowFunction) {
    //  //LOG.info("getValueString");
    MutableString buffer = new MutableString();

    buffer.append(entry.toString());
    buffer.replace("\n", "<br>");

    if (this.isPaired()) {
      buffer.append("----------------------" + "<br>");
      buffer.append("Pair start = " + getMate().positionString() + "<br>");
      buffer.append("Pair is mapped = " + (getMate().isMapped() ? "yes" : "no") + "<br>");
      // buf.append("Pair is proper = " + (getProperPairFlag() ? "yes" : "no") + "<br>");
      if (getChr().equals(getMate().getChr())) {
        buffer.append("Insert size = " + getInferredInsertSize() + "<br>");
      }
      if (getPairOrientation().length() > 0) {
        buffer.append("Pair orientation = " + getPairOrientation() + "<br>");
      }
      if (isFirstOfPair()) {
        buffer.append("First of pair <br>");
      }
      if (isSecondOfPair()) {
        buffer.append("Second of pair <br>");
      }
    }
    return buffer.toString();
  }
Exemplo n.º 8
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  /**
   * Determine if this iterator has more alignment entries in the given window.
   *
   * @return True if next() will return an alignment, False otherwise.
   */
  public boolean hasNext() {
    /*    LOG.debug(String.format("previousPosition: %d endReferencePosition %d previousReferenceIndex %d targetIndex %d",
            previousPosition, endReferencePosition, previousReferenceIndex, targetIndex)
    ); */
    // Fetch the next entry with skipTo
    if (nextEntry != null) return true;

    try {
      if (!useWindow) {
        // all results are returned
        if (!reader.hasNext()) return false;
        nextEntry = reader.next();
      } else {
        // we return only within a window
        nextEntry = reader.skipTo(targetIndex, startReferencePosition);

        if (nextEntry == null
            || (nextEntry.getTargetIndex() != targetIndex
                || nextEntry.getPosition() < startReferencePosition
                || nextEntry.getPosition() > endReferencePosition)) {
          // No next entry, on a different target sequence, or before the position of interest:
          nextEntry = null;
        }
      }
    } catch (IOException e) {
      nextEntry = null;
      LOG.error(e);
      //  throw new RuntimeException("IO error reading next Goby alignment entry", e);
      return false;
    } catch (GobyRuntimeException e) {
      nextEntry = null;
      LOG.error(e);
      //  throw new RuntimeException("IO error reading next Goby alignment entry", e);
      return false;
    }

    final boolean result = nextEntry != null;
    // LOG.debug("hasNext returning :" + result);
    return result;
  }
Exemplo n.º 9
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  /**
   * Verify that the list has an appropriate unbroken chain of back links.
   *
   * @param list the list of splices to validate
   * @return true if the list has an unbroken chain of back links
   */
  boolean spliceListIsValid(final ObjectArrayList<GobyAlignment> list) {

    if (list != null && list.size() > 1) {
      Alignments.AlignmentEntry prevEntry = list.get(0).entry;
      for (int i = 1; i < list.size(); i++) {
        Alignments.AlignmentEntry currentEntry = list.get(i).entry;
        if (!currentEntry.hasSplicedBackwardAlignmentLink()) return false;
        else {
          Alignments.RelatedAlignmentEntry currentBackwardLink =
              currentEntry.getSplicedBackwardAlignmentLink();

          if ((prevEntry.getQueryIndex() != currentEntry.getQueryIndex())
              || (prevEntry.getFragmentIndex() != currentBackwardLink.getFragmentIndex())
              || (prevEntry.getPosition() != currentBackwardLink.getPosition())
              || (prevEntry.getTargetIndex() != currentBackwardLink.getTargetIndex())) {
            return false;
          }
        }
        prevEntry = currentEntry;
      }
    }
    return true;
  }
Exemplo n.º 10
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 public boolean isNegativeStrand() {
   //     //LOG.info("isNegativeStrand");
   return entry.getMatchingReverseStrand();
 }
Exemplo n.º 11
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  /**
   * Construct alignment blocks from the Goby alignment entry. This method uses the convention that
   * '=' denotes a match to the reference.
   *
   * <p>Conventions for storing sequence variations in Goby alignments are described <a
   * href="http://tinyurl.com/goby-sequence-variations">here</a>
   *
   * @param alignmentEntry The Goby alignment entry to use
   */
  public void buildBlocks(Alignments.AlignmentEntry alignmentEntry) {

