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Reorganized init() to check for RODs (reference / truth) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6050 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:54:48 +00:00
parent 6f5a08ddc6
commit 3f974c62e6
1 changed files with 58 additions and 100 deletions
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158
java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java
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@ -8,13 +8,16 @@ import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import java.io.PrintStream; import java.io.PrintStream;
import org.apache.commons.math.util.*; import org.apache.commons.math.util.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.*; import java.util.*;
@ -30,8 +33,6 @@ import java.util.regex.Pattern;
* A reference sample name must be provided and it must be barcoded uniquely. * A reference sample name must be provided and it must be barcoded uniquely.
*/ */
public class ReplicationValidationWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> { public class ReplicationValidationWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
@Argument(shortName="refSample", fullName="reference_sample_name", doc="reference sample name", required=true)
String referenceSampleName = "NA12878";
@Argument(shortName="nsamples", fullName="number_of_samples", doc="Number of samples in the dataset (not counting the reference sample).", required=true) @Argument(shortName="nsamples", fullName="number_of_samples", doc="Number of samples in the dataset (not counting the reference sample).", required=true)
int nSamples = -1; int nSamples = -1;
@ -52,36 +53,28 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
PrintStream out; PrintStream out;
int maxAlleleCount; int maxAlleleCount;
List<LaneData> lanes; String referenceSampleName;
boolean USE_TRUTH_ROD;
private class LaneData { final String REFERENCE_ROD_NAME = "reference";
String id; final String TRUTH_ROD_NAME = "truth";
List <String> sampleNames;
String referenceSample;
public String getId() {
return id; /**
} * GATK Engine creates readgroups of the form XXX.Y.Z
* XXX.Y is the unique lane identifier.
public void setId(String id) { * Z is the id of the sample to make the read group id unique
this.id = id; * This function returns a list of unique lane identifiers.
} * @param readGroups readGroups A collection of read group strings (obtained from the alignment context pileup)
* @return a collection of lane ids.
public List<String> getSampleNames() { */
return sampleNames; private Set<String> getLaneIDs(Collection<String> readGroups) {
} HashSet<String> result = new HashSet<String>();
for (String rgid : readGroups) {
public void setSampleNames(List<String> sampleNames) { String [] parsedId = rgid.split("\\.");
this.sampleNames = sampleNames; result.add(parsedId[0] + "." + parsedId[1]);
}
public String getReferenceSample() {
return referenceSample;
}
public void setReferenceSample(String referenceSample) {
this.referenceSample = referenceSample;
} }
return result;
} }
/** /**
@ -107,7 +100,12 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
return model; return model;
} }
// buildErrorModel helper functions /**
* Returns the number of mismatching bases in a pileup
* @param data the bases of a pileup
* @param refBase the reference sample base to compare to
* @return number of bases in data that are different from refBase
*/
private int getNumberOfMismatches(byte[] data, byte refBase) { private int getNumberOfMismatches(byte[] data, byte refBase) {
int mismatches = 0; int mismatches = 0;
for (byte seqBase : data) { for (byte seqBase : data) {
@ -117,41 +115,35 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
return mismatches; return mismatches;
} }
// private String getLaneId (SAMReadGroupRecord rg) {
// String [] idParts = rg.getPlatformUnit().split("\\.");
// return idParts[0] + idParts[1]; // 0 is run_id, 1 is lane_number.
// }
//
// private List<LaneData> createLanesList () {
// List<SAMReadGroupRecord> rgs = getToolkit().getSAMFileHeader().getReadGroups();
// for(SAMReadGroupRecord rg : rgs) {
// String laneId = getLaneId(rg);
// }
//
// return new LinkedList<LaneData>();
// }
//
// private int getNumberOfSamples() {
// int nSamples = 0;
// List<Set<String>> readers = getToolkit().getSamplesByReaders();
// for(Set<String> reader : readers) {
// nSamples += reader.size();
// if (reader.contains(referenceSampleName))
// nSamples--;
// }
// return nSamples;
// }
public void initialize() { public void initialize() {
if (overrideMaxAlleleCount > 0)
maxAlleleCount = overrideMaxAlleleCount; // Set the max allele count (defines the size of the error model array)
else maxAlleleCount = (overrideMaxAlleleCount > 0) ? overrideMaxAlleleCount : nSamples*nChromosomes;
maxAlleleCount = nSamples*nChromosomes;
// Look for the reference ROD and the optional truth ROD. If truth is provided, set the truth "test" mode ON.
