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package org.broadinstitute.gatk.tools.walkers.diagnostics;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.report.GATKReport;
import org.broadinstitute.gatk.engine.walkers.LocusWalker;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.Map;
/**
* Simple walker to plot the coverage distribution per base
*
* <p>
* Features of this walker:
* <li>includes a smart counting of uncovered bases without visiting the uncovered loci</li>
* <li>includes reads with deletions in the loci (optionally can be turned off)</li>
* </p>
*
* <h3>Input</h3>
* <p>
* The BAM file and an optional interval list (works for WGS as well)
* </p>
*
* <h3>Output</h3>
* <p>
* A GATK Report with the coverage distribution per base
*
* <p/>
* <h3>Examples</h3>
* <pre>
* java -Xmx4g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T BaseCoverageDistribution \
* -I myData.bam \
* -L interesting.intervals \
* -fd \
* -o report.grp
* </pre>
*
* @author carneiro
* @since 1/27/13
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
public class BaseCoverageDistribution extends LocusWalker<ArrayList<Integer>, Map<Integer, ArrayList<Long>>> {
/**
* The output GATK Report table
*/
@Output(doc = "The output GATK Report table")
private PrintStream out;
/**
* Whether or not a deletion should be counted towards the coverage of a site
*/
@Argument(required = false, shortName="del", fullName = "include_deletions", doc ="whether or not to include reads with deletions on the loci in the pileup")
private boolean includeDeletions = true;
/**
* Whether or not to calculate and output a filtered coverage distribution. Bases will be filtered according to the
* minimum_mapping_quality and minimum_base_quality parameters below.
*/
@Argument(required = false, shortName="fd", fullName = "filtered_distribution", doc ="calculate and report the filtered coverage distribution of bases")
private boolean calculateFilteredDistribution = false;
/**
* The minimum mapping quality a read must have to be counted towards the filtered coverage of a site
*/
@Argument(required = false, shortName="mmq", fullName = "minimum_mapping_quality", doc ="minimum mapping quality of a read to include it in the filtered coverage distribution")
private byte minMappingQuality = 20;
/**
* The minimum base quality a base must have to be counted towards the filtered coverage of a site
*/
@Argument(required = false, shortName="mbq", fullName = "minimum_base_quality", doc ="minimum base quality of a base to include it in the filtered coverage distribution")
private byte minBaseQuality = 17;
private GenomeLoc previousLocus = null;
private long uncoveredBases = 0L;
private final LinkedList<GenomeLoc> intervalList = new LinkedList<GenomeLoc>();
@Override
public boolean includeReadsWithDeletionAtLoci() {
return includeDeletions;
}
@Override
public void initialize() {
if (getToolkit().getIntervals() != null)
intervalList.addAll(getToolkit().getIntervals()); // if the user provided intervals, keep track of them for uncovered bases calculation
}
@Override
public ArrayList<Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
ArrayList<Integer> result = new ArrayList<Integer>(2);
GenomeLoc currentLocus = ref.getLocus();
tallyUncoveredBases(currentLocus);
previousLocus = currentLocus;
result.add(context.getBasePileup().getReads().size()); // I want the reads instead of the base pileup because I want to count deletions.
if (calculateFilteredDistribution)
result.add(context.getBasePileup().getBaseAndMappingFilteredPileup(minBaseQuality, minMappingQuality).getReads().size()); // filtered pileup
else {
result.add(result.get(0)); // repeat the same value as the unfiltered pileup if filters are not on
}
return result;
}
@Override
public Map<Integer, ArrayList<Long>> reduceInit() {
return new HashMap<Integer, ArrayList<Long>>(10000);
}
@Override
public Map<Integer, ArrayList<Long>> reduce(ArrayList<Integer> value, Map<Integer, ArrayList<Long>> sum) {
final int unfilteredCoverage = value.get(0);
final int filteredCoverage = value.get(1);
incrementSumArray(sum, unfilteredCoverage, 0);
incrementSumArray(sum, filteredCoverage, 1);
return sum;
}
@Override
public void onTraversalDone(Map<Integer, ArrayList<Long>> result) {
tallyUncoveredBasesTillEndOfTraversal();
GATKReport report;
if (calculateFilteredDistribution) {
report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count", "Filtered");
} else {
report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count");
report.addRow(0, uncoveredBases); // preemptively add the uncovered bases row (since they'll never exist in the Map)
}
for (Map.Entry<Integer, ArrayList<Long>> entry : result.entrySet()) {
final ArrayList<Long> values = entry.getValue();
final int coverage = entry.getKey();
if (calculateFilteredDistribution) {
if (coverage == 0) { // special case for the uncovered bases. The filtered pileups may have an entry, but the unfiltered ones won't.
report.addRow(coverage, uncoveredBases, uncoveredBases + values.get(1));
} else {
report.addRow(coverage, values.get(0), values.get(1));
}
} else {
report.addRow(coverage, values.get(0));
}
}
// In case the filtered distribution never had a pileup filtered down to zero coverage, output the overall uncovered bases for both
if (calculateFilteredDistribution && !result.containsKey(0)) {
report.addRow(0, uncoveredBases, uncoveredBases);
}
report.print(out);
}
/**
* Initializes the ArrayList if needed. Returns the initialized element (or previously initialized)
* this method is used directly by the incrementSumArray.