    ObjectArrayList<AlignmentBlock> blocks = new ObjectArrayList<AlignmentBlock>();
    ObjectArrayList<AlignmentBlock> insertionBlocks = new ObjectArrayList<AlignmentBlock>();

    int start = alignmentEntry.getPosition();
    ByteArrayList bases = new ByteArrayList();
    ByteArrayList scores = new ByteArrayList();
    int readLength = alignmentEntry.getQueryLength();

    byte[] readBases = new byte[readLength];
    byte[] readQual = new byte[readLength];
    Arrays.fill(readBases, (byte) '=');
    if (alignmentEntry.hasReadQualityScores()) {
      readQual = alignmentEntry.getReadQualityScores().toByteArray();
    } else {
      Arrays.fill(readQual, (byte) 40);
    }
    int j = 0;
    int insertedBases = 0;
    int deletedBases = 0;
    final int leftPadding = alignmentEntry.getQueryPosition();
    boolean showSoftClipped =
        PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_SOFT_CLIPPED);
    if (showSoftClipped && entry.hasSoftClippedBasesLeft()) {
      int clipLength = entry.getSoftClippedBasesLeft().length();

      addSoftClipBlock(
          blocks,
          Math.max(0, entry.getPosition() - clipLength),
          entry.getSoftClippedBasesLeft(),
          readQual,
          entry.hasSoftClippedQualityLeft(),
          entry.getSoftClippedQualityLeft().toByteArray(),
          0);
    }
    for (Alignments.SequenceVariation var : alignmentEntry.getSequenceVariationsList()) {
      final String from = var.getFrom();
      final int fromLength = from.length();
      final String to = var.getTo();
      final int toLength = from.length();
      final int sequenceVariationLength = Math.max(fromLength, toLength);
      final ByteString toQuality = var.getToQuality();

      if (hasReadInsertion(from)) {
        bases.clear();
        scores.clear();
        for (int i = 0; i < sequenceVariationLength; i++) {
          final char toChar = i >= toLength ? '-' : to.charAt(i);
          int size = toQuality.size();
          final byte qual = size > 0 && i < size ? toQuality.byteAt(i) : 40;

          bases.add((byte) toChar);
          scores.add(qual);
          deletedBases++;
        }
        addBlock(insertionBlocks, alignmentEntry.getPosition() + var.getPosition(), bases, scores);
        bases.clear();
        scores.clear();
      } else if (!to.contains("-")) {
        for (int i = 0; i < toLength; i++) {
          final int offset = j + var.getPosition() + i - 1 + leftPadding - insertedBases;
          if (offset > 0 && offset < readBases.length) {
            readBases[offset] = (byte) to.charAt(i);
            if (i < toQuality.size()) {
              readQual[offset] = toQuality.byteAt(i);
            }
          }
        }
      } else {
        // has read deletion:
        insertedBases++;
      }
    }

    int pos = start;
    int matchLength = alignmentEntry.getQueryAlignedLength() - deletedBases;
    int endAlignmentRefPosition = matchLength + start;
    bases.clear();
    scores.clear();
    int maxIndex = Math.min(readBases.length, readQual.length);
    while (pos < endAlignmentRefPosition) {
      final int index = pos - start + leftPadding;
      if (index < maxIndex) {
        bases.add(readBases[index]);
        scores.add(readQual[index]);
      } else {
        break;
      }
      ++pos;
    }

    addBlock(blocks, start, bases, scores);
    blocks = introduceDeletions(blocks, entry);
    if (showSoftClipped && entry.hasSoftClippedBasesRight()) {

