Quick QC walkers to look at the error profile of indels in the read
This commit is contained in:
Mauricio Carneiro
parent
24173d860a
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08dbd756f3
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package org.broadinstitute.sting.gatk.walkers.qc;
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import net.sf.samtools.CigarOperator;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.report.GATKReport;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import java.io.PrintStream;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Map;
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/**
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* Walks over the input data set, counting the number of reads ending in insertions/deletions or soft-clips
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*
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* <h2>Input</h2>
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* <p>
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* One or more BAM files.
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* </p>
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*
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* <h2>Output</h2>
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* <p>
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* Number of reads ending in each category.
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* </p>
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*
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* <h2>Examples</h2>
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* <pre>
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* java -Xmx2g -jar GenomeAnalysisTK.jar \
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* -R ref.fasta \
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* -T ReadEndIndels \
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* -o output.grp \
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* -I input.bam \
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* [-L input.intervals]
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* </pre>
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*/
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@Requires({DataSource.READS, DataSource.REFERENCE})
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public class CountReadEventsWalker extends ReadWalker<Map<CigarOperator, ArrayList<Integer>> , Map<Integer, Map<CigarOperator, Long>>> {
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@Output (doc = "GATKReport table output")
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PrintStream out;
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public Map<CigarOperator, ArrayList<Integer>> map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
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return ReadUtils.getCigarOperatorForAllBases(read);
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}
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public Map<Integer, Map<CigarOperator, Long>> reduceInit() {
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return new HashMap<Integer, Map<CigarOperator, Long>>();
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}
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public Map<Integer, Map<CigarOperator, Long>> reduce(Map<CigarOperator, ArrayList<Integer>> value, Map<Integer, Map<CigarOperator, Long>> sum) {
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for (Map.Entry<CigarOperator, ArrayList<Integer>> entry : value.entrySet()) {
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CigarOperator op = entry.getKey();
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ArrayList<Integer> positions = entry.getValue();
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for (int p : positions) {
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Map<CigarOperator, Long> operatorCount = sum.get(p);
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if (operatorCount == null) {
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operatorCount = new HashMap<CigarOperator, Long>();
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sum.put(p, operatorCount);
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}
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Long count = operatorCount.get(op);
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if (count == null)
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count = 0L;
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count++;
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operatorCount.put(op, count);
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}
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}
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return sum;
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}
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@Override
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public void onTraversalDone(Map<Integer, Map<CigarOperator, Long>> result) {
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GATKReport report = GATKReport.newSimpleReport("Events", "Position", "Event", "Observations");
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for (Map.Entry<Integer, Map<CigarOperator, Long>> entry : result.entrySet()) {
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int position = entry.getKey();
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Map<CigarOperator, Long> operatorCount = entry.getValue();
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for (Map.Entry<CigarOperator, Long> subEntry: operatorCount.entrySet()) {
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String operator = subEntry.getKey().name();
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Long observations = subEntry.getValue();
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report.addRow(position, operator, observations);
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}
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}
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report.print(out);
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}
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}
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@ -0,0 +1,70 @@
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package org.broadinstitute.sting.gatk.walkers.qc;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.CigarOperator;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import java.util.List;
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/**
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* Walks over the input data set, counting the number of reads ending in insertions/deletions or soft-clips
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*
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* <h2>Input</h2>
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* <p>
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* One or more BAM files.
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* </p>
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*
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* <h2>Output</h2>
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* <p>
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* Number of reads ending in each category.
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* </p>
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*
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* <h2>Examples</h2>
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* <pre>
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* java -Xmx2g -jar GenomeAnalysisTK.jar \
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* -R ref.fasta \
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* -T ReadEndIndels \
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* -o output.txt \
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* -I input.bam \
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* [-L input.intervals]
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* </pre>
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*/
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@Requires({DataSource.READS, DataSource.REFERENCE})
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public class CountTerminusEventWalker extends ReadWalker<Pair<Long, Long>, Pair<Long, Long>> {
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public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) {
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List<CigarElement> cigarElements = read.getCigar().getCigarElements();
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CigarElement lastElement = null;
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for (CigarElement element : cigarElements) {
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if (element.getOperator() != CigarOperator.HARD_CLIP)
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lastElement = element;
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}
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if (lastElement == null)
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throw new UserException.MalformedBAM(read, "read does not have any bases, it's all hard clips");
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long endsInIndel = lastElement.getOperator() == CigarOperator.INSERTION || lastElement.getOperator() == CigarOperator.DELETION? 1 : 0;
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long endsInSC = lastElement.getOperator() == CigarOperator.SOFT_CLIP ? 1 : 0;
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return new Pair<Long, Long>(endsInIndel, endsInSC);
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}
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public Pair<Long, Long> reduceInit() { return new Pair<Long, Long>(0L, 0L); }
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public Pair<Long, Long> reduce(Pair<Long, Long> value, Pair<Long, Long> sum) {
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sum.set(sum.getFirst() + value.getFirst(), sum.getSecond() + value.getSecond());
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return sum;
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}
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@Override
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public void onTraversalDone(Pair<Long, Long> result) {
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System.out.println(String.format("\tReads ending in indels : %d\n\tReads ending in soft-clips: %d\n", result.getFirst(), result.getSecond()));
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}
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}
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@ -783,4 +783,43 @@ public class ReadUtils {
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return location;
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}
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/**
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* Creates a map with each event in the read (cigar operator) and the read coordinate where it happened.
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*
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* Example:
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* D -> 2, 34, 75
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* I -> 55
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* S -> 0, 101
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* H -> 101
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*
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* @param read the read
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* @return a map with the properties described above. See example
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*/
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public static Map<CigarOperator, ArrayList<Integer>> getCigarOperatorForAllBases (GATKSAMRecord read) {
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Map<CigarOperator, ArrayList<Integer>> events = new HashMap<CigarOperator, ArrayList<Integer>>();
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int position = 0;
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for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
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CigarOperator op = cigarElement.getOperator();
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if (op.consumesReadBases()) {
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ArrayList<Integer> list = events.get(op);
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if (list == null) {
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list = new ArrayList<Integer>();
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events.put(op, list);
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}
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for (int i = position; i < cigarElement.getLength(); i++)
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list.add(position++);
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}
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else {
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ArrayList<Integer> list = events.get(op);
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if (list == null) {
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list = new ArrayList<Integer>();
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events.put(op, list);
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}
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list.add(position);
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}
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}
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return events;
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}
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}
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