*
* @param sum the map
* @param coverage the key to the map to extract the array list
* @return if the ArrayList exists, return it. Otherwise, initialize it with 0 counters.
*/
private ArrayList<Long> initializeSumArray(final Map<Integer, ArrayList<Long>> sum, final int coverage) {
ArrayList<Long> curr = sum.get(coverage);
if (curr == null) {
curr = new ArrayList<Long>(2);
curr.add(0L); // number of bases with this unfiltered coverage
curr.add(0L); // number of bases with this filtered coverage
sum.put(coverage, curr);
}
return curr;
}
/**
* Increments the counter for the given arrayindex (type of coverage : filtered or unfiltered) initializing if necessary
*
* @param sum the hash
* @param coverage the hash key
* @param arrayIndex which distribution to increment, 0 for unfiltered, 1 for filtered.
*/
private void incrementSumArray(final Map<Integer, ArrayList<Long>> sum, final int coverage, final int arrayIndex) {
final ArrayList<Long> currentTally = initializeSumArray(sum, coverage);
currentTally.set(arrayIndex, currentTally.get(arrayIndex) + 1);
}
/**
* Counts all the uncovered loci after the end of traversal.
*
* - Modifies the global variable uncoveredBases
* - Uses global variables: intervalList and previousLocus
*
* takes into account that the traversal may have been due over a set of intervals, or over the whole genome.
*/
private void tallyUncoveredBasesTillEndOfTraversal() {
GenomeLocParser parser = getToolkit().getGenomeLocParser();
GenomeLoc lastLocus;
if (intervalList.isEmpty()) { // whole genome, add up all contigs past previousLocus
final int lastContigIndex = getToolkit().getSAMFileHeader().getSequenceDictionary().size() - 1;
final int lastContigLength = getToolkit().getSAMFileHeader().getSequence(lastContigIndex).getSequenceLength();
final String lastContigName = getToolkit().getSAMFileHeader().getSequence(lastContigIndex).getSequenceName();
lastLocus = parser.createGenomeLoc(lastContigName, lastContigIndex, lastContigLength, lastContigLength);
} else {
GenomeLoc lastInterval = intervalList.getLast();
lastLocus = parser.createGenomeLoc(lastInterval.getContig(), lastInterval.getContigIndex(), lastInterval.getStop(), lastInterval.getStop());
}
tallyUncoveredBases(lastLocus);
}
/**
* Counts all the uncovered loci that have been skipped since the last visited locus. This method allows coverage
* tools to run with @By(DataSource.READS) instead of @By(DataSource.REFERENCE), while still accurately calculating
* uncovered bases
*
* //todo -- make this a generic capability of Coverage and DiagnoseTargets
*
* - Modifies the global variable uncoveredBases
* - Uses global variables: intervalList and previousLocus
*
* takes into account that the traversal may have been due over a set of intervals, or over the whole genome.
*
* @param currentLocus the locus we are visiting right now
*/
private void tallyUncoveredBases(GenomeLoc currentLocus) {
long distance = 0;
if (previousLocus == null) { // first base visited
GenomeLocParser parser = getToolkit().getGenomeLocParser();
if (intervalList.isEmpty()) { // if this is whole genome (no intervals requested), add what we missed.
final GenomeLoc zeroLoc = parser.createGenomeLoc(getToolkit().getSAMFileHeader().getSequence(0).getSequenceName(), 0, 1, 1);
distance += currentLocus.distanceAcrossContigs(zeroLoc, getToolkit().getSAMFileHeader());
} else { // if we are running on an interval list, add all intervals before the current locus to the uncovered bases counter
while (!intervalList.peek().containsP(currentLocus)) {
GenomeLoc interval = intervalList.removeFirst();
distance += interval.size();
}
distance += currentLocus.getStart() - intervalList.peek().getStart(); // now this is the interval that contains the current locus. Discount the bases from the beginning.
}
} else {
final GenomeLoc previousInterval = intervalList.peekFirst(); // peekFirst returns null if interval list is empty (WGS).
distance = currentLocus.distanceAcrossContigs(previousLocus, getToolkit().getSAMFileHeader()) - 1;
if (previousInterval != null && !previousInterval.containsP(currentLocus)) {
intervalList.removeFirst(); // we're done with the previous interval
final GenomeLoc currentInterval = intervalList.peekFirst();
distance -= currentInterval.distanceAcrossContigs(previousInterval, getToolkit().getSAMFileHeader()) - 1;
}
}
uncoveredBases += distance;
}
}