Ejemplo n.º 1
0
  /**
   * Returns the coverage distribution of a single read within the desired region.
   *
   * <p>Note: This function counts DELETIONS as coverage (since the main purpose is to downsample
   * reads for variant regions, and deletions count as variants)
   *
   * @param read the read to get the coverage distribution of
   * @param startLocation the first reference coordinate of the region (inclusive)
   * @param stopLocation the last reference coordinate of the region (inclusive)
   * @return an array with the coverage of each position from startLocation to stopLocation
   */
  public static int[] getCoverageDistributionOfRead(
      GATKSAMRecord read, int startLocation, int stopLocation) {
    int[] coverage = new int[stopLocation - startLocation + 1];
    int refLocation = read.getSoftStart();
    for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
      switch (cigarElement.getOperator()) {
        case S:
        case M:
        case EQ:
        case N:
        case X:
        case D:
          for (int i = 0; i < cigarElement.getLength(); i++) {
            if (refLocation >= startLocation && refLocation <= stopLocation) {
              int baseCount =
                  read.isReducedRead()
                      ? read.getReducedCount(refLocation - read.getSoftStart())
                      : 1;
              coverage[refLocation - startLocation] +=
                  baseCount; // this may be a reduced read, so add the proper number of bases
            }
            refLocation++;
          }
          break;

        case P:
        case I:
        case H:
          break;
      }

      if (refLocation > stopLocation) break;
    }
    return coverage;
  }
Ejemplo n.º 2
0
  public static int getMeanRepresentativeReadCount(GATKSAMRecord read) {
    if (!read.isReducedRead()) return 1;

    // compute mean representative read counts
    final byte[] counts = read.getReducedReadCounts();
    return (int) Math.round((double) MathUtils.sum(counts) / counts.length);
  }