@Override
public String toString() {
final StringBuilder sb = new StringBuilder();
final int[] assignment = new int[mStrains];
int currentIndex = 0;
int last = -1;
while (currentIndex > 0 || last <= max(assignment, currentIndex)) {
assignment[currentIndex++] = last + 1;
while (currentIndex < assignment.length) {
assignment[currentIndex++] = 0;
}
int countIndex = 0;
for (int i = 0; i < mStride.length; i++) {
countIndex += assignment[i] * mStride[i];
}
sb.append(Arrays.toString(assignment));
sb.append(" = ");
sb.append(mCounts[countIndex]);
sb.append("\t");
sb.append(Utils.realFormat((double) mCounts[countIndex] / mTotal, 6));
sb.append(StringUtils.LS);
last = assignment[--currentIndex];
while (last == max(assignment, currentIndex) + 1 && currentIndex > 0) {
last = assignment[--currentIndex];
}
}
return sb.toString();
}
String countsString() {
return mReadGroup
+ "\t"
+ mTotalReference
+ "\t"
+ mLengthDist.count()
+ "\t"
+ Utils.realFormat(mLengthDist.sum())
+ "\t"
+ Utils.realFormat(mLengthDist.sumSq())
+ "\t"
+ mFragmentSizeDist.count()
+ "\t"
+ Utils.realFormat(mFragmentSizeDist.sum())
+ "\t"
+ Utils.realFormat(mFragmentSizeDist.sumSq())
+ "\t"
+ mGapSizeDist.count()
+ "\t"
+ Utils.realFormat(mGapSizeDist.sum())
+ "\t"
+ Utils.realFormat(mGapSizeDist.sumSq())
+ "\t"
+ mMaxAlignment
+ "\t"
+ mProper
+ "\t"
+ mDiscordant
+ "\t"
+ mUnmated;
}
@Override
public String toString() {
return id()
+ "\t"
+ Utils.realFormat(meanLength(), 5)
+ "\t"
+ Utils.realFormat(fragmentMean(), 5)
+ "\t"
+ Utils.realFormat(fragmentStdDev(), 5)
+ "\t"
+ Utils.realFormat(gapMean(), 5)
+ "\t"
+ Utils.realFormat(gapStdDev(), 5)
+ "\t"
+ Utils.realFormat(maxAlignment(), 5)
+ "\t"
+ Utils.realFormat(properRate(), 6)
+ "\t"
+ Utils.realFormat(properRandomRate(), 6)
+ "\t"
+ Utils.realFormat(discordantRate(), 6)
+ "\t"
+ Utils.realFormat(unmatedRate(), 6);
}
/**
* @param calibrator the mapping calibration stats to use when computing coverage
* @param defaultSequenceLengths map of sequence names to sequence length, used if not already set
* in the calibrator
* @param readGroupToSampleId read group to sample id
* @param restriction a region restriction, may be null
*/
public CalibratedPerSequenceExpectedCoverage(
Calibrator calibrator,
Map<String, Integer> defaultSequenceLengths,
Map<String, String> readGroupToSampleId,
RegionRestriction restriction) {
mSequenceSampleCoverages = new HashMap<>();
mSumCoverages = new HashMap<>();
mSamples = Collections.unmodifiableSet(new HashSet<>(readGroupToSampleId.values()));
final Map<String, Integer> sequenceLengths =
calibrator.hasLengths() ? calibrator.getSequenceLengths() : defaultSequenceLengths;
if (calibrator.getCovariateIndex(CovariateEnum.SEQUENCE)
== -1) { // No per sequence separation in calibration data, calculate per-genome coverage
// level
long length = 0;
for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
length += entry.getValue();
}
final Map<String, HashMap<String, CalibrationStats>> local = new HashMap<>();
findIndividualGlobalCoverage(calibrator, readGroupToSampleId, local);
double currentMax = 0;
double currentSum = 0;
for (Map.Entry<String, HashMap<String, CalibrationStats>> e : local.entrySet()) {
final HashMap<String, CalibrationStats> map = e.getValue();
if (map.containsKey(DUMMY_SEQ)) {
final double currentCov =
(length == 0) ? 0 : (double) map.get(DUMMY_SEQ).getTotalLength() / length;
final String sampleName = e.getKey();
Diagnostic.userLog(
"Average coverage for sample "
+ sampleName
+ " is "
+ Utils.realFormat(currentCov, 2));
for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
final String seqName = entry.getKey();
Map<String, Double> samples = mSequenceSampleCoverages.get(seqName);
if (samples == null) {
samples = new HashMap<>();
mSequenceSampleCoverages.put(seqName, samples);
}
samples.put(sampleName, currentCov);
}
currentSum += currentCov;
if (currentCov > currentMax) {
currentMax = currentCov;
}
}
}
Diagnostic.userLog("Average combined coverage is " + Utils.realFormat(currentSum, 2));
for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
final String seqName = entry.getKey();
mSumCoverages.put(seqName, currentSum);
}
} else { // Per-sequence separation is in calibration data, calculate per-sequence coverage
// level
final Map<String, HashMap<String, CalibrationStats>> local = new HashMap<>();
findIndividualPerSequenceCoverage(
calibrator, sequenceLengths, readGroupToSampleId, local, restriction);
for (final Map.Entry<String, Integer> entry : sequenceLengths.entrySet()) {
final String seqName = entry.getKey();
if (restriction != null && !seqName.equals(restriction.getSequenceName())) {
continue;
}
final int seqLength = entry.getValue();
double currentMax = 0;
double currentSum = 0;
for (Map.Entry<String, HashMap<String, CalibrationStats>> e : local.entrySet()) {
final HashMap<String, CalibrationStats> map = e.getValue();
if (map.containsKey(seqName)) {
final double currentCov =
(seqLength == 0) ? 0 : (double) map.get(seqName).getTotalLength() / seqLength;
final String sampleName = e.getKey();
Diagnostic.userLog(
"Average coverage across sequence "
+ seqName
+ " for sample "
+ sampleName
+ " is "
+ Utils.realFormat(currentCov, 2));
Map<String, Double> samples = mSequenceSampleCoverages.get(seqName);
if (samples == null) {
samples = new HashMap<>();
mSequenceSampleCoverages.put(seqName, samples);
}
samples.put(sampleName, currentCov);
currentSum += currentCov;
if (currentCov > currentMax) {
currentMax = currentCov;
}
}
}
Diagnostic.userLog(
"Average combined coverage for sequence "
+ seqName
+ " is "
+ Utils.realFormat(currentSum, 2));
mSumCoverages.put(seqName, currentSum);
}
}
}