Now outputs VCF (as standard output associated with -o)! Can also outptut, in parallel, a lightweight bed and fully annotated .txt (old verbose format) with --bed and --verbose, respectively
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4128 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache
parent
dfae48cee0
commit
9b3ffa5f64
|
|
@ -30,7 +30,10 @@ import net.sf.samtools.CigarElement;
|
|||
import net.sf.samtools.CigarOperator;
|
||||
import net.sf.samtools.SAMRecord;
|
||||
import org.broad.tribble.FeatureSource;
|
||||
import org.broad.tribble.dbsnp.DbSNPCodec;
|
||||
import org.broad.tribble.util.variantcontext.Allele;
|
||||
import org.broad.tribble.util.variantcontext.VariantContext;
|
||||
import org.broad.tribble.util.variantcontext.Genotype;
|
||||
import org.broad.tribble.vcf.*;
|
||||
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
|
||||
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
|
||||
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
|
||||
|
|
@ -38,25 +41,25 @@ import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
|
|||
import org.broadinstitute.sting.gatk.refdata.*;
|
||||
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
|
||||
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
|
||||
import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
|
||||
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
|
||||
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
|
||||
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSource;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
import org.broadinstitute.sting.utils.vcf.VCFUtils;
|
||||
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
|
||||
import org.broadinstitute.sting.utils.collections.CircularArray;
|
||||
import org.broadinstitute.sting.utils.collections.PrimitivePair;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.commandline.CommandLineUtils;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.io.PrintStream;
|
||||
import java.io.*;
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
|
|
@ -71,44 +74,60 @@ import java.util.*;
|
|||
*/
|
||||
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class})
|
||||
public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
||||
@Output
|
||||
PrintStream out;
|
||||
// @Output
|
||||
// PrintStream out;
|
||||
@Output(doc="File to which variants should be written",required=true)
|
||||
protected VCFWriter vcf_writer = null;
|
||||
|
||||
@Argument(fullName="outputFile", shortName="O", doc="output file name (defaults to BED format)", required=true)
|
||||
java.io.File bed_file;
|
||||
@Argument(fullName="outputFile", shortName="O", doc="output file name (BED format). DEPRECATED> Use --bed", required=true)
|
||||
@Deprecated
|
||||
java.io.File output_file;
|
||||
|
||||
@Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print callability metrics output", required = false)
|
||||
public PrintStream metricsWriter = null;
|
||||
|
||||
@Argument(fullName="1kg_format", shortName="1kg", doc="output in 1000 genomes format", required=false)
|
||||
boolean FORMAT_1KG = false;
|
||||
// @Argument(fullName="vcf_format", shortName="vcf", doc="generate output file in VCF format", required=false)
|
||||
// boolean FORMAT_VCF = false;
|
||||
|
||||
@Argument(fullName="somatic", shortName="somatic",
|
||||
doc="Perform somatic calls; two input alignment files (-I option) must be specified. Calls are performed from the second file (\"tumor\") against the first one (\"normal\").", required=false)
|
||||
boolean call_somatic = false;
|
||||
@Argument(fullName="verbose", shortName="verbose",
|
||||
doc="Prints all calls (both germline and somatic if --somatic is used) with additional read/mismatch statistics into GATK output stream (redirect with -o).", required=false)
|
||||
boolean verbose = false;
|
||||
|
||||
@Argument(fullName="verboseOutput", shortName="verbose",
|
||||
doc="Verbose output file in text format", required=false)
|
||||
java.io.File verboseOutput = null;
|
||||
|
||||
@Argument(fullName="bedOutput", shortName="bed",
|
||||
doc="Lightweight bed output file (only positions and events, no stats/annotations)", required=false)
|
||||
java.io.File bedOutput = null;
|
||||
|
||||
@Argument(fullName="minCoverage", shortName="minCoverage",
|
||||
doc="indel calls will be made only at sites with coverage of minCoverage or more reads; with --somatic this value is applied to tumor sample", required=false)
