Computes additional stats we want to use later for filtering: median and mad for indel position with respect to starts and ends of all the reads that support it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5803 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache
parent
5c889580c4
commit
befbcd274b
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@ -199,6 +199,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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private long lastGenotypedPosition = -1; // last position on the currentGenotypeInterval, for which a call was already printed;
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// can be 1 base before lastGenotyped start
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// "/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"
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private Set<VCFHeaderLine> getVCFHeaderInfo() {
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@ -211,12 +212,10 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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// FORMAT and INFO fields
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// headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());
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headerInfo.addAll(VCFIndelAttributes.getAttributeHeaderLines());
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if ( call_somatic ) {
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headerInfo.addAll(VCFIndelAttributes.getAttributeHeaderLines("N_","In NORMAL: "));
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headerInfo.addAll(VCFIndelAttributes.getAttributeHeaderLines("T_","In TUMOR: "));
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headerInfo.add(new VCFInfoHeaderLine(VCFConstants.SOMATIC_KEY, 0, VCFHeaderLineType.Flag, "Somatic event"));
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} else {
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headerInfo.addAll(VCFIndelAttributes.getAttributeHeaderLines("",""));
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}
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// all of the arguments from the argument collection
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@ -602,7 +601,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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continue; // re-enter the loop to check against the interval we just loaded
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}
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// we reach tjis point only if p is inside current genotyping interval; set the flag and bail out:
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// we reach this point only if p is inside current genotyping interval; set the flag and bail out:
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genotype = true;
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break;
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}
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@ -1005,19 +1004,22 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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Map<String,Genotype> genotypes = new HashMap<String,Genotype>();
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for ( String sample : normalSamples ) {
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Map<String,?> attrs = call.makeStatsAttributes(null);
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if ( call.isCall() ) // we made a call - put actual het genotype here:
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genotypes.put(sample,new Genotype(sample, alleles));
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genotypes.put(sample,new Genotype(sample,alleles,Genotype.NO_NEG_LOG_10PERROR,null,attrs,false));
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else // no call: genotype is ref/ref (but alleles still contain the alt if we observed anything at all)
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genotypes.put(sample,new Genotype(sample, homref_alleles));
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genotypes.put(sample,new Genotype(sample, homref_alleles,Genotype.NO_NEG_LOG_10PERROR,null,attrs,false));
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}
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Set<String> filters = null;
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if ( call.getVariant() != null && ! call.isCall() ) {
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filters = new HashSet<String>();
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filters.add("NOCALL");
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filters.add("NoCall");
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}
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VariantContext vc = new VariantContext("IGv2_Indel_call", refName, start, stop, alleles, genotypes,
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-1.0 /* log error */, filters, call.makeStatsAttributes("",null));
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-1.0 /* log error */, filters, null);
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vcf.add(vc,refBases[(int)start-1]);
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}
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@ -1051,8 +1053,10 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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if ( start == 0 )
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return;
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Map<String,Object> attrs = nCall.makeStatsAttributes("N_",null);
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attrs = tCall.makeStatsAttributes("T_",attrs);
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Map<String,Object> attrsNormal = nCall.makeStatsAttributes(null);
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Map<String,Object> attrsTumor = tCall.makeStatsAttributes(null);
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Map<String,Object> attrs = new HashMap();
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boolean isSomatic = false;
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if ( nCall.getCoverage() >= minNormalCoverage && nCall.getVariant() == null && tCall.getVariant() != null ) {
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@ -1090,25 +1094,25 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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Map<String,Genotype> genotypes = new HashMap<String,Genotype>();
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for ( String sample : normalSamples ) {
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genotypes.put(sample,new Genotype(sample, homRefN ? homRefAlleles : alleles,0));
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genotypes.put(sample,new Genotype(sample, homRefN ? homRefAlleles : alleles,Genotype.NO_NEG_LOG_10PERROR,null,attrsNormal,false));
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}
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for ( String sample : tumorSamples ) {
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genotypes.put(sample,new Genotype(sample, homRefT ? homRefAlleles : alleles,0) );
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genotypes.put(sample,new Genotype(sample, homRefT ? homRefAlleles : alleles,Genotype.NO_NEG_LOG_10PERROR,null,attrsTumor,false) );
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}
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Set<String> filters = null;
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if ( tCall.getVariant() != null && ! tCall.isCall() ) {
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filters = new HashSet<String>();
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filters.add("NOCALL");
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filters.add("NoCall");
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}
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if ( nCall.getCoverage() < minNormalCoverage ) {
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if ( filters == null ) filters = new HashSet<String>();
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filters.add("NCOV");
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filters.add("NCov");
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}
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if ( tCall.getCoverage() < minCoverage ) {
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if ( filters == null ) filters = new HashSet<String>();
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filters.add("TCOV");
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filters.add("TCov");
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}
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VariantContext vc = new VariantContext("IGv2_Indel_call", refName, start, stop, alleles, genotypes,
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@ -1160,6 +1164,8 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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public static enum Type { I, D};
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private String bases;
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private Type type;
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private ArrayList<Integer> fromStartOffsets = null;
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private ArrayList<Integer> fromEndOffsets = null;
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private Set<ExpandedSAMRecord> reads = new HashSet<ExpandedSAMRecord>(); // keep track of reads that have this indel
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private Set<String> samples = new HashSet<String>(); // which samples had the indel described by this object
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@ -1168,6 +1174,8 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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this.type = type;
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this.bases = bases.toUpperCase();
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addObservation(read);
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fromStartOffsets = new ArrayList<Integer>();
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fromEndOffsets = new ArrayList<Integer>();
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}
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/** Adds another observation for the current indel. It is assumed that the read being registered
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@ -1207,6 +1215,14 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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samples.add(sample);
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}
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public void addReadPositions(int fromStart, int fromEnd) {
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fromStartOffsets.add(fromStart);
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fromEndOffsets.add(fromEnd);
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}
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public List<Integer> getOffsetsFromStart() { return fromStartOffsets ; }
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public List<Integer> getOffsetsFromEnd() { return fromEndOffsets; }
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public String getSamples() {
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StringBuffer sb = new StringBuffer();
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Iterator<String> i = samples.iterator();
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@ -1283,6 +1299,11 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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private PrimitivePair.Int all_indel_read_orientation_cnt = new PrimitivePair.Int();
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private PrimitivePair.Int all_read_orientation_cnt = new PrimitivePair.Int();
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private int from_start_median = 0;
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private int from_start_mad = 0;
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private int from_end_median = 0;
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private int from_end_mad = 0;
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/** Makes an empty call (no-call) with all stats set to 0
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*
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* @param position
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@ -1388,6 +1409,43 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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// }
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}
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// compute median/mad for offsets from the read starts/ends
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if ( consensus_indel != null ) {
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from_start_median = median(consensus_indel.getOffsetsFromStart()) ;
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from_start_mad = mad(consensus_indel.getOffsetsFromStart(),from_start_median);
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from_end_median = median(consensus_indel.getOffsetsFromEnd()) ;
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from_end_mad = mad(consensus_indel.getOffsetsFromEnd(),from_end_median);
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}
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}
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/** As a side effect will sort l!
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*
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* @param l
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* @return
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*/
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private int median(List<Integer> l) {
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Collections.sort(l);
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int k = l.size()/2;
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return ( l.size() % 2 == 0 ?
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(l.get(k-1).intValue()+l.get(k).intValue())/2 :
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l.get(k).intValue());
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}
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private int median(int[] l) {
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Arrays.sort(l);
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int k = l.length/2;
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return ( l.length % 2 == 0 ?
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(l[k-1]+l[k])/2 :
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l[k]);
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}
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private int mad(List<Integer> l, int med) {
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int [] diff = new int[l.size()];
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for ( int i = 0; i < l.size(); i++ ) {
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diff[i] = Math.abs(l.get(i).intValue() - med);
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}
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return median(diff);
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}
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public long getPosition() { return pos; }
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@ -1589,40 +1647,51 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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PrimitivePair.Int strand_ref = getRefStrandCounts();
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message.append('\t');
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message.append(prefix+"STRAND_COUNTS[C/C/R/R]:"+strand_cons.first+"/"+strand_cons.second+"/"+strand_ref.first+"/"+strand_ref.second);
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message.append('\t');
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message.append(prefix+"OFFSET_RSTART:"+from_start_median+"/"+from_start_mad);
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message.append('\t');
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message.append(prefix+"OFFSET_REND:"+from_end_median+"/"+from_end_mad);
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return message.toString();
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}
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/**
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* Places alignment statistics into attribute map and returns the map. If attr parameter is null,
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* a new map is allocated, filled and returned. If attr is not null, new attributes are added to that
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* preexisting map, and the same instance of the (updated) map is returned.
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* @param prefix
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*
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* @param attr
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* @return
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*/
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public Map<String,Object> makeStatsAttributes(String prefix, Map<String,Object> attr) {
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public Map<String,Object> makeStatsAttributes(Map<String,Object> attr) {
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if ( attr == null ) attr = new HashMap<String, Object>();
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VCFIndelAttributes.recordDepth(prefix,getConsensusVariantCount(),getAllVariantCount(),getCoverage(),attr);
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VCFIndelAttributes.recordDepth(getConsensusVariantCount(),getAllVariantCount(),getCoverage(),attr);
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VCFIndelAttributes.recordAvMM(prefix,getAvConsensusMismatches(),getAvRefMismatches(),attr);
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VCFIndelAttributes.recordAvMM(getAvConsensusMismatches(),getAvRefMismatches(),attr);
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VCFIndelAttributes.recordAvMapQ(prefix,getAvConsensusMapq(),getAvRefMapq(),attr);
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VCFIndelAttributes.recordAvMapQ(getAvConsensusMapq(),getAvRefMapq(),attr);
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VCFIndelAttributes.recordNQSMMRate(prefix,getNQSConsensusMMRate(),getNQSRefMMRate(),attr);
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VCFIndelAttributes.recordNQSMMRate(getNQSConsensusMMRate(),getNQSRefMMRate(),attr);
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VCFIndelAttributes.recordNQSAvQ(prefix,getNQSConsensusAvQual(),getNQSRefAvQual(),attr);
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VCFIndelAttributes.recordNQSAvQ(getNQSConsensusAvQual(),getNQSRefAvQual(),attr);
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VCFIndelAttributes.recordOffsetFromStart(from_start_median,from_start_mad,attr);
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VCFIndelAttributes.recordOffsetFromEnd(from_end_median,from_end_mad,attr);
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PrimitivePair.Int strand_cons = getConsensusStrandCounts();
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PrimitivePair.Int strand_ref = getRefStrandCounts();
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VCFIndelAttributes.recordStrandCounts(prefix,strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,attr);
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VCFIndelAttributes.recordStrandCounts(strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,attr);
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return attr;
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}
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}
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interface IndelListener {
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public void addObservation(int pos, IndelVariant.Type t, String bases, ExpandedSAMRecord r);
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public void addObservation(int pos, IndelVariant.Type t, String bases, int fromStart, int fromEnd, ExpandedSAMRecord r);
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}
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class WindowContext implements IndelListener {
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@ -1751,7 +1820,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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reads.add(er);
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}
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public void addObservation(int pos, IndelVariant.Type type, String bases, ExpandedSAMRecord rec) {
