Пример #1
0
 /**
  * Throw an exception if all the "to" sequence names in the chains are not found in the given
  * sequence dictionary.
  */
 public void validateToSequences(final SAMSequenceDictionary sequenceDictionary) {
   for (final Chain chain : chains.getAll()) {
     if (sequenceDictionary.getSequence(chain.toSequenceName) == null) {
       throw new PicardException(
           "Sequence "
               + chain.toSequenceName
               + " from chain file is not found in sequence dictionary.");
     }
   }
 }
Пример #2
0
  /**
   * Lift over the given interval to the new genome build.
   *
   * @param interval Interval to be lifted over.
   * @param liftOverMinMatch Minimum fraction of bases that must remap.
   * @return Interval in the output build coordinates, or null if it cannot be lifted over.
   */
  public Interval liftOver(final Interval interval, final double liftOverMinMatch) {
    if (interval.length() == 0) {
      throw new IllegalArgumentException(
          "Zero-length interval cannot be lifted over.  Interval: " + interval.getName());
    }
    Chain chainHit = null;
    TargetIntersection targetIntersection = null;
    // Number of bases in interval that can be lifted over must be >= this.
    double minMatchSize = liftOverMinMatch * interval.length();

    // Find the appropriate Chain, and the part of the chain corresponding to the interval to be
    // lifted over.
    for (final Chain chain : chains.getOverlaps(interval)) {
      final TargetIntersection candidateIntersection = targetIntersection(chain, interval);
      if (candidateIntersection != null
          && candidateIntersection.intersectionLength >= minMatchSize) {
        if (chainHit != null) {
          // In basic liftOver, multiple hits are not allowed.
          return null;
        }
        chainHit = chain;
        targetIntersection = candidateIntersection;
      } else if (candidateIntersection != null) {
        LOG.info(
            "Interval "
                + interval.getName()
                + " failed to match chain "
                + chain.id
                + " because intersection length "
                + candidateIntersection.intersectionLength
                + " < minMatchSize "
                + minMatchSize
                + " ("
                + (candidateIntersection.intersectionLength / (float) interval.length())
                + " < "
                + liftOverMinMatch
                + ")");
      }
    }
    if (chainHit == null) {
      // Can't be lifted over.
      return null;
    }

    return createToInterval(interval.getName(), targetIntersection);
  }
Пример #3
0
 public List<PartialLiftover> diagnosticLiftover(final Interval interval) {
   final List<PartialLiftover> ret = new ArrayList<PartialLiftover>();
   if (interval.length() == 0) {
     throw new IllegalArgumentException(
         "Zero-length interval cannot be lifted over.  Interval: " + interval.getName());
   }
   for (final Chain chain : chains.getOverlaps(interval)) {
     Interval intersectingChain = interval.intersect(chain.interval);
     final TargetIntersection targetIntersection = targetIntersection(chain, intersectingChain);
     if (targetIntersection == null) {
       ret.add(new PartialLiftover(intersectingChain, chain.id));
     } else {
       Interval toInterval = createToInterval(interval.getName(), targetIntersection);
       float percentLiftedOver = targetIntersection.intersectionLength / (float) interval.length();
       ret.add(
           new PartialLiftover(
               intersectingChain, toInterval, targetIntersection.chain.id, percentLiftedOver));
     }
   }
   return ret;
 }