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nothing fancy, just a wrapper (aka struct) to pass around a bunch of counts 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@327 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-04-08 01:58:57 +00:00
parent 453d13415d
commit 62d75ced3c
1 changed files with 46 additions and 0 deletions
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java/src/org/broadinstitute/sting/playground/utils/TrioConcordanceRecord.java 100644
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package org.broadinstitute.sting.playground.utils;
/**
* This class is a trivial wrapper for keeping together and passing around counts of different possible outcomes of
* comparisons in a trio. Mendelian walker uses this class to classify/accumulate events such as consistent snp, inconsistent snp
* (e.g. only in a kid, but not in parents), loci with no calls etc.
* @author asivache
*
*/
public class TrioConcordanceRecord {
public long assessed_loci = 0; // number of loci with all 3 genotypes available at or above the specified cutoff
public long consistent_ref = 0; // number of assessed loci, where all 3 people have homogeneous reference allele
public int consistent_snp = 0; // number of assessed loci where a SNP is observed in at least one individual and genotyping calls are consistent between the trio members
public int inconsistent_snp = 0; // number of assessed loci where a SNP is observed in at least one individual and genotyping calls are inconsistent
public int inconsistent_snp_in_parent = 0; // number of inconsistent snps (see above), where parent(s) have a snp but the kid does not while she should
public int inconsistent_snp_in_kid = 0; // number of inconsistent snps (see above), where kid has a snp but the parents do not while they should
public int consistent_indels = 0; // *_indels are same as *_snps, see above
public int inconsistent_indels = 0 ;
public int inconsistent_indels_in_parent = 0 ;
public int inconsistent_indels_in_kid = 0 ;
public int non_biallelic = 0; // number of variant calls that are not biallelic
public TrioConcordanceRecord add(TrioConcordanceRecord other) {
this.assessed_loci += other.assessed_loci;
this.consistent_ref += other.consistent_ref;
this.consistent_snp += other.consistent_snp;
this.inconsistent_snp += other.inconsistent_snp;
this.inconsistent_snp_in_parent += other.inconsistent_snp_in_parent;
this.inconsistent_snp_in_kid += other.inconsistent_snp_in_kid;
this.consistent_indels += other.consistent_indels;
this.inconsistent_indels += other.inconsistent_indels;
this.inconsistent_indels_in_parent += other.inconsistent_indels_in_parent;
this.inconsistent_indels_in_kid += other.inconsistent_indels_in_kid;
this.non_biallelic += other.non_biallelic;
return this;
}
public int totalSNP() { return consistent_snp + inconsistent_snp + non_biallelic; }
public String toString() {
return String.format("assessed: %d; reference: %d (%3.2f); total snp: %d; consistent snp: %d (%3.2f); multiallelic: %d (%3.2f); " ,
assessed_loci, consistent_ref, ((double)consistent_ref*100.00)/assessed_loci,totalSNP(), consistent_snp, ((double)consistent_snp*100.0)/totalSNP(),
non_biallelic, ((double)non_biallelic*100.0)/totalSNP());
}
}