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public void addObservation(int pos, IndelVariant.Type type, String bases, int fromStart, int fromEnd, ExpandedSAMRecord rec) {
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List<IndelVariant> indelsAtSite;
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try {
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indelsAtSite = indels.get(pos);
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@ -1770,19 +1839,20 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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indels.set(pos, indelsAtSite);
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}
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boolean found = false;
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IndelVariant indel = null;
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for ( IndelVariant v : indelsAtSite ) {
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if ( ! v.equals(type, bases) ) continue;
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v.addObservation(rec);
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found = true;
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indel = v;
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indel.addObservation(rec);
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break;
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}
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if ( ! found ) {
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IndelVariant v = new IndelVariant(rec, type, bases);
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indelsAtSite.add(v);
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if ( indel == null ) { // not found:
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indel = new IndelVariant(rec, type, bases);
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indelsAtSite.add(indel);
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}
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indel.addReadPositions(fromStart,fromEnd);
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}
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public List<IndelVariant> indelsAt( final long refPos ) {
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@ -1818,9 +1888,30 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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Cigar c = read.getCigar();
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final int nCigarElems = c.numCigarElements();
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int readLength = 0; // length of the aligned part of the read NOT counting clipped bases
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for ( CigarElement cel : c.getCigarElements() ) {
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switch(cel.getOperator()) {
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case H:
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case S:
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case D:
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case N:
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case P:
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break; // do not count gaps or clipped bases
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case I:
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case M:
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readLength += cel.getLength();
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break; // advance along the gapless block in the alignment
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default :
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throw new IllegalArgumentException("Unexpected operator in cigar string: "+cel.getOperator());
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}
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}
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int fromStart = 0;
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int posOnRead = 0;
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int posOnRef = 0; // the chunk of reference ref[] that we have access to is aligned with the read:
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// its start on the actual full reference contig is r.getAlignmentStart()
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// its start on the actual full reference contig is r.getAlignmentStart()
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for ( int i = 0 ; i < nCigarElems ; i++ ) {
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final CigarElement ce = c.getCigarElement(i);
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@ -1854,6 +1945,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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}
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expanded_quals[posOnRef] = read.getBaseQualities()[posOnRead];
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}
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fromStart += ce.getLength();
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break; // advance along the gapless block in the alignment
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default :
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throw new IllegalArgumentException("Unexpected operator in cigar string: "+ce.getOperator());
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@ -1867,7 +1959,13 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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// note that here we will be assigning indels to the first deleted base or to the first
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// base after insertion, not to the last base before the event!
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l.addObservation((int)(offset+eventPosition), type, indel_bases, this);
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int fromEnd = readLength - fromStart;
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if ( type == IndelVariant.Type.I ) fromEnd -= ce.getLength();
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l.addObservation((int)(offset+eventPosition), type, indel_bases, fromStart, fromEnd, this);
