IndelSummary now emits all of the underlying counts for ratios, percentages, etc it computes
This commit is contained in:
Mark DePristo
parent
542a8e3306
commit
23ccf772d4
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@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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@ -41,51 +40,81 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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public class IndelSummary extends VariantEvaluator implements StandardEval {
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final protected static Logger logger = Logger.getLogger(IndelSummary.class);
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//
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// counts of snps and indels
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//
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@DataPoint(description = "Number of SNPs", format = "%d")
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public int n_SNPs = 0;
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@DataPoint(description = "Number of singleton SNPs", format = "%d")
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public int n_singleton_SNPs = 0;
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@DataPoint(description = "Number of Indels", format = "%d")
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@DataPoint(description = "Number of indels", format = "%d")
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public int n_indels = 0;
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// Number of Indels Sites (counts one for any number of alleles at site)
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public int nIndelSites = 0;
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@DataPoint(description = "Number of singleton Indels", format = "%d")
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@DataPoint(description = "Number of singleton indels", format = "%d")
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public int n_singleton_indels = 0;
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//
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// gold standard
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//
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@DataPoint(description = "Number of Indels overlapping gold standard sites", format = "%d")
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public int n_indels_matching_gold_standard = 0;
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@DataPoint(description = "Percent of indels overlapping gold standard sites")
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public String gold_standard_matching_rate;
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//
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// multi-allelics
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//
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// Number of Indels Sites (counts one for any number of alleles at site)
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public int nIndelSites = 0;
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@DataPoint(description = "Number of sites with where the number of alleles is greater than 2")
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public int n_multiallelic_indel_sites = 0;
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@DataPoint(description = "Percent of indel sites that are multi-allelic")
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public String percent_of_sites_with_more_than_2_alleles;
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//
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// snp : indel ratios
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//
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@DataPoint(description = "SNP to indel ratio")
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public String SNP_to_indel_ratio;
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@DataPoint(description = "Singleton SNP to indel ratio")
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public String SNP_to_indel_ratio_for_singletons;
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//
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// novelty
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//
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@DataPoint(description = "Number of novel indels", format = "%d")
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public int n_novel_indels = 0;
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@DataPoint(description = "Indel novelty rate")
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public String indel_novelty_rate;
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@DataPoint(description = "Frameshift percent")
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public String frameshift_rate_for_coding_indels;
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//
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// insertions to deletions
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//
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@DataPoint(description = "Number of insertion indels")
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public int n_insertions = 0;
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@DataPoint(description = "Number of deletion indels")
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public int n_deletions = 0;
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@DataPoint(description = "Insertion to deletion ratio")
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public String insertion_to_deletion_ratio;
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@DataPoint(description = "Number of large (>10 bp) deletions")
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public int n_large_deletions = 0;
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@DataPoint(description = "Number of large (>10 bp) insertions")
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public int n_large_insertions = 0;
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@DataPoint(description = "Ratio of large (>10 bp) insertions to deletions")
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public String insertion_to_deletion_ratio_for_large_indels;
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//
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// Frameshifts
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//
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@ -95,6 +124,9 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
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@DataPoint(description = "Number of indels in protein-coding regions not labeled as frameshift")
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public int n_coding_indels_in_frame = 0;
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@DataPoint(description = "Frameshift percent")
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public String frameshift_rate_for_coding_indels;
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//
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// Het : hom ratios
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//
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@ -106,8 +138,6 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
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int nSNPHets = 0, nSNPHoms = 0, nIndelHets = 0, nIndelHoms = 0;
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int nKnownIndels = 0, nInsertions = 0;
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int[] insertionCountByLength = new int[]{0, 0, 0, 0}; // note that the first element isn't used
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int[] deletionCountByLength = new int[]{0, 0, 0, 0}; // note that the first element isn't used
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@ -129,15 +159,6 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
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public final static int LARGE_INDEL_SIZE_THRESHOLD = 10;
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@DataPoint(description = "Number of large (>10 bp) deletions")
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public int n_large_deletions = 0;
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@DataPoint(description = "Number of large (>10 bp) insertions")
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public int n_large_insertions = 0;
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@DataPoint(description = "Ratio of large (>10 bp) insertions to deletions")
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public String insertion_to_deletion_ratio_for_large_indels;
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@Override public int getComparisonOrder() { return 2; }
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public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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@ -171,13 +192,14 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
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for ( Allele alt : eval.getAlternateAlleles() ) {
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n_indels++; // +1 for each alt allele
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if ( variantWasSingleton(eval) ) n_singleton_indels++;
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if ( comp != null ) nKnownIndels++; // TODO -- make this test allele specific?
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if ( comp == null ) n_novel_indels++; // TODO -- make this test allele specific?
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if ( gold != null ) n_indels_matching_gold_standard++;
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// ins : del ratios
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final int alleleSize = alt.length() - eval.getReference().length();
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if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
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if ( alleleSize > 0 ) nInsertions++;
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if ( alleleSize > 0 ) n_insertions++;
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if ( alleleSize < 0 ) n_deletions++;
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// requires snpEFF annotations
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if ( eval.getAttributeAsString("SNPEFF_GENE_BIOTYPE", "missing").equals("protein_coding") ) {
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@ -220,7 +242,7 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
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SNP_to_indel_ratio_for_singletons = Utils.formattedRatio(n_singleton_SNPs, n_singleton_indels);
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gold_standard_matching_rate = Utils.formattedPercent(n_indels_matching_gold_standard, n_indels);
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indel_novelty_rate = Utils.formattedNoveltyRate(nKnownIndels, n_indels);
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indel_novelty_rate = Utils.formattedNoveltyRate(n_indels - n_novel_indels, n_indels);
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frameshift_rate_for_coding_indels = Utils.formattedPercent(n_coding_indels_frameshifting, n_coding_indels_in_frame + n_coding_indels_frameshifting);
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ratio_of_1_and_2_to_3_bp_deletions = Utils.formattedRatio(deletionCountByLength[1] + deletionCountByLength[2], deletionCountByLength[3]);
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@ -229,7 +251,7 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
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SNP_het_to_hom_ratio = Utils.formattedRatio(nSNPHets, nSNPHoms);
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indel_het_to_hom_ratio = Utils.formattedRatio(nIndelHets, nIndelHoms);
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insertion_to_deletion_ratio = Utils.formattedRatio(nInsertions, n_indels - nInsertions);
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insertion_to_deletion_ratio = Utils.formattedRatio(n_insertions, n_deletions);
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insertion_to_deletion_ratio_for_large_indels = Utils.formattedRatio(n_large_insertions, n_large_deletions);
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}
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