示例#1
0
  /** Note: this is the only getKey function that handles unmapped reads specially! */
  public static long getKey(final SAMRecord rec) {
    final int refIdx = rec.getReferenceIndex();
    final int start = rec.getAlignmentStart();

    if (!(rec.getReadUnmappedFlag() || refIdx < 0 || start < 0)) return getKey(refIdx, start);

    // Put unmapped reads at the end, but don't give them all the exact same
    // key so that they can be distributed to different reducers.
    //
    // A random number would probably be best, but to ensure that the same
    // record always gets the same key we use a fast hash instead.
    //
    // We avoid using hashCode(), because it's not guaranteed to have the
    // same value across different processes.

    int hash = 0;
    byte[] var;
    if ((var = rec.getVariableBinaryRepresentation()) != null) {
      // Undecoded BAM record: just hash its raw data.
      hash = (int) MurmurHash3.murmurhash3(var, hash);
    } else {
      // Decoded BAM record or any SAM record: hash a few representative
      // fields together.
      hash = (int) MurmurHash3.murmurhash3(rec.getReadName(), hash);
      hash = (int) MurmurHash3.murmurhash3(rec.getReadBases(), hash);
      hash = (int) MurmurHash3.murmurhash3(rec.getBaseQualities(), hash);
      hash = (int) MurmurHash3.murmurhash3(rec.getCigarString(), hash);
    }
    return getKey0(Integer.MAX_VALUE, hash);
  }
示例#2
0
  /**
   * HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY
   *
   * @param read
   */
  public GATKSAMRecord(final SAMRecord read) {
    super(read.getHeader());
    super.setReferenceIndex(read.getReferenceIndex());
    super.setAlignmentStart(read.getAlignmentStart());
    super.setReadName(read.getReadName());
    super.setMappingQuality(read.getMappingQuality());
    // indexing bin done below
    super.setCigar(read.getCigar());
    super.setFlags(read.getFlags());
    super.setMateReferenceIndex(read.getMateReferenceIndex());
    super.setMateAlignmentStart(read.getMateAlignmentStart());
    super.setInferredInsertSize(read.getInferredInsertSize());
    SAMReadGroupRecord samRG = read.getReadGroup();
    SAMBinaryTagAndValue samAttr = GATKBin.getReadBinaryAttributes(read);
    if (samAttr == null) {
      clearAttributes();
    } else {
      setAttributes(samAttr);
    }
    if (samRG != null) {
      GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
      setReadGroup(rg);
    }

    super.setFileSource(read.getFileSource());
    super.setReadName(read.getReadName());
    super.setCigarString(read.getCigarString());
    super.setReadBases(read.getReadBases());
    super.setBaseQualities(read.getBaseQualities());
    // From SAMRecord constructor: Do this after the above because setCigarString will clear it.
    GATKBin.setReadIndexingBin(this, GATKBin.getReadIndexingBin(read));
  }
  private boolean isOutOfOrder(final SAMRecord last, final SAMRecord cur) {
    if (last == null || cur.getReadUnmappedFlag()) return false;
    else {
      if (last.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX
          || last.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
        throw new UserException.MalformedBAM(
            last, String.format("read %s has inconsistent mapping information.", last.format()));
      if (cur.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX
          || cur.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
        throw new UserException.MalformedBAM(
            last, String.format("read %s has inconsistent mapping information.", cur.format()));

      return (last.getReferenceIndex() > cur.getReferenceIndex())
          || (last.getReferenceIndex().equals(cur.getReferenceIndex())
              && last.getAlignmentStart() > cur.getAlignmentStart());
    }
  }