fixing missing sample genotype bug, missing AD/DP bug, and putting annotations in more natural order (Ref/Alt)
This commit is contained in:
Andrey Sivachenko
parent
ac5e58a265
commit
b4fbf6280a
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@ -438,8 +438,6 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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location = getToolkit().getGenomeLocParser().createGenomeLoc(getToolkit().getSAMFileHeader().getSequence(0).getSequenceName(),1);
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normalSamples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeaders().get(0));
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try {
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// we already checked that bedOutput and output_file are not set simultaneously
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if ( bedOutput != null ) bedWriter = new FileWriter(bedOutput);
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@ -1152,8 +1150,9 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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GenotypesContext genotypes = GenotypesContext.create();
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for ( String sample : normalSamples ) {
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final GenotypeBuilder gb = new GenotypeBuilder(sample);
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gb.attributes(call.makeStatsAttributes(null));
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GenotypeBuilder gb = new GenotypeBuilder(sample);
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gb=call.addStatsAttributes(gb);
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gb.alleles(! discard_event
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? alleles // we made a call - put actual het genotype here:
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: homref_alleles); // no call: genotype is ref/ref (but alleles still contain the alt if we observed anything at all)
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@ -1200,8 +1199,11 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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if ( start == 0 )
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return;
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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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GenotypeBuilder nGB = new GenotypeBuilder();
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GenotypeBuilder tGB = new GenotypeBuilder();
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nCall.addStatsAttributes(nGB);
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tCall.addStatsAttributes(tGB);
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Map<String,Object> attrs = new HashMap();
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@ -1242,11 +1244,11 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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GenotypesContext genotypes = GenotypesContext.create();
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for ( String sample : normalSamples ) {
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genotypes.add(GenotypeBuilder.create(sample, homRefN ? homRefAlleles : alleles, attrsNormal));
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genotypes.add(nGB.name(sample).alleles(homRefN ? homRefAlleles : alleles).make());
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}
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for ( String sample : tumorSamples ) {
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genotypes.add(GenotypeBuilder.create(sample, homRefT ? homRefAlleles : alleles, attrsTumor));
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genotypes.add(tGB.name(sample).alleles(homRefT ? homRefAlleles : alleles).make());
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}
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Set<String> filters = null;
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@ -1254,14 +1256,6 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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filters = new HashSet<String>();
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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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}
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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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}
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VariantContext vc = new VariantContextBuilder("IGv2_Indel_call", refName, start, stop, alleles)
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.genotypes(genotypes).filters(filters).attributes(attrs).make();
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@ -1844,6 +1838,38 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
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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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* Adds alignment statistics directly into the genotype builder object.
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*
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* @param gb
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* @return
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*/
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public GenotypeBuilder addStatsAttributes(GenotypeBuilder gb) {
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if ( gb == null ) gb = new GenotypeBuilder();
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gb = VCFIndelAttributes.recordDepth(getConsensusVariantCount(),getAllVariantCount(),getCoverage(),gb);
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gb = VCFIndelAttributes.recordAvMM(getAvConsensusMismatches(),getAvRefMismatches(),gb);
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gb = VCFIndelAttributes.recordAvMapQ(getAvConsensusMapq(),getAvRefMapq(),gb);
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gb = VCFIndelAttributes.recordNQSMMRate(getNQSConsensusMMRate(),getNQSRefMMRate(),gb);
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gb = VCFIndelAttributes.recordNQSAvQ(getNQSConsensusAvQual(),getNQSRefAvQual(),gb);
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gb = VCFIndelAttributes.recordOffsetFromStart(from_start_median,from_start_mad,gb);
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gb = VCFIndelAttributes.recordOffsetFromEnd(from_end_median,from_end_mad,gb);
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PrimitivePair.Int strand_cons = getConsensusStrandCounts();
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PrimitivePair.Int strand_ref = getRefStrandCounts();
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gb = VCFIndelAttributes.recordStrandCounts(strand_cons.first,strand_cons.second,strand_ref.first,strand_ref.second,gb);
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return gb;
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}
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}
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interface IndelListener {
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@ -2181,7 +2207,7 @@ class VCFIndelAttributes {
