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package org.broadinstitute.gatk.utils.recalibration;
import com.google.java.contract.Ensures;
import com.google.java.contract.Invariant;
import com.google.java.contract.Requires;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.engine.report.GATKReport;
import org.broadinstitute.gatk.engine.report.GATKReportTable;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.io.PrintStream;
import java.util.*;
/**
* A general algorithm for quantizing quality score distributions to use a specific number of levels
*
* Takes a histogram of quality scores and a desired number of levels and produces a
* map from original quality scores -> quantized quality scores.
*
* Note that this data structure is fairly heavy-weight, holding lots of debugging and
* calculation information. If you want to use it efficiently at scale with lots of
* read groups the right way to do this:
*
* Map<ReadGroup, List<Byte>> map
* for each read group rg:
* hist = getQualHist(rg)
* QualQuantizer qq = new QualQuantizer(hist, nLevels, minInterestingQual)
* map.set(rg, qq.getOriginalToQuantizedMap())
*
* This map would then be used to look up the appropriate original -> quantized
* quals for each read as it comes in.
*
* @author Mark Depristo
* @since 3/2/12
*/
public class QualQuantizer {
final private static Set<QualInterval> MY_EMPTY_SET = Collections.emptySet();
private static Logger logger = Logger.getLogger(QualQuantizer.class);
/**
* Inputs to the QualQuantizer
*/
final int nLevels, minInterestingQual;
final List<Long> nObservationsPerQual;
/**
* Map from original qual (e.g., Q30) to new quantized qual (e.g., Q28).
*
* Has the same range as nObservationsPerQual
*/
final List<Byte> originalToQuantizedMap;
/** Sorted set of qual intervals.
*
* After quantize() this data structure contains only the top-level qual intervals
*/
final TreeSet<QualInterval> quantizedIntervals;
/**
* Protected creator for testng use only
*/
protected QualQuantizer(final int minInterestingQual) {
this.nObservationsPerQual = Collections.emptyList();
this.nLevels = 0;
this.minInterestingQual = minInterestingQual;
this.quantizedIntervals = null;
this.originalToQuantizedMap = null;
}
/**
* Creates a QualQuantizer for the histogram that has nLevels
*
* Note this is the only interface to the system. After creating this object
* the map can be obtained via getOriginalToQuantizedMap()
*
* @param nObservationsPerQual A histogram of counts of bases with quality scores. Note that
* this histogram must start at 0 (i.e., get(0) => count of Q0 bases) and must include counts all the
* way up to the largest quality score possible in the reads. OK if the histogram includes many 0
* count bins, as these are quantized for free.
* @param nLevels the desired number of distinct quality scores to represent the full original range. Must
* be at least 1.
* @param minInterestingQual All quality scores <= this value are considered uninteresting and are freely
* merged together. For example, if this value is 10, then Q0-Q10 are all considered free to merge, and
* quantized into a single value. For ILMN data with lots of Q2 bases this results in a Q2 bin containing
* all data with Q0-Q10.
*/
public QualQuantizer(final List<Long> nObservationsPerQual, final int nLevels, final int minInterestingQual) {
this.nObservationsPerQual = nObservationsPerQual;
this.nLevels = nLevels;
this.minInterestingQual = minInterestingQual;
// some sanity checking
if ( Collections.min(nObservationsPerQual) < 0 ) throw new ReviewedGATKException("Quality score histogram has negative values at: " + Utils.join(", ", nObservationsPerQual));
if ( nLevels < 0 ) throw new ReviewedGATKException("nLevels must be >= 0");
if ( minInterestingQual < 0 ) throw new ReviewedGATKException("minInterestingQual must be >= 0");
// actually run the quantizer
this.quantizedIntervals = quantize();
// store the map
this.originalToQuantizedMap = intervalsToMap(quantizedIntervals);
}
/**
* Represents an contiguous interval of quality scores.