|
||||
int minCoverage = 6;
|
||||
|
||||
@Argument(fullName="minNormalCoverage", shortName="minNormalCoverage",
|
||||
doc="used only with --somatic; normal sample must have at least minNormalCoverage or more reads at the site to call germline/somatic indel, otherwise the indel (in tumor) is ignored", required=false)
|
||||
int minNormalCoverage = 4;
|
||||
|
||||
@Argument(fullName="minFraction", shortName="minFraction",
|
||||
doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for making a call"+
|
||||
" (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false)
|
||||
double minFraction = 0.3;
|
||||
|
||||
@Argument(fullName="minConsensusFraction", shortName="minConsensusFraction",
|
||||
doc="Indel call is made only if fraction of CONSENSUS indel observations at a site wrt all indel observations at the site exceeds this threshold", required=false)
|
||||
double minConsensusFraction = 0.7;
|
||||
|
||||
@Argument(fullName="minIndelCount", shortName="minCnt",
|
||||
doc="Minimum count of reads supporting consensus indel required for making the call. "+
|
||||
" This filter supercedes minFraction, i.e. indels with acceptable minFraction at low coverage "+
|
||||
"(minIndelCount not met) will not pass.", required=false)
|
||||
int minIndelCount = 0;
|
||||
|
||||
@Argument(fullName="refseq", shortName="refseq",
|
||||
doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with GENOMIC/UTR/INTRON/CODING and with the gene name", required=false)
|
||||
String RefseqFileName = null;
|
||||
|
||||
@Argument(fullName="blacklistedLanes", shortName="BL",
|
||||
doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+
|
||||
"by this application, so they will not contribute indels to consider and will not be counted.", required=false)
|
||||
|
|
@ -138,6 +157,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
private int NQS_WIDTH = 5; // 5 bases on each side of the indel for NQS-style statistics
|
||||
|
||||
private Writer bedWriter = null;
|
||||
private Writer verboseWriter = null;
|
||||
|
||||
|
||||
private static String annGenomic = "GENOMIC";
|
||||
private static String annIntron = "INTRON";
|
||||
|
|
@ -146,14 +168,55 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
private static String annUnknown = "UNKNOWN";
|
||||
|
||||
private SAMRecord lastRead;
|
||||
private byte[] refBases;
|
||||
private ReferenceDataSource refData;
|
||||
|
||||
// "/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"
|
||||
|
||||
private Set<VCFHeaderLine> getVCFHeaderInfo() {
|
||||
Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
|
||||
|
||||
// first, the basic info
|
||||
headerInfo.add(new VCFHeaderLine("source", "IndelGenotyperV2"));
|
||||
headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
|
||||
|
||||
// FORMAT and INFO fields
|
||||
// headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());
|
||||
|
||||
if ( call_somatic ) {
|
||||
headerInfo.addAll(VCFIndelAttributes.getAttributeHeaderLines("N_","In NORMAL: "));
|
||||
headerInfo.addAll(VCFIndelAttributes.getAttributeHeaderLines("T_","In TUMOR: "));
|
||||
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.SOMATIC_KEY, 0, VCFHeaderLineType.Flag, "Somatic event"));
|
||||
} else {
|
||||
headerInfo.addAll(VCFIndelAttributes.getAttributeHeaderLines("",""));
|
||||
}
|
||||
|
||||
// all of the arguments from the argument collection
|
||||
Set<Object> args = new HashSet<Object>();
|
||||
args.add(this);
|
||||
args.addAll(getToolkit().getFilters());
|
||||
Map<String,String> commandLineArgs = CommandLineUtils.getApproximateCommandLineArguments(args);
|
||||
for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() )
|
||||
headerInfo.add(new VCFHeaderLine(String.format("IGv2_%s", commandLineArg.getKey()), commandLineArg.getValue()));
|
||||
// also, the list of input bams
|
||||
for ( File file : getToolkit().getArguments().samFiles )
|
||||
headerInfo.add(new VCFHeaderLine("IGv2_bam_file_used", file.getName()));
|
||||
|
||||
return headerInfo;
|
||||
}
|
||||
|
||||
// "/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"
|
||||
|
||||
@Override
|
||||
public void initialize() {
|
||||
normal_context = new WindowContext(0,WINDOW_SIZE);
|
||||
|
||||
if ( bedOutput != null && output_file != null ) {
|
||||
throw new StingException("-O option is deprecated and -bed option replaces it; you can not use both at the same time");
|
||||
}