List<ReferenceOrderedDataSource> rods = getToolkit().getRodDataSources();
if (rods.size() < 1) {
throw new IllegalArgumentException("You must provide a reference ROD.");
}
boolean foundReferenceROD = false;
boolean foundTruthROD = false;
for (ReferenceOrderedDataSource rod : rods) {
if (rod.getName().equals(REFERENCE_ROD_NAME)) {
foundReferenceROD = true;
}
if (rod.getName().equals(TRUTH_ROD_NAME)) {
foundReferenceROD = true;
}
}
if (!foundReferenceROD) {
throw new IllegalArgumentException("You haven't provided a reference ROD. Note that the reference ROD must be labeled " + REFERENCE_ROD_NAME + ".");
}
if (rods.size() > 1 && !foundTruthROD) {
throw new IllegalArgumentException("You haven't provided a truth ROD. Note that the reference ROD must be labeled " + TRUTH_ROD_NAME + ".");
}
USE_TRUTH_ROD = foundTruthROD;
} }
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
ReadBackedPileup contextPileup = context.getBasePileup(); ReadBackedPileup contextPileup = context.getBasePileup();
Set<String> lanesInLocus = getLaneIDs(contextPileup.getReadGroups()); Set<String> lanesInLocus = getLaneIDs(contextPileup.getReadGroups());
@ -175,7 +167,9 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
if (referenceSamplePileup != null && !referenceSamplePileup.isEmpty() && !poolPileup.isEmpty()) { if (referenceSamplePileup != null && !referenceSamplePileup.isEmpty() && !poolPileup.isEmpty()) {
// Build error model // Build error model
double [] errorModel = buildErrorModel(poolPileup.getBases(), referenceSamplePileup.getBases()[0], defaultPrior); //TODO: Build a reference sample VCF and get true reference base from there.
byte trueReferenceBase = referenceSamplePileup.getBases()[0]; // THIS IS A QUICK FIX JUST TO BE ABLE TO TEST -- IT IS WRONG!
double [] errorModel = buildErrorModel(referenceSamplePileup.getBases(), trueReferenceBase, defaultPrior);
// Debug error model // Debug error model
System.out.println(laneID + ":"); System.out.println(laneID + ":");
@ -191,44 +185,8 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
return 1; return 1;
} }
/**
* GATK Engine creates readgroups of the form XXX.Y.Z
* XXX.Y is the unique lane identifier.
* Z is the id of the sample to make the read group id unique
* This function returns a map that groups together all samples that were run in the same lane:
* XXX.Y -> {Z1, Z2, Z3, ... Zn}
* @param readGroups A collection of read group strings (obtained from the alignment context pileup)
* @return A map of lanes and samples, as described above
*/
// private HashMap<String, ArrayList<String>> decodeReadIDs(Collection<String> readGroups) {
// HashMap<String, ArrayList<String>> result = new HashMap<String, ArrayList<String>>();
// for (String rgid : readGroups) {
// String [] parsedId = rgid.split("\\.");
// String lane = parsedId[0] + "." + parsedId[1];
// String id = parsedId[2];
// ArrayList<String> idList = (result.get(lane) == null) ? (new ArrayList<String>()) : result.get(lane);
// idList.add(id);
// result.put(lane, idList);
// }
// return result;
// }
/**
* GATK Engine creates readgroups of the form XXX.Y.Z
* XXX.Y is the unique lane identifier.
* Z is the id of the sample to make the read group id unique
* This function returns a list of unique lane identifiers.
* @param readGroups readGroups A collection of read group strings (obtained from the alignment context pileup)
* @return a collection of lane ids.
*/
private Set<String> getLaneIDs(Collection<String> readGroups) {
HashSet<String> result = new HashSet<String>();
for (String rgid : readGroups) {
String [] parsedId = rgid.split("\\.");
result.add(parsedId[0] + "." + parsedId[1]);
}
return result;
}
public Long reduceInit() { public Long reduceInit() {