*
* qStart and qEnd are inclusive, so qStart = qEnd = 2 is the quality score bin of 2
*/
@Invariant({
"qStart <= qEnd",
"qStart >= 0",
"qEnd <= 1000",
"nObservations >= 0",
"nErrors >= 0",
"nErrors <= nObservations",
"fixedQual >= -1 && fixedQual <= QualityUtils.MAX_SAM_QUAL_SCORE",
"mergeOrder >= 0"})
protected final class QualInterval implements Comparable<QualInterval> {
final int qStart, qEnd, fixedQual, level;
final long nObservations, nErrors;
final Set<QualInterval> subIntervals;
/** for debugging / visualization. When was this interval created? */
int mergeOrder;
protected QualInterval(final int qStart, final int qEnd, final long nObservations, final long nErrors, final int level) {
this(qStart, qEnd, nObservations, nErrors, level, -1, MY_EMPTY_SET);
}
protected QualInterval(final int qStart, final int qEnd, final long nObservations, final long nErrors, final int level, final Set<QualInterval> subIntervals) {
this(qStart, qEnd, nObservations, nErrors, level, -1, subIntervals);
}
protected QualInterval(final int qStart, final int qEnd, final long nObservations, final long nErrors, final int level, final int fixedQual) {
this(qStart, qEnd, nObservations, nErrors, level, fixedQual, MY_EMPTY_SET);
}
@Requires("level >= 0")
public QualInterval(final int qStart, final int qEnd, final long nObservations, final long nErrors, final int level, final int fixedQual, final Set<QualInterval> subIntervals) {
this.qStart = qStart;
this.qEnd = qEnd;
this.nObservations = nObservations;
this.nErrors = nErrors;
this.fixedQual = fixedQual;
this.level = level;
this.mergeOrder = 0;
this.subIntervals = Collections.unmodifiableSet(subIntervals);
}
/**
* @return Human readable name of this interval: e.g., 10-12
*/
public String getName() {
return qStart + "-" + qEnd;
}
@Override
public String toString() {
return "QQ:" + getName();
}
/**
* @return the error rate (in real space) of this interval, or 0 if there are no observations
*/
@Ensures("result >= 0.0")
public double getErrorRate() {
if ( hasFixedQual() )
return QualityUtils.qualToErrorProb((byte)fixedQual);
else if ( nObservations == 0 )
return 0.0;
else
return (nErrors+1) / (1.0 * (nObservations+1));
}
/**
* @return the QUAL of the error rate of this interval, or the fixed qual if this interval was created with a fixed qual.
*/
@Ensures("result >= 0 && result <= QualityUtils.MAX_SAM_QUAL_SCORE")
public byte getQual() {
if ( ! hasFixedQual() )
return QualityUtils.errorProbToQual(getErrorRate());
else
return (byte)fixedQual;
}
/**
* @return true if this bin is using a fixed qual
*/
public boolean hasFixedQual() {
return fixedQual != -1;
}
@Override
public int compareTo(final QualInterval qualInterval) {
return Integer.valueOf(this.qStart).compareTo(qualInterval.qStart);
}
/**
* Create a interval representing the merge of this interval and toMerge
*
* Errors and observations are combined
* Subintervals updated in order of left to right (determined by qStart)
* Level is 1 + highest level of this and toMerge
* Order must be updated elsewhere
*
* @param toMerge
* @return newly created merged QualInterval
*/
@Requires({"toMerge != null"})
@Ensures({
"result != null",
"result.nObservations >= this.nObservations",
"result.nObservations >= toMerge.nObservations",
"result.nErrors >= this.nErrors",
"result.nErrors >= toMerge.nErrors",
"result.qStart == Math.min(this.qStart, toMerge.qStart)",
"result.qEnd == Math.max(this.qEnd, toMerge.qEnd)",
"result.level > Math.max(this.level, toMerge.level)",
"result.subIntervals.size() == 2"
})
public QualInterval merge(final QualInterval toMerge) {
final QualInterval left = this.compareTo(toMerge) < 0 ? this : toMerge;
final QualInterval right = this.compareTo(toMerge) < 0 ? toMerge : this;
if ( left.qEnd + 1 != right.qStart )
throw new ReviewedGATKException("Attempting to merge non-contiguous intervals: left = " + left + " right = " + right);
final long nCombinedObs = left.nObservations + right.nObservations;
final long nCombinedErr = left.nErrors + right.nErrors;
final int level = Math.max(left.level, right.level) + 1;
final Set<QualInterval> subIntervals = new HashSet<QualInterval>(Arrays.asList(left, right));