      int targetAlignedLength = entry.getTargetAlignedLength();
      addSoftClipBlock(
          blocks,
          entry.getPosition() + targetAlignedLength,
          entry.getSoftClippedBasesRight(),
          readQual,
          entry.hasSoftClippedQualityRight(),
          entry.getSoftClippedQualityRight().toByteArray(),
          entry.getQueryAlignedLength() + entry.getSoftClippedBasesLeft().length());
    }
    block = blocks.toArray(new AlignmentBlock[blocks.size()]);
    Arrays.sort(block, blockComparator);
    insertionBlock = insertionBlocks.toArray(new AlignmentBlock[insertionBlocks.size()]);
    Arrays.sort(insertionBlock, blockComparator);
    ObjectArrayList<GobyAlignment> list = null;

    if (alignmentEntry.hasSplicedForwardAlignmentLink()
        || alignmentEntry.hasSplicedBackwardAlignmentLink()) {
      // if has a forward link, store a reference to this alignment in the reader (which represents
      // the window scope)
      list = iterator.cacheSpliceComponent(this);
      if (list.size() > 1 && spliceListIsValid(list)) {

        final GobyAlignment spliceHeadAlignment = list.get(0);

        ObjectArrayList<AlignmentBlock> splicedBlocks = new ObjectArrayList<AlignmentBlock>();
        splicedBlocks.addAll(ObjectArrayList.wrap(spliceHeadAlignment.block));
        splicedBlocks.addAll(blocks);
        spliceHeadAlignment.block = splicedBlocks.toArray(new AlignmentBlock[splicedBlocks.size()]);

        ObjectArrayList<AlignmentBlock> splicedInsertionBlocks =
            new ObjectArrayList<AlignmentBlock>();
        splicedInsertionBlocks.addAll(ObjectArrayList.wrap(spliceHeadAlignment.insertionBlock));
        splicedInsertionBlocks.addAll(insertionBlocks);
        spliceHeadAlignment.insertionBlock =
            splicedInsertionBlocks.toArray(new AlignmentBlock[splicedInsertionBlocks.size()]);

        if (spliceHeadAlignment.gapTypes == null) {
          spliceHeadAlignment.gapTypes = new CharArrayList(10);
        }
        spliceHeadAlignment.gapTypes.add(SamAlignment.SKIPPED_REGION);

        // Since the previous alignment carries this information, we clear up block and
        // insertionBlock
        // in this alignment, but keep any softClips:
        this.block = keepSoftClips(block);
        this.insertionBlock = new AlignmentBlock[0];
      }
    }
  }
Exemplo n.º 12
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  /**
   * Transform the read index into a readname:
   *
   * @return
   */
  public String getReadName() {

    return Integer.toString(entry.getQueryIndex());
  }
Exemplo n.º 13
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  /** Get the reference id from the iterator, prepend "chr". */
  public String getChromosome() {

    return "chr" + iterator.indexToReferenceId.getId(entry.getTargetIndex()).toString();
  }
Exemplo n.º 14
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 public float getScore() {
   // LOG.info("getScore");
   return entry.getScore();
 }
Exemplo n.º 15
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 public int getStart() {
   //      //LOG.info("getStart");
   return entry.getPosition();
 }
Exemplo n.º 16
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 public int getInferredInsertSize() {
   if (entry.hasInsertSize()) {
     return entry.getInsertSize();
   } else return 0;
 }
Exemplo n.º 17
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  @Test
  public void testLastToCompact1() throws IOException {

    // test LastToCompact convert+filtering

    // read fake data and convert+filter
    final LastToCompactMode processor = new LastToCompactMode();
    final int LAST_TO_COMPACT_M_PARAM = 2;
    processor.setAmbiguityThreshold(LAST_TO_COMPACT_M_PARAM);
    processor.setInputFile("test-results/alignments/last-to-compact/last-101.maf");
    processor.setOutputFile("test-results/alignments/last-to-compact/last-101.compact");
    processor.setTargetReferenceIdsFilename(
        "test-results/alignments/last-to-compact/last-reference.compact-reads");
    processor.setOnlyMafFile(true);
    processor.setNumberOfReads(2857819);
    processor.setLargestQueryIndex(2857819);
    processor.setSmallestQueryIndex(0);
    processor.setPropagateQueryIds(false);
    processor.setPropagateTargetIds(true);
    processor.execute();

    // read compact alignment results
    final AlignmentReaderImpl reader = new AlignmentReaderImpl(processor.getOutputFile());
    reader.readHeader();
    assertEquals(2857819, reader.getNumberOfQueries());
    assertEquals(1, reader.getNumberOfTargets());
    assertTrue(reader.hasQueryIndexOccurrences());

    // lookup tables
    final Int2IntOpenHashMap queryIndex2NumberOfHits = new Int2IntOpenHashMap();

    final Int2FloatOpenHashMap queryIndex2Score = new Int2FloatOpenHashMap();
    final Int2IntOpenHashMap queryIndex2Multiplicity = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2NumberOfIndels = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2NumberOfMismatches = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2Position = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2QueryAlignedLength = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2QueryPosition = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2TargetIndex = new Int2IntOpenHashMap();
    final Int2BooleanOpenHashMap queryIndex2MatchingReverseStrand = new Int2BooleanOpenHashMap();
    final Int2IntOpenHashMap queryIndex2TargetAlignedLength = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2QueryIndexOcc = new Int2IntOpenHashMap();
    final Int2IntOpenHashMap queryIndex2Ambiguity = new Int2IntOpenHashMap();

    // enter alignment data
    int qii;
    while (reader.hasNext()) {

      final Alignments.AlignmentEntry aln = reader.next();
      qii = aln.getQueryIndex();

      final int numHits = queryIndex2NumberOfHits.get(qii);

      queryIndex2NumberOfHits.put(qii, numHits + 1);

      queryIndex2Score.put(qii, aln.getScore());
      queryIndex2Multiplicity.put(qii, aln.getMultiplicity());
      queryIndex2NumberOfIndels.put(qii, aln.getNumberOfIndels());
      queryIndex2NumberOfMismatches.put(qii, aln.getNumberOfMismatches());
      queryIndex2Position.put(qii, aln.getPosition());
      queryIndex2QueryAlignedLength.put(qii, aln.getQueryAlignedLength());
      queryIndex2QueryPosition.put(qii, aln.getQueryPosition());
      queryIndex2TargetIndex.put(qii, aln.getTargetIndex());
      queryIndex2MatchingReverseStrand.put(qii, aln.getMatchingReverseStrand());
      queryIndex2TargetAlignedLength.put(qii, aln.getTargetAlignedLength());
      queryIndex2QueryIndexOcc.put(qii, aln.getQueryIndexOccurrences());
      queryIndex2Ambiguity.put(qii, aln.getAmbiguity());
    }

    //
    // validate alignment data using values from getMafInput() below
    //

    // there are a total of 5 entries with ID 2857818
    // 2 entries have score = 35 (the maximum score for this ID)
    // 3 entries are filtered b/c their scores are below 35
    qii = 2857818;
    assertEquals(queryIndex2NumberOfHits.get(qii), 2);
    assertEquals((int) queryIndex2Score.get(qii), 35);
    assertEquals(queryIndex2Multiplicity.get(qii), 1);
    assertEquals(queryIndex2NumberOfIndels.get(qii), 0);
    assertEquals(queryIndex2NumberOfMismatches.get(qii), 0);
    assertEquals(queryIndex2Position.get(qii), 1614); // last entry added
    assertEquals(queryIndex2QueryAlignedLength.get(qii), 35);
    assertEquals(queryIndex2QueryPosition.get(qii), 0);
    assertEquals(queryIndex2TargetIndex.get(qii), 0);
    assertEquals(queryIndex2MatchingReverseStrand.get(qii), false);
    assertEquals(queryIndex2TargetAlignedLength.get(qii), 35);
    assertEquals(2, queryIndex2QueryIndexOcc.get(qii));
    assertEquals(2, queryIndex2Ambiguity.get(qii));

    // there are 5 entries with the score = 35 (the maximum score for this ID)
    // filtered due to ambiguity
    qii = 577287;
    assertEquals(queryIndex2NumberOfHits.get(qii), 0);
    assertEquals((int) queryIndex2Score.get(qii), 0);
    assertEquals(queryIndex2Multiplicity.get(qii), 0);
    assertEquals(queryIndex2NumberOfIndels.get(qii), 0);
    assertEquals(queryIndex2NumberOfMismatches.get(qii), 0);
    assertEquals(queryIndex2Position.get(qii), 0);
    assertEquals(queryIndex2QueryAlignedLength.get(qii), 0);
    assertEquals(queryIndex2QueryPosition.get(qii), 0);
    assertEquals(queryIndex2TargetIndex.get(qii), 0);
    assertEquals(queryIndex2MatchingReverseStrand.get(qii), false);
    assertEquals(queryIndex2TargetAlignedLength.get(qii), 0);
    assertEquals(0, queryIndex2QueryIndexOcc.get(qii));
    assertEquals(0, queryIndex2Ambiguity.get(qii));

    //
    reader.close();
  }
Exemplo n.º 18
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  /**
   * Test the parsing of sequence variations from Last MAF file.
   *
   * @throws IOException
   */
  @Test
  public void testLastToCompactVariations() throws IOException {

    // test LastToCompact convert+filtering

    // read fake data and convert+filter
    final LastToCompactMode processor = new LastToCompactMode();
    final int LAST_TO_COMPACT_M_PARAM = 2;
    processor.setAmbiguityThreshold(LAST_TO_COMPACT_M_PARAM);
    processor.setInputFile("test-results/alignments/last-to-compact/last-103-variations.maf");
    processor.setOutputFile("test-results/alignments/last-to-compact/last-103-variations");
    processor.setTargetReferenceIdsFilename(
        "test-results/alignments/last-to-compact/last-reference.compact-reads");
    processor.setOnlyMafFile(true);
    processor.setNumberOfReads(2857822);
    processor.setLargestQueryIndex(2857822);
    processor.setSmallestQueryIndex(0);
    processor.setPropagateQueryIds(false);
    processor.setPropagateTargetIds(true);
    processor.setQualityFilterParameters(
        "threshold=1"); // allow everything to pass through, important to detect all variations in
    // this test.
    processor.execute();

    // read compact alignment results
    final AlignmentReaderImpl reader = new AlignmentReaderImpl(processor.getOutputFile());
    reader.readHeader();
    assertEquals(2857822, reader.getNumberOfQueries());
    assertEquals(1, reader.getNumberOfTargets());
    int entryIndex = 0;
    while (reader.hasNext()) {
      final Alignments.AlignmentEntry alignmentEntry = reader.next();

      System.out.println(entryIndex + " entry : " + alignmentEntry);
      switch (entryIndex) {
        case 0:
          assertEquals(2, alignmentEntry.getSequenceVariationsCount());
          final Alignments.SequenceVariation var1 = alignmentEntry.getSequenceVariations(0);
          assertEquals("C", var1.getTo());
          assertEquals("G", var1.getFrom());
          assertEquals(1, var1.getPosition());

          final Alignments.SequenceVariation var2 = alignmentEntry.getSequenceVariations(1);
          assertEquals("C", var2.getTo());
          assertEquals("A", var2.getFrom());
          assertEquals(11, var2.getPosition());
          break;

        case 1:
          assertEquals(1, alignmentEntry.getSequenceVariationsCount());
          final Alignments.SequenceVariation var1_0 = alignmentEntry.getSequenceVariations(0);
          assertEquals("---", var1_0.getTo());
          assertEquals("TTT", var1_0.getFrom());
          assertEquals(3, var1_0.getPosition());
          break;

        case 2:
          assertEquals(2, alignmentEntry.getSequenceVariationsCount());
          final Alignments.SequenceVariation var2_1 = alignmentEntry.getSequenceVariations(0);
          assertEquals("A", var2_1.getTo());
          assertEquals("G", var2_1.getFrom());
          assertEquals(2, var2_1.getPosition());

          final Alignments.SequenceVariation var2_2 = alignmentEntry.getSequenceVariations(1);
          assertEquals("A", var2_2.getTo());
          assertEquals("-", var2_2.getFrom());
          assertEquals(29, var2_2.getPosition());
          break;
        default:
          break;
      }
      entryIndex++;
    }
    assertEquals(4, entryIndex);
  }
Exemplo n.º 19
0
 public int getAlignmentEnd() {
   // LOG.info("getAlignmentEnd");
   return entry.getPosition() + entry.getTargetAlignedLength();
 }