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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"));
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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"));
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lines.add(new VCFFormatHeaderLine(STRAND_COUNT_KEY, 4, VCFHeaderLineType.Integer, "Strandness: counts of forward-/reverse-aligned reference and indel-supporting reads (FwdRef,RevRef,FwdIndel,RevIndel)"));
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lines.add(new VCFFormatHeaderLine(RSTART_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the starts of the reads"));
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lines.add(new VCFFormatHeaderLine(REND_OFFSET_KEY, 2, VCFHeaderLineType.Integer, "Median/mad of indel offsets from the ends of the reads"));
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@ -2194,39 +2220,72 @@ class VCFIndelAttributes {
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return attrs;
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}
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public static GenotypeBuilder recordStrandCounts(int cnt_cons_fwd, int cnt_cons_rev, int cnt_ref_fwd, int cnt_ref_rev,
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GenotypeBuilder gb) {
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return gb.attribute(STRAND_COUNT_KEY, new Integer[] {cnt_ref_fwd, cnt_ref_rev,cnt_cons_fwd, cnt_cons_rev } );
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}
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public static Map<String,Object> recordDepth(int cnt_cons, int cnt_indel, int cnt_total, Map<String,Object> attrs) {
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attrs.put(ALLELIC_DEPTH_KEY, new Integer[] {cnt_cons, cnt_indel} );
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attrs.put(ALLELIC_DEPTH_KEY, new Integer[] {cnt_total-cnt_indel, cnt_cons} );
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attrs.put(DEPTH_TOTAL_KEY, cnt_total);
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return attrs;
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}
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public static GenotypeBuilder recordDepth(int cnt_cons, int cnt_indel, int cnt_total, GenotypeBuilder gb) {
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return gb.AD(new int[] {cnt_total-cnt_indel,cnt_cons} ).DP(cnt_total);
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}
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public static Map<String,Object> recordAvMapQ(double cons, double ref, Map<String,Object> attrs) {
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attrs.put(MAPQ_KEY, new Float[] {(float)cons, (float)ref} );
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attrs.put(MAPQ_KEY, new Float[] {(float)ref, (float)cons} );
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return attrs;
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}
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public static GenotypeBuilder recordAvMapQ(double cons, double ref, GenotypeBuilder gb) {
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return gb.attribute(MAPQ_KEY,new float[] {(float)ref, (float)cons} );
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}
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public static Map<String,Object> recordAvMM(double cons, double ref, Map<String,Object> attrs) {
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attrs.put(MM_KEY, new Float[] {(float)cons, (float)ref} );
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attrs.put(MM_KEY, new Float[] {(float)ref, (float)cons} );
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return attrs;
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}
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public static GenotypeBuilder recordAvMM(double cons, double ref, GenotypeBuilder gb) {
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return gb.attribute(MM_KEY, new float[] {(float)ref, (float)cons} );
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}
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public static Map<String,Object> recordNQSMMRate(double cons, double ref, Map<String,Object> attrs) {
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attrs.put(NQS_MMRATE_KEY, new Float[] {(float)cons, (float)ref} );
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attrs.put(NQS_MMRATE_KEY, new Float[] {(float)ref, (float)cons} );
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return attrs;
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}
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public static GenotypeBuilder recordNQSMMRate(double cons, double ref, GenotypeBuilder gb) {
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return gb.attribute(NQS_MMRATE_KEY, new float[] {(float)ref, (float)cons} );
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}
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public static Map<String,Object> recordNQSAvQ(double cons, double ref, Map<String,Object> attrs) {
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attrs.put(NQS_AVQ_KEY, new Float[] {(float)cons, (float)ref} );
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attrs.put(NQS_AVQ_KEY, new float[] {(float)ref, (float)cons} );
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return attrs;
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}
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public static GenotypeBuilder recordNQSAvQ(double cons, double ref, GenotypeBuilder gb) {
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return gb.attribute(NQS_AVQ_KEY, new float[] {(float)ref, (float)cons} );
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}
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public static Map<String,Object> recordOffsetFromStart(int median, int mad, Map<String,Object> attrs) {
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attrs.put(RSTART_OFFSET_KEY, new Integer[] {median, mad} );
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return attrs;
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}
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public static GenotypeBuilder recordOffsetFromStart(int median, int mad, GenotypeBuilder gb) {
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return gb.attribute(RSTART_OFFSET_KEY, new int[] {median, mad} );
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}
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public static Map<String,Object> recordOffsetFromEnd(int median, int mad, Map<String,Object> attrs) {
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attrs.put(REND_OFFSET_KEY, new Integer[] {median, mad} );
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return attrs;
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}
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public static GenotypeBuilder recordOffsetFromEnd(int median, int mad, GenotypeBuilder gb) {
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return gb.attribute(REND_OFFSET_KEY, new int[] {median, mad} );
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}
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}
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