|
||||
|
||||
if ( RefseqFileName != null ) {
|
||||
logger.info("Using RefSeq annotations from "+RefseqFileName);
|
||||
|
||||
TribbleRMDTrackBuilder builder = new TribbleRMDTrackBuilder();
|
||||
FeatureSource refseq = builder.createFeatureReader(RefSeqCodec.class,new File(RefseqFileName)).first;
|
||||
|
||||
|
|
@ -162,10 +225,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
} catch (IOException e) {
|
||||
throw new StingException("Unable to open file " + RefseqFileName, e);
|
||||
}
|
||||
logger.info("Using RefSeq annotations from "+RefseqFileName);
|
||||
}
|
||||
|
||||
if ( refseqIterator == null ) logger.info("No annotations available");
|
||||
if ( refseqIterator == null ) logger.info("No gene annotations available");
|
||||
|
||||
int nSams = getToolkit().getArguments().samFiles.size();
|
||||
|
||||
|
|
@ -192,11 +254,21 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
"WARNING: Without --somatic option they will be merged and processed as a single sample");
|
||||
}
|
||||
|
||||
try {
|
||||
output = new java.io.FileWriter(bed_file);
|
||||
} catch (IOException e) {
|
||||
throw new StingException("Failed to open file for writing BED output");
|
||||
}
|
||||
try {
|
||||
// we already checked that bedOutput and output_file are not set simultaneously
|
||||
if ( bedOutput != null ) bedWriter = new FileWriter(bedOutput);
|
||||
if ( output_file != null ) bedWriter = new FileWriter(output_file);
|
||||
} catch (java.io.IOException e) {
|
||||
throw new StingException("Failed to open BED file for writing. "+ e.getMessage());
|
||||
}
|
||||
try {
|
||||
if ( verboseOutput != null ) verboseWriter = new FileWriter(verboseOutput);
|
||||
} catch (java.io.IOException e) {
|
||||
throw new StingException("Failed to open verbose file for writing. "+ e.getMessage());
|
||||
}
|
||||
|
||||
vcf_writer.writeHeader(new VCFHeader(getVCFHeaderInfo(), SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()))) ;
|
||||
refData = new ReferenceDataSource(getToolkit().getArguments().referenceFile);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -238,6 +310,8 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
normal_context.clear(); // reset coverage window; this will also set reference position to 0
|
||||
if ( call_somatic) tumor_context.clear();
|
||||
|
||||
refBases = new String(refData.getReference().getSequence(read.getReferenceName()).getBases()).toUpperCase().getBytes();
|
||||
}
|
||||
|
||||
// we have reset the window to the new contig if it was required and emitted everything we collected
|
||||
|
|
@ -317,9 +391,9 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream. RG is required for somatic calls.");
|
||||
|
||||
if ( normalReadGroups.contains(rg) ) {
|
||||
normal_context.add(read,ref.getBasesAsChars());
|
||||
normal_context.add(read,ref.getBases());
|
||||
} else if ( tumorReadGroups.contains(rg) ) {
|
||||
tumor_context.add(read,ref.getBasesAsChars());
|
||||
tumor_context.add(read,ref.getBases());
|
||||
} else {
|
||||
throw new StingException("Unrecognized read group in merged stream: "+rg);
|
||||
}
|
||||
|
|
@ -338,7 +412,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
|
||||
} else {
|
||||
normal_context.add(read, ref.getBasesAsChars());
|
||||
normal_context.add(read, ref.getBases());
|
||||
if ( normal_context.getReads().size() > MAX_READ_NUMBER ) {
|
||||
System.out.println("WARNING: a count of "+MAX_READ_NUMBER+" reads reached in a window "+
|
||||
refName+':'+normal_context.getStart()+'-'+normal_context.getStop()+". The whole window will be dropped");
|
||||
|
|
@ -350,12 +424,12 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
}
|
||||
|
||||
|
||||
/** Output indel calls up to the specified position and shift the window: after this method is executed, the
|
||||
* first element of the window maps onto 'position', if possible, or at worst a few bases to the left of 'position' if we may need more
|
||||
* reads to get full NQS-style statistics for an indel in the close proximity of 'position'.
|
||||
*
|
||||
* @param position
|
||||
*/
|
||||
/** Output indel calls up to the specified position and shift the window: after this method is executed, the
|
||||
* first element of the window maps onto 'position', if possible, or at worst a few bases to the left of 'position' if we may need more
|
||||
* reads to get full NQS-style statistics for an indel in the close proximity of 'position'.