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if ( type == IndelVariant.Type.I ) fromStart += ce.getLength();
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}
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}
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@ -1894,10 +1992,10 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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class VCFIndelAttributes {
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public static String DEPTH_INDEL_KEY = VCFConstants.ALLELE_COUNT_KEY;
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public static String ALLELIC_DEPTH_KEY = "AD";
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public static String DEPTH_TOTAL_KEY = VCFConstants.DEPTH_KEY;
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public static String MAPQ_KEY = "MQ";
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public static String MAPQ_KEY = "MQS";
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public static String MM_KEY = "MM";
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@ -1906,54 +2004,69 @@ class VCFIndelAttributes {
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public static String NQS_AVQ_KEY = "NQSBQ";
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public static String STRAND_COUNT_KEY = "SC";
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public static String RSTART_OFFSET_KEY = "RStart";
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public static String REND_OFFSET_KEY = "REnd";
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public static Set<VCFInfoHeaderLine> getAttributeHeaderLines(String prefix, String descr_prefix) {
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Set<VCFInfoHeaderLine> lines = new HashSet<VCFInfoHeaderLine>();
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public static Set<? extends VCFHeaderLine> getAttributeHeaderLines() {
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Set<VCFHeaderLine> lines = new HashSet<VCFHeaderLine>();
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lines.add(new VCFInfoHeaderLine(prefix+DEPTH_INDEL_KEY, 2, VCFHeaderLineType.Integer, descr_prefix+"# of reads supporting consensus indel/any indel at the site"));
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lines.add(new VCFInfoHeaderLine(prefix+DEPTH_TOTAL_KEY, 1, VCFHeaderLineType.Integer, descr_prefix+"total coverage at the site"));
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lines.add(new VCFFormatHeaderLine(ALLELIC_DEPTH_KEY, 2, VCFHeaderLineType.Integer, "# of reads supporting consensus indel/reference at the site"));
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lines.add(new VCFFormatHeaderLine(DEPTH_TOTAL_KEY, 1, VCFHeaderLineType.Integer, "Total coverage at the site"));
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lines.add(new VCFInfoHeaderLine(prefix+MAPQ_KEY, 2, VCFHeaderLineType.Float, descr_prefix+"average mapping quality of consensus indel-supporting reads/reference-supporting reads"));
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lines.add(new VCFFormatHeaderLine(MAPQ_KEY, 2, VCFHeaderLineType.Float, "Average mapping qualities of consensus indel-supporting reads/reference-supporting reads"));
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lines.add(new VCFInfoHeaderLine(prefix+MM_KEY, 2, VCFHeaderLineType.Float, descr_prefix+"average # of mismatches per consensus indel-supporting read/per reference-supporting read"));
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lines.add(new VCFFormatHeaderLine(MM_KEY, 2, VCFHeaderLineType.Float, "Average # of mismatches per consensus indel-supporting read/per reference-supporting read"));
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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"));
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lines.add(new VCFFormatHeaderLine(NQS_MMRATE_KEY, 2, VCFHeaderLineType.Float, "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 VCFFormatHeaderLine(NQS_AVQ_KEY, 2, VCFHeaderLineType.Float, "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"));
|
||||
lines.add(new VCFFormatHeaderLine(STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, "Strandness: counts of forward-/reverse-aligned indel-supporting reads / forward-/reverse-aligned reference supporting reads"));
|
||||
|
||||
lines.add(new VCFFormatHeaderLine(RSTART_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the starts of the reads"));
|
||||
lines.add(new VCFFormatHeaderLine(REND_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the ends of the 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} );
|
||||
public static Map<String,Object> recordStrandCounts(int cnt_cons_fwd, int cnt_cons_rev, int cnt_ref_fwd, int cnt_ref_rev, Map<String,Object> attrs) {
|
||||
attrs.put(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);
|
||||
public static Map<String,Object> recordDepth(int cnt_cons, int cnt_indel, int cnt_total, Map<String,Object> attrs) {
|
||||
attrs.put(ALLELIC_DEPTH_KEY, new Integer[] {cnt_cons, cnt_indel} );
|
||||
attrs.put(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} );
|
||||
public static Map<String,Object> recordAvMapQ(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(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} );
|
||||
public static Map<String,Object> recordAvMM(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(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} );
|
||||
public static Map<String,Object> recordNQSMMRate(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(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} );
|
||||
public static Map<String,Object> recordNQSAvQ(double cons, double ref, Map<String,Object> attrs) {
|
||||
attrs.put(NQS_AVQ_KEY, new Float[] {(float)cons, (float)ref} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordOffsetFromStart(int median, int mad, Map<String,Object> attrs) {
|
||||
attrs.put(RSTART_OFFSET_KEY, new Integer[] {median, mad} );
|
||||
return attrs;
|
||||
}
|
||||
|
||||
public static Map<String,Object> recordOffsetFromEnd(int median, int mad, Map<String,Object> attrs) {
|
||||
attrs.put(REND_OFFSET_KEY, new Integer[] {median, mad} );
|
||||
return attrs;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue