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lots of changes to facilitate calling indels and 1kG 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@666 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-12 15:11:42 +00:00
parent add7b6cf65
commit 313a6d0fb5
1 changed files with 122 additions and 8 deletions
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130
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
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@ -5,7 +5,9 @@ import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.playground.utils.*;
import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods.IndelCall;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.BasicPileup;
import org.broadinstitute.sting.utils.ReadBackedPileup;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
@ -18,26 +20,32 @@ import java.util.*;
// Draft single sample genotyper
// j.maguire 3-7-2009
public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, Integer> {
public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, String>
{
@Argument(fullName="metrics", shortName="met", doc="metrics", required=false) public String metricsFileName = "/dev/null";
@Argument(fullName="metInterval", shortName="mi", doc="metInterval", required=false) public Integer metricsInterval = 50000;
@Argument(fullName="printMetrics", shortName="printMetrics", doc="printMetrics", required=false) public Boolean printMetrics = true;
@Argument(fullName="lodThreshold", shortName="lod", doc="lodThreshold", required=false) public Double lodThreshold = 5.0;
@Argument(fullName="fourBaseMode", shortName="fb", doc="fourBaseMode", required=false) public Boolean fourBaseMode = false;
@Argument(fullName="retest", shortName="re", doc="retest", required=false) public Boolean retest = false;
@Argument(fullName="call_indels", shortName="call_indels", doc="Call Indels", required=false) public Boolean call_indels = false;
@Argument(fullName="qHom", shortName="qHom", doc="qHom", required=false) public Double qHom = 0.04;
@Argument(fullName="qHet", shortName="qHet", doc="qHet", required=false) public Double qHet = 0.49;
@Argument(fullName="qHomNonRef", shortName="qHomNonRef", doc="qHomNonRef", required=false) public Double qHomNonRef = 0.97;
public AlleleMetrics metrics;
public String sample_name;
public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) { return true; }
public boolean requiresReads() { return true; }
public void initialize() { metrics = new AlleleMetrics(metricsFileName, lodThreshold); }
public void initialize() { metrics = new AlleleMetrics(metricsFileName, lodThreshold); sample_name = null; }
public AlleleFrequencyEstimate map(RefMetaDataTracker tracker, char ref, LocusContext context) {
String rodString = getRodString(tracker);
if (ref == 'N') { return null; }
/*
AlleleFrequencyEstimate freq;
if (fourBaseMode) {
@ -57,8 +65,21 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
freq = getOneProbAlleleFrequency(ref, context, rodString);
}
*/
if (context.getReads().size() != 0)
{
SAMRecord read = context.getReads().get(0);
String RG = (String)(read.getAttribute("RG"));
String local_sample_name = read.getHeader().getReadGroup(RG).getSample();
if (sample_name == null) { sample_name = local_sample_name; }
else
{
if (! sample_name.equals(local_sample_name)) { System.out.printf("SAMPLE NAME MIXUP: %s vs. %s\n", sample_name, local_sample_name); }
assert(sample_name.equals(local_sample_name));
}
}
AlleleFrequencyEstimate freq = getOneProbAlleleFrequency(ref, context, rodString);
AlleleFrequencyEstimate freq = getOneProbAlleleFrequency(ref, context, rodString, sample_name);
if (printMetrics) {
if (freq != null) { metrics.nextPosition(freq, tracker); }
@ -151,7 +172,8 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
probs.length,
ReadBackedPileup.basePileupAsString(context.getReads(), context.getOffsets()),
probs,
posteriors);
posteriors,
"unknown_sample");
return freq;
}
@ -250,14 +272,29 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
return secondaryBaseCounts;
}
private AlleleFrequencyEstimate getOneProbAlleleFrequency(char ref, LocusContext context, String rodString) {
private AlleleFrequencyEstimate getOneProbAlleleFrequency(char ref, LocusContext context, String rodString, String sample_name) {
ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases();
List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets();
ref = Character.toUpperCase(ref);
// Handle indels.
if (call_indels)
{
String[] indels = BasicPileup.indelPileup(reads, offsets);
IndelCall indel_call = GenotypeLikelihoods.callIndel(indels);
if (indel_call != null)
{
if (! indel_call.type.equals("ref"))
{
System.out.printf("INDEL %s %s\n", context.getLocation(), indel_call);
}
}
}
// Handle single-base polymorphisms.
GenotypeLikelihoods G = new GenotypeLikelihoods();
for ( int i = 0; i < reads.size(); i++ )
{
@ -272,7 +309,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
G.applyFourBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
}
return G.toAlleleFrequencyEstimate(context.getLocation(), ref, bases.length(), bases, G.likelihoods);
return G.toAlleleFrequencyEstimate(context.getLocation(), ref, bases.length(), bases, G.likelihoods, sample_name);
}
private String getRodString(RefMetaDataTracker tracker) {
@ -300,6 +337,83 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
}
// Given result of map function
public Integer reduceInit() { return 0; }
public Integer reduce(AlleleFrequencyEstimate value, Integer sum) { return 0; }
private String confident_ref_interval_contig = "";
private long confident_ref_interval_start = 0;
private double confident_ref_interval_LOD_sum = 0;
private double confident_ref_interval_length = 0;
private long last_position_considered = -1;
private boolean inside_confident_ref_interval = false;
public String reduceInit()
{
confident_ref_interval_contig = "";
confident_ref_interval_start = 0;
confident_ref_interval_LOD_sum = 0;
confident_ref_interval_length = 0;
last_position_considered = -1;
inside_confident_ref_interval = false;
return "";
}
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{
// Print RESULT data for confident calls
long current_offset = alleleFreq.location.getStart(); //Integer.parseInt(tokens[1]);
if (inside_confident_ref_interval &&
((alleleFreq.lodVsRef > -5.0) || (current_offset != last_position_considered + 1)) )
{
// No longer hom-ref, so output a ref line.
double lod = confident_ref_interval_LOD_sum / confident_ref_interval_length;
out.format("%s\tCALLER\tREFERENCE\t%d\t%d\t%f\t.\t.\tLENGTH %d\n",
confident_ref_interval_contig,
confident_ref_interval_start,
last_position_considered,
lod,
(int)(confident_ref_interval_length));
inside_confident_ref_interval = false;
}
else if (inside_confident_ref_interval && (alleleFreq.lodVsRef <= -5.0))
{
// Still hom-ref so increment the counters.
confident_ref_interval_LOD_sum += alleleFreq.lodVsRef;
confident_ref_interval_length += 1;
}
else if ((!inside_confident_ref_interval) && (alleleFreq.lodVsRef > -5.0))
{
// do nothing.
}
else if ((!inside_confident_ref_interval) && (alleleFreq.lodVsRef <= -5.0))
{
// We moved into a hom-ref region so start a new interval.
confident_ref_interval_contig = alleleFreq.location.getContig();
confident_ref_interval_start = alleleFreq.location.getStart();
confident_ref_interval_LOD_sum = alleleFreq.lodVsRef;
confident_ref_interval_length = 1;
inside_confident_ref_interval = true;
}
last_position_considered = current_offset;
if (alleleFreq.lodVsRef >= 5) {
out.print(alleleFreq.asGFFString());
/*
String gtype = genotypeTypeString(alleleFreq.qstar, alleleFreq.N);
System.out.print("DEBUG " + gtype + " ");
if (gtype.contentEquals("het")) {
System.out.println(alleleFreq.ref + "" + alleleFreq.alt);
} else if (gtype.contentEquals("hom")) {
System.out.println(alleleFreq.ref + "" + alleleFreq.ref);
} else {
System.out.println(alleleFreq.alt + "" + alleleFreq.alt);
}
*/
}
return "";
}
}