|
||||
*
|
||||
* @param position
|
||||
*/
|
||||
private void emit(long position, boolean force) {
|
||||
|
||||
long adjustedPosition = adjustPosition(position);
|
||||
|
|
@ -405,31 +479,25 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
location = GenomeLocParser.setStart(location,pos);
|
||||
location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
|
||||
RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
|
||||
|
||||
if ( normalCall.failsNQSMismatch() ) {
|
||||
String fullRecord = makeFullRecord(normalCall);
|
||||
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
|
||||
out.println(fullRecord+
|
||||
"SAMPLE_TOO_DIRTY\t"+annotationString);
|
||||
normal_context.indelsAt(pos).clear();
|
||||
// we dealt with this indel; don't want to see it again
|
||||
// (we might otherwise in the case when 1) there is another indel that follows
|
||||
// within MISMATCH_WIDTH bases and 2) we'd need to wait for more coverage for that next indel)
|
||||
continue; // too dirty
|
||||
}
|
||||
|
||||
if ( normalCall.isCall() ) {
|
||||
normalCallsMade++;
|
||||
String message = normalCall.makeBedLine(output);
|
||||
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
|
||||
printVCFLine(vcf_writer,normalCall);
|
||||
if ( bedWriter != null ) normalCall.printBedLine(bedWriter);
|
||||
|
||||
StringBuilder fullRecord = new StringBuilder();
|
||||
fullRecord.append(makeFullRecord(normalCall));
|
||||
if ( verboseWriter != null ) {
|
||||
|
||||
if ( verbose ) {
|
||||
if ( refseqIterator == null ) out.println(fullRecord + "\t");
|
||||
else out.println(fullRecord + "\t"+ annotationString);
|
||||
RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
|
||||
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
|
||||
|
||||
StringBuilder fullRecord = new StringBuilder();
|
||||
fullRecord.append(makeFullRecord(normalCall));
|
||||
fullRecord.append(annotationString);
|
||||
try {
|
||||
verboseWriter.write(fullRecord.toString());
|
||||
} catch (IOException e) {
|
||||
throw new StingException("Write failed (verbose writer). "+e.getMessage());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -564,52 +632,33 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
location = GenomeLocParser.setStart(location,pos);
|
||||
location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
|
||||
RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
|
||||
|
||||
if ( normalCall.failsNQSMismatch() ) {
|
||||
String fullRecord = makeFullRecord(normalCall,tumorCall);
|
||||
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
|
||||
out.println(fullRecord+
|
||||
"NORMAL_TOO_DIRTY\t"+annotationString);
|
||||
tumor_context.indelsAt(pos).clear();
|
||||
normal_context.indelsAt(pos).clear();
|
||||
// we dealt with this indel; don't want to see it again
|
||||
// (we might otherwise in the case when 1) there is another indel that follows
|
||||
// within MISMATCH_WIDTH bases and 2) we'd need to wait for more coverage for that next indel)
|
||||
continue; // too dirty
|
||||
}
|
||||
if ( tumorCall.failsNQSMismatch() ) {
|
||||
String fullRecord = makeFullRecord(normalCall,tumorCall);
|
||||
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
|
||||
out.println(fullRecord+
|
||||
"TUMOR_TOO_DIRTY\t"+annotationString);
|
||||
tumor_context.indelsAt(pos).clear();
|
||||
normal_context.indelsAt(pos).clear();
|
||||
// we dealt with this indel; don't want to see it again
|
||||
// (we might otherwise in the case when 1) there is another indel that follows
|
||||
// within MISMATCH_WIDTH bases and 2) we'd need to wait for more coverage for that next indel)
|
||||
continue; // too dirty
|
||||
}
|
||||
|
||||
if ( tumorCall.isCall() ) {
|
||||
tumorCallsMade++;
|
||||
String message = tumorCall.makeBedLine(output);
|
||||
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
|
||||
|
||||
StringBuilder fullRecord = new StringBuilder();
|
||||
fullRecord.append(makeFullRecord(normalCall,tumorCall));
|
||||
printVCFLine(vcf_writer,normalCall,tumorCall);
|
||||
|
||||
if ( normalCall.getVariant() == null ) {
|
||||
fullRecord.append("SOMATIC");
|
||||
} else {
|
||||
fullRecord.append("GERMLINE");
|
||||
}
|
||||
if ( verbose ) {
|
||||
if ( refseqIterator == null ) out.println(fullRecord + "\t");
|
||||
else out.println(fullRecord + "\t"+ annotationString);
|
||||
if ( bedWriter != null ) tumorCall.printBedLine(bedWriter);
|
||||
|
||||
if ( verboseWriter != null ) {
|
||||
RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
|
||||
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
|
||||
|
||||
StringBuilder fullRecord = new StringBuilder();
|
||||
fullRecord.append(makeFullRecord(normalCall,tumorCall));
|
||||
|
||||
if ( normalCall.getVariant() == null ) {
|
||||
fullRecord.append("SOMATIC");
|
||||
} else {
|
||||
fullRecord.append("GERMLINE");
|
||||
}
|
||||
try {
|
||||
verboseWriter.write(fullRecord + "\t"+ annotationString);
|
||||
} catch (IOException e) {
|
||||
throw new StingException("Write failed (verbose writer). "+e.getMessage());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
tumor_context.indelsAt(pos).clear();
|
||||
normal_context.indelsAt(pos).clear();
|
||||
// we dealt with this indel; don't want to see it again
|
||||
|
|
@ -668,6 +717,57 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
}
|
||||
|
||||
public void printVCFLine(VCFWriter vcf, IndelPrecall call) {
|
||||
int event_length = call.getVariant().lengthOnRef();
|
||||
if ( event_length < 0 ) event_length = 0;
|
||||
|
||||
long start = call.getPosition()-1;
|
||||
long stop = start;
|
||||
|
||||
List<Allele> alleles = new ArrayList<Allele>(2);
|
||||
|
||||
if ( event_length == 0 ) { // insertion
|
||||
alleles.add( Allele.create(Allele.NULL_ALLELE_STRING,true) );
|
||||
alleles.add( Allele.create(call.getVariant().getBases(), false ));
|
||||
} else { //deletion:
|
||||
alleles.add( Allele.create(Allele.NULL_ALLELE_STRING,false) );
|
||||
alleles.add( Allele.create(call.getVariant().getBases(), true ));
|
||||
stop += event_length;
|
||||
}
|
||||
|
||||
VariantContext vc = new VariantContext("IGv2_Indel_call", refName, start, stop, alleles, VariantContext.NO_GENOTYPES /* genotypes */,
|
||||
-1.0 /* log error */, null /* filters */, call.makeStatsAttributes("",null));
|
||||
vcf.add(vc,refBases[(int)start-1]);
|
||||
}
|
||||
|
||||
public void printVCFLine(VCFWriter vcf, IndelPrecall nCall, IndelPrecall tCall) {
|
||||
int event_length = tCall.getVariant().lengthOnRef();
|
||||
if ( event_length < 0 ) event_length = 0;
|
||||
|
||||
long start = tCall.getPosition()-1;
|
||||
long stop = start;
|
||||
|
||||
List<Allele> alleles = new ArrayList<Allele>(2);
|
||||
|
||||
if ( event_length == 0 ) { // insertion
|
||||
alleles.add( Allele.create(Allele.NULL_ALLELE_STRING,true) );
|
||||
alleles.add( Allele.create(tCall.getVariant().getBases(), false ));
|
||||
} else { //deletion:
|
||||
alleles.add( Allele.create(Allele.NULL_ALLELE_STRING,false) );
|
||||
alleles.add( Allele.create(tCall.getVariant().getBases(), true ));
|
||||
stop += event_length;
|
||||
}
|
||||
|
||||
Map<String,Object> attrs = nCall.makeStatsAttributes("N_",null);
|
||||
attrs = tCall.makeStatsAttributes("T_",attrs);
|
||||
|
||||
if ( nCall.getVariant() == null ) attrs.put(VCFConstants.SOMATIC_KEY,true);
|
||||
|
||||
VariantContext vc = new VariantContext("IGv2_Indel_call", refName, start, stop, alleles, VariantContext.NO_GENOTYPES /* genotypes */,
|
||||
-1.0 /* log error */, null /* filters */, attrs);
|
||||
vcf.add(vc,refBases[(int)start-1]);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void onTraversalDone(Integer result) {
|
||||
if ( call_somatic ) emit_somatic(1000000000, true);
|
||||
|
|
@ -676,10 +776,12 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
if ( metricsWriter != null ) {
|
||||
metricsWriter.println(String.format("Normal calls made %d", normalCallsMade));
|
||||
metricsWriter.println(String.format("Tumor calls made %d", tumorCallsMade));
|
||||
metricsWriter.close();
|
||||
}
|
||||
|
||||
try {
|
||||
output.close();
|
||||
if ( bedWriter != null ) bedWriter.close();
|
||||
if ( verboseWriter != null ) verboseWriter.close();
|
||||
} catch (IOException e) {
|
||||
System.out.println("Failed to close output BED file gracefully, data may be lost");
|
||||
e.printStackTrace();
|
||||
|
|
@ -1022,16 +1124,16 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
public int getAllVariantCount() { return all_indel_count; }
|
||||
public int getConsensusVariantCount() { return consensus_indel_count; }
|
||||
|
||||
public boolean failsNQSMismatch() {
|
||||
//TODO wrong fraction: mismatches are counted only in indel-containing reads, but total_coverage is used!
|
||||
return ( indel_read_mismatches_in_nqs_window > NQS_MISMATCH_CUTOFF ) ||
|
||||
( indel_read_mismatches_in_nqs_window > total_coverage * AV_MISMATCHES_PER_READ );
|
||||
}
|
||||
// public boolean failsNQSMismatch() {
|
||||
// //TODO wrong fraction: mismatches are counted only in indel-containing reads, but total_coverage is used!
|
||||
// return ( indel_read_mismatches_in_nqs_window > NQS_MISMATCH_CUTOFF ) ||
|
||||
// ( indel_read_mismatches_in_nqs_window > total_coverage * AV_MISMATCHES_PER_READ );
|
||||
// }
|
||||
|
||||
public IndelVariant getVariant() { return consensus_indel; }
|
||||
|
||||
public boolean isCall() {
|
||||
boolean ret = ! failsNQSMismatch() && ( consensus_indel_count >= minIndelCount &&
|
||||
boolean ret = ( consensus_indel_count >= minIndelCount &&
|
||||
(double)consensus_indel_count > minFraction * total_coverage &&
|
||||
(double) consensus_indel_count > minConsensusFraction*all_indel_count );
|
||||
if ( DEBUG && ! ret ) System.out.println("DEBUG>> NOT a call: count="+consensus_indel_count+
|
||||
|
|
@ -1062,27 +1164,20 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
}
|
||||
|
||||
|
||||
public String makeBedLine(java.io.Writer bedOutput) {
|
||||
|
||||
public void printBedLine(Writer bed) {
|
||||
int event_length = consensus_indel.lengthOnRef();
|
||||
if ( event_length < 0 ) event_length = 0;
|
||||
|
||||
StringBuffer message = new StringBuffer();
|
||||
message.append(refName+"\t"+(pos-1)+"\t");
|
||||
if ( FORMAT_1KG )
|
||||
message.append(consensus_indel.getBases().length() + "\t" + (event_length > 0 ? "D" : "I") + "\t" +
|
||||
consensus_indel.getBases() + "\t" + consensus_indel.getSamples());
|
||||
else
|
||||
message.append((pos-1+event_length)+"\t"+(event_length>0? "-":"+")+consensus_indel.getBases() +":"+all_indel_count+"/"+total_coverage);
|
||||
message.append((pos-1+event_length)+"\t"+(event_length>0? "-":"+")+consensus_indel.getBases() +":"+all_indel_count+"/"+total_coverage);
|
||||
|
||||
if ( bedOutput != null ) {
|
||||
try {
|
||||
bedOutput.write(message.toString()+"\n");
|
||||
} catch (IOException e) {
|
||||
System.out.println(e.getMessage());
|
||||
e.printStackTrace();
|
||||
throw new StingException("Error encountered while writing into output BED file");
|
||||
}
|
||||
}
|
||||
return message.toString();
|
||||
try {
|
||||
bed.write(message.toString()+"\n");
|
||||
} catch (IOException e) {
|
||||
throw new StingException("Error encountered while writing into output BED file");
|
||||
}
|
||||
}
|
||||
|
||||
public String makeEventString() {
|
||||
|
|
@ -1121,6 +1216,33 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
return message.toString();
|
||||
}
|
||||
|
||||
/**
|
||||
* Places alignment statistics into attribute map and returns the map. If attr parameter is null,
|
||||
* a new map is allocated, filled and returned. If attr is not null, new attributes are added to that
|
||||
* preexisting map, and the same instance of the (updated) map is returned.
|
||||
* @param prefix
|
||||
* @param attr
|
||||
* @return
|
||||
*/
|
||||
public Map<String,Object> makeStatsAttributes(String prefix, Map<String,Object> attr) {
|
||||
if ( attr == null ) attr = new HashMap<String, Object>();
|
||||
|
||||
VCFIndelAttributes.recordDepth(prefix,getConsensusVariantCount(),getAllVariantCount(),getCoverage(),attr);
|
||||
|
||||
VCFIndelAttributes.recordAvMM(prefix,getAvConsensusMismatches(),getAvRefMismatches(),attr);
|
||||
|
||||
VCFIndelAttributes.recordAvMapQ(prefix,getAvConsensusMapq(),getAvRefMapq(),attr);
|
||||
|
||||
VCFIndelAttributes.recordNQSMMRate(prefix,getNQSConsensusMMRate(),getNQSRefMMRate(),attr);
|
||||
|
||||
VCFIndelAttributes.recordNQSAvQ(prefix,getNQSConsensusAvQual(),getNQSRefAvQual(),attr);
|
||||
|
||||
PrimitivePair.Int strand_cons = getConsensusStrandCounts();
|
||||
PrimitivePair.Int strand_ref = getRefStrandCounts();
|
||||
|
||||
VCFIndelAttributes.recordStrandCounts(prefix,strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,attr);
|
||||
return attr;
|
||||
}
|
||||
}
|
||||
|
||||
interface IndelListener {
|
||||
|
|
@ -1243,7 +1365,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
}
|
||||
}
|
||||
|
||||
public void add(SAMRecord read, char [] ref) {
|
||||
public void add(SAMRecord read, byte [] ref) {
|
||||
|
||||
if ( read.getAlignmentStart() < start ) return; // silently ignore reads starting before the window start
|
||||
|
||||
|
|
@ -1303,12 +1425,14 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
private byte[] expanded_quals;
|
||||
private int mms;
|
||||
|
||||
public ExpandedSAMRecord(SAMRecord r, char [] ref, long offset, IndelListener l) {
|
||||
public ExpandedSAMRecord(SAMRecord r, byte [] ref, long offset, IndelListener l) {
|
||||
|
||||
read = r;
|
||||
final long rStart = read.getAlignmentStart();
|
||||
final long rStop = read.getAlignmentEnd();
|
||||
final String readBases = read.getReadString().toUpperCase();
|
||||
final byte[] readBases = read.getReadString().toUpperCase().getBytes();
|
||||
|
||||
ref = new String(ref).toUpperCase().getBytes();
|
||||
|
||||
mismatch_flags = new byte[(int)(rStop-rStart+1)];
|
||||
expanded_quals = new byte[(int)(rStop-rStart+1)];
|
||||
|
|
@ -1325,31 +1449,30 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
final CigarElement ce = c.getCigarElement(i);
|
||||
IndelVariant.Type type = null;
|
||||
String bases = null;
|
||||
String indel_bases = null;
|
||||
int eventPosition = posOnRef;
|
||||
|
||||
switch(ce.getOperator()) {
|
||||
case H: break; // hard clipped reads do not have clipped bases in their sequence, so we just ignore the H element...
|
||||
case H: break; // hard clipped reads do not have clipped indel_bases in their sequence, so we just ignore the H element...
|
||||
case I:
|
||||
type = IndelVariant.Type.I;
|
||||
bases = readBases.substring(posOnRead,posOnRead+ce.getLength());
|
||||
indel_bases = read.getReadString().substring(posOnRead,posOnRead+ce.getLength());
|
||||
// will increment position on the read below, there's no 'break' statement yet...
|
||||
case S:
|
||||
// here we also skip soft-clipped bases on the read; according to SAM format specification,
|
||||
// here we also skip soft-clipped indel_bases on the read; according to SAM format specification,
|
||||
// alignment start position on the reference points to where the actually aligned
|
||||
// (not clipped) bases go, so we do not need to increment reference position here
|
||||
// (not clipped) indel_bases go, so we do not need to increment reference position here
|
||||
posOnRead += ce.getLength();
|
||||
break;
|
||||
case D:
|
||||
type = IndelVariant.Type.D;
|
||||
bases = new String( ref, posOnRef, ce.getLength() );
|
||||
indel_bases = new String( ref, posOnRef, ce.getLength() );
|
||||
for( int k = 0 ; k < ce.getLength(); k++, posOnRef++ ) mismatch_flags[posOnRef] = expanded_quals[posOnRef] = -1;
|
||||
|
||||
break;
|
||||
case M:
|
||||
for ( int k = 0; k < ce.getLength(); k++, posOnRef++, posOnRead++ ) {
|
||||
if ( readBases.charAt(posOnRead) != //note: readBases was uppercased above!