QualInterval merged = new QualInterval(left.qStart, right.qEnd, nCombinedObs, nCombinedErr, level, subIntervals);
return merged;
}
public double getPenalty() {
return calcPenalty(getErrorRate());
}
/**
* Calculate the penalty of this interval, given the overall error rate for the interval
*
* If the globalErrorRate is e, this value is:
*
* sum_i |log10(e_i) - log10(e)| * nObservations_i
*
* each the index i applies to all leaves of the tree accessible from this interval
* (found recursively from subIntervals as necessary)
*
* @param globalErrorRate overall error rate in real space against which we calculate the penalty
* @return the cost of approximating the bins in this interval with the globalErrorRate
*/
@Requires("globalErrorRate >= 0.0")
@Ensures("result >= 0.0")
private double calcPenalty(final double globalErrorRate) {
if ( globalErrorRate == 0.0 ) // there were no observations, so there's no penalty
return 0.0;
if ( subIntervals.isEmpty() ) {
// this is leave node
if ( this.qEnd <= minInterestingQual )
// It's free to merge up quality scores below the smallest interesting one
return 0;
else {
return (Math.abs(Math.log10(getErrorRate()) - Math.log10(globalErrorRate))) * nObservations;
}
} else {
double sum = 0;
for ( final QualInterval interval : subIntervals )
sum += interval.calcPenalty(globalErrorRate);
return sum;
}
}
}
/**
* Main method for computing the quantization intervals.
*
* Invoked in the constructor after all input variables are initialized. Walks
* over the inputs and builds the min. penalty forest of intervals with exactly nLevel
* root nodes. Finds this min. penalty forest via greedy search, so is not guarenteed
* to find the optimal combination.
*
* TODO: develop a smarter algorithm
*
* @return the forest of intervals with size == nLevels
*/
@Ensures({"! result.isEmpty()", "result.size() == nLevels"})
private TreeSet<QualInterval> quantize() {
// create intervals for each qual individually
final TreeSet<QualInterval> intervals = new TreeSet<QualInterval>();
for ( int qStart = 0; qStart < getNQualsInHistogram(); qStart++ ) {
final long nObs = nObservationsPerQual.get(qStart);
final double errorRate = QualityUtils.qualToErrorProb((byte)qStart);
final double nErrors = nObs * errorRate;
final QualInterval qi = new QualInterval(qStart, qStart, nObs, (int)Math.floor(nErrors), 0, (byte)qStart);
intervals.add(qi);
}
// greedy algorithm:
// while ( n intervals >= nLevels ):
// find intervals to merge with least penalty
// merge it
while ( intervals.size() > nLevels ) {
mergeLowestPenaltyIntervals(intervals);
}
return intervals;
}
/**
* Helper function that finds and merges together the lowest penalty pair of intervals
* @param intervals
*/
@Requires("! intervals.isEmpty()")
private void mergeLowestPenaltyIntervals(final TreeSet<QualInterval> intervals) {
// setup the iterators
final Iterator<QualInterval> it1 = intervals.iterator();
final Iterator<QualInterval> it1p = intervals.iterator();
it1p.next(); // skip one
// walk over the pairs of left and right, keeping track of the pair with the lowest merge penalty
QualInterval minMerge = null;
if ( logger.isDebugEnabled() ) logger.debug("mergeLowestPenaltyIntervals: " + intervals.size());
int lastMergeOrder = 0;
while ( it1p.hasNext() ) {
final QualInterval left = it1.next();
final QualInterval right = it1p.next();
final QualInterval merged = left.merge(right);
lastMergeOrder = Math.max(Math.max(lastMergeOrder, left.mergeOrder), right.mergeOrder);
if ( minMerge == null || (merged.getPenalty() < minMerge.getPenalty() ) ) {
if ( logger.isDebugEnabled() ) logger.debug(" Updating merge " + minMerge);
minMerge = merged;
}
}
// now actually go ahead and merge the minMerge pair
if ( logger.isDebugEnabled() ) logger.debug(" => final min merge " + minMerge);
intervals.removeAll(minMerge.subIntervals);
intervals.add(minMerge);
minMerge.mergeOrder = lastMergeOrder + 1;
if ( logger.isDebugEnabled() ) logger.debug("updated intervals: " + intervals);
}
/**
* Given a final forest of intervals constructs a list mapping
* list.get(i) => quantized qual to use for original quality score i
*
* This function should be called only once to initialize the corresponding
* cached value in this object, as the calculation is a bit costly.
*
* @param intervals
* @return
*/
@Ensures("result.size() == getNQualsInHistogram()")
private List<Byte> intervalsToMap(final TreeSet<QualInterval> intervals) {
final List<Byte> map = new ArrayList<Byte>(getNQualsInHistogram());
map.addAll(Collections.nCopies(getNQualsInHistogram(), Byte.MIN_VALUE));
for ( final QualInterval interval : intervals ) {
for ( int q = interval.qStart; q <= interval.qEnd; q++ ) {
map.set(q, interval.getQual());
}
}
if ( Collections.min(map) == Byte.MIN_VALUE )
throw new ReviewedGATKException("quantized quality score map contains an un-initialized value");
return map;
}
@Ensures("result > 0")
private final int getNQualsInHistogram() {
return nObservationsPerQual.size();
}
/**
* Write out a GATKReport to visualize the QualQuantization process of this data
* @param out
*/
public void writeReport(PrintStream out) {
final GATKReport report = new GATKReport();
addQualHistogramToReport(report);
addIntervalsToReport(report);
report.print(out);
}
private final void addQualHistogramToReport(final GATKReport report) {
report.addTable("QualHistogram", "Quality score histogram provided to report", 2);
GATKReportTable table = report.getTable("QualHistogram");
table.addColumn("qual");
table.addColumn("count");
for ( int q = 0; q < nObservationsPerQual.size(); q++ ) {
table.set(q, "qual", q);
table.set(q, "count", nObservationsPerQual.get(q));
}
}
private final void addIntervalsToReport(final GATKReport report) {
report.addTable("QualQuantizerIntervals", "Table of QualQuantizer quantization intervals", 10);
GATKReportTable table = report.getTable("QualQuantizerIntervals");
table.addColumn("name");
table.addColumn("qStart");
table.addColumn("qEnd");
table.addColumn("level");
table.addColumn("merge.order");
table.addColumn("nErrors");
table.addColumn("nObservations");
table.addColumn("qual");
table.addColumn("penalty");
table.addColumn("root.node");
//table.addColumn("subintervals", "NA");
for ( QualInterval interval : quantizedIntervals )
addIntervalToReport(table, interval, true);
}
private final void addIntervalToReport(final GATKReportTable table, final QualInterval interval, final boolean atRootP) {
final String name = interval.getName();
table.set(name, "name", name);
table.set(name, "qStart", interval.qStart);
table.set(name, "qEnd", interval.qEnd);
table.set(name, "level", interval.level);
table.set(name, "merge.order", interval.mergeOrder);
table.set(name, "nErrors", interval.nErrors);
table.set(name, "nObservations", interval.nObservations);
table.set(name, "qual", interval.getQual());
table.set(name, "penalty", String.format("%.1f", interval.getPenalty()));
table.set(name, "root.node", atRootP);
for ( final QualInterval sub : interval.subIntervals )
addIntervalToReport(table, sub, false);
}
public List<Byte> getOriginalToQuantizedMap() {
return originalToQuantizedMap;
}
}