|
||||
Character.toUpperCase(ref[posOnRef]) ) { // mismatch!
|
||||
if ( readBases[posOnRead] != ref[posOnRef] ) { // mismatch!
|
||||
mms++;
|
||||
mismatch_flags[posOnRef] = 1;
|
||||
}
|
||||
|
|
@ -1368,7 +1491,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
// note that here we will be assigning indels to the first deleted base or to the first
|
||||
// base after insertion, not to the last base before the event!
|
||||
l.addObservation((int)(offset+eventPosition), type, bases, this);
|
||||
l.addObservation((int)(offset+eventPosition), type, indel_bases, this);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -1390,4 +1513,71 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
|
|||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
class VCFIndelAttributes {
|
||||
public static String DEPTH_INDEL_KEY = VCFConstants.ALLELE_COUNT_KEY;
|
||||
public static String DEPTH_TOTAL_KEY = VCFConstants.DEPTH_KEY;
|
||||
|
||||
public static String MAPQ_KEY = "MQ";
|
||||
|
||||
public static String MM_KEY = "MM";
|
||||
|
||||
public static String NQS_MMRATE_KEY = "NQSMM";
|
||||
|
||||
public static String NQS_AVQ_KEY = "NQSBQ";
|
||||
|
||||
public static String STRAND_COUNT_KEY = "SC";
|
||||
|
||||
public static Set<VCFInfoHeaderLine> getAttributeHeaderLines(String prefix, String descr_prefix) {
|
||||
Set<VCFInfoHeaderLine> lines = new HashSet<VCFInfoHeaderLine>();
|
||||
|
||||
lines.add(new VCFInfoHeaderLine(prefix+DEPTH_INDEL_KEY, 2, VCFHeaderLineType.Integer, descr_prefix+"# of reads supporting consensus indel/any indel at the site"));
|
||||
lines.add(new VCFInfoHeaderLine(prefix+DEPTH_TOTAL_KEY, 1, VCFHeaderLineType.Integer, descr_prefix+"total coverage at the site"));
|
||||
|
||||
lines.add(new VCFInfoHeaderLine(prefix+MAPQ_KEY, 2, VCFHeaderLineType.Float, descr_prefix+"average mapping quality of consensus indel-supporting reads/reference-supporting reads"));
|
||||
|
||||
lines.add(new VCFInfoHeaderLine(prefix+MM_KEY, 2, VCFHeaderLineType.Float, descr_prefix+"average # of mismatches per consensus indel-supporting read/per reference-supporting read"));
|
||||
|
||||
lines.add(new VCFInfoHeaderLine(prefix+NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, descr_prefix+"Within NQS window: fraction of mismatching bases in consensus indel-supporting reads/in reference-supporting reads"));
|
||||
|
||||
lines.add(new VCFInfoHeaderLine(prefix+NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, descr_prefix+"Within NQS window: average quality of bases from consensus indel-supporting reads/from reference-supporting reads"));
|
||||
|
||||
lines.add(new VCFInfoHeaderLine(prefix+STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, descr_prefix+"strandness: counts of forward-/reverse-aligned indel-supporting reads / forward-/reverse-aligned reference supporting reads"));
|
||||
|
||||
return lines;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordStrandCounts(String prefix, int cnt_cons_fwd, int cnt_cons_rev, int cnt_ref_fwd, int cnt_ref_rev, Map<String,Object> attrs) {
|
||||
attrs.put(prefix+STRAND_COUNT_KEY, new Integer[] {cnt_cons_fwd, cnt_cons_rev, cnt_ref_fwd, cnt_ref_rev} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordDepth(String prefix, int cnt_cons, int cnt_indel, int cnt_total, Map<String,Object> attrs) {
|
||||
attrs.put(prefix+DEPTH_INDEL_KEY, new Integer[] {cnt_cons, cnt_indel} );
|
||||
attrs.put(prefix+DEPTH_TOTAL_KEY, cnt_total);
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordAvMapQ(String prefix, double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(prefix+MAPQ_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordAvMM(String prefix, double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(prefix+MM_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordNQSMMRate(String prefix, double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(prefix+NQS_MMRATE_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordNQSAvQ(String prefix, double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(prefix+NQS_AVQ_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
return attrs;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue