updated
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@800 348d0f76-0448-11de-a6fe-93d51630548a
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asivache
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@ -10,89 +10,123 @@ import org.broadinstitute.sting.utils.Utils;
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*
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*/
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public class TrioConcordanceRecord {
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public long assessed_loci = 0; // number of loci with all 3 genotypes available at or above the specified cutoff
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public long consistent_ref = 0; // number of assessed loci, where all 3 people have homogeneous reference allele
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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
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public int inconsistent_snp = 0; // number of assessed loci where a SNP is observed in at least one individual and genotyping calls are inconsistent
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public int missing_snp_in_parents = 0; // number of inconsistent snps (see above), where parent(s) have a snp but the kid does not while she should
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public int missing_snp_in_kid = 0; // number of inconsistent snps (see above), where kid has a snp but the parents do not while they should
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public int consistent_indels = 0; // *_indels are same as *_snps, see above
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public int consistent_indels_in_mother = 0; // *_indels are same as *_snps, see above
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public int consistent_indels_in_father = 0; // *_indels are same as *_snps, see above
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public int inconsistent_indels = 0 ;
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public int missing_indels_in_parents = 0 ;
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public int missing_indels_in_kid = 0 ;
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public int non_biallelic_snp = 0; // number of variant calls that are not biallelic
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public int non_biallelic_indel = 0; // number of variant calls that are not biallelic
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public long mom_assessed = 0; // number of assessed loci for mother (i.e. passing confidence threshold filter)
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public long dad_assessed = 0;
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public long kid_assessed = 0;
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public long mom_ref = 0; // number of reference calls (out of total assessed)
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public long dad_ref = 0;
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public long kid_ref = 0;
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public long mom_snp = 0; // number of snp calls (out of total assessed)
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public long dad_snp = 0;
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public long kid_snp = 0;
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public long mom_indel = 0; // number of snp calls (out of total assessed)
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public long dad_indel = 0;
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public long kid_indel = 0;
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public long unclassified_events = 0;
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public GenotypingCallStats mom;
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public GenotypingCallStats dad;
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public GenotypingCallStats kid;
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public GenotypingCallStats trio;
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// public long mom_assessed_ref; // number of ref calls in mother on positions assessed *in all 3 individuals*
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// public long dad_assessed_ref; // ditto
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// public long kid_assessed_ref;
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// public int mom_assessed_variant; // number of variant calls in mother on positions assessed *in all 3 individuals*
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// public int dad_assessed_variant; // ditto
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// public int kid_assessed_variant;
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public int missing_variant_in_kid;
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public int nonmatching_variant_in_kid;
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public int missing_variant_in_parents;
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public int mom_passed_variant;
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public int dad_passed_variant;
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// public long consistent_ref = 0; // number of assessed loci, where all 3 people have homogeneous reference allele
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// public int consistent_variant = 0; // number of assessed loci where a variant is observed in at least one individual and genotyping calls are consistent between the trio members
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// public int inconsistent_variant = 0; // number of assessed loci where a variant is observed in at least one individual and genotyping calls are inconsistent
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// public int missing_variant_in_parents = 0; // number of inconsistent variants (see above), where parent(s) have a variant but the kid does not while she should
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// public int missing_variant_in_kid = 0; // number of inconsistent variants (see above), where kid has a snp but the parents do not while they should
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// public int consistent_variant_passed = 0; // variants that are consistent and *passed* (i.e. present in kid and one of the parents)
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// public int non_biallelic_variant = 0; // number of variant calls that are not biallelic
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// public long unclassified_events = 0;
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public TrioConcordanceRecord() {
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mom = new GenotypingCallStats();
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dad = new GenotypingCallStats();
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kid = new GenotypingCallStats();
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trio = new GenotypingCallStats();
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}
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public TrioConcordanceRecord add(TrioConcordanceRecord other) {
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this.assessed_loci += other.assessed_loci;
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this.consistent_ref += other.consistent_ref;
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this.consistent_snp += other.consistent_snp;
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this.inconsistent_snp += other.inconsistent_snp;
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this.missing_snp_in_parents += other.missing_snp_in_parents;
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this.missing_snp_in_kid += other.missing_snp_in_kid;
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this.consistent_indels += other.consistent_indels;
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this.consistent_indels_in_mother += other.consistent_indels_in_mother;
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this.consistent_indels_in_father += other.consistent_indels_in_father;
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this.inconsistent_indels += other.inconsistent_indels;
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this.missing_indels_in_parents += other.missing_indels_in_parents;
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this.missing_indels_in_kid += other.missing_indels_in_kid;
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this.non_biallelic_snp += other.non_biallelic_snp;
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this.non_biallelic_indel += other.non_biallelic_indel;
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this.mom_assessed += other.mom_assessed;
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this.dad_assessed += other.dad_assessed;
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this.kid_assessed += other.kid_assessed;
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this.mom_ref += other.mom_ref;
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this.dad_ref += other.dad_ref;
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this.kid_ref += other.kid_ref;
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this.mom_snp += other.mom_snp;
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this.dad_snp += other.dad_snp;
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this.kid_snp += other.kid_snp;
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this.mom_indel += other.mom_indel;
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this.dad_indel += other.dad_indel;
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this.kid_indel += other.kid_indel;
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this.unclassified_events += other.unclassified_events;
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this.mom.add(other.mom);
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this.dad.add(other.dad);
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this.kid.add(other.kid);
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this.trio.add(other.trio);
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// this.mom_assessed_ref += other.mom_assessed_ref;
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// this.dad_assessed_ref += other.dad_assessed_ref;
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// this.kid_assessed_ref += other.kid_assessed_ref;
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// this.mom_assessed_variant += other.mom_assessed_variant;
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// this.dad_assessed_variant += other.dad_assessed_ref;
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// this.kid_assessed_variant += other.kid_assessed_variant;
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this.missing_variant_in_kid += other.missing_variant_in_kid ;
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this.nonmatching_variant_in_kid += other.nonmatching_variant_in_kid ;
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this.missing_variant_in_parents += other.missing_variant_in_parents ;
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this.mom_passed_variant += other.mom_passed_variant;
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this.dad_passed_variant += other.dad_passed_variant;
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// this.consistent_ref += other.consistent_ref;
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// this.consistent_variant += other.consistent_variant;
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// this.inconsistent_variant += other.inconsistent_variant;
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// this.missing_variant_in_parents += other.missing_variant_in_parents;
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// this.missing_variant_in_kid += other.missing_variant_in_kid;
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// this.consistent_variant_passed += other.consistent_variant_passed;
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// this.non_biallelic_variant += other.non_biallelic_variant;
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// this.unclassified_events += other.unclassified_events;
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return this;
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}
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public int totalSNP() { return consistent_snp + inconsistent_snp + non_biallelic_snp; }
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public int totalIndels() { return consistent_indels + inconsistent_indels + non_biallelic_indel; }
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public int totalVariants() { return trio.consistent_variant + trio.inconsistent_variant + trio.non_biallelic_variant; }
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public String toString() {
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StringBuilder b = new StringBuilder();
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b.append(String.format("%ntotal assessed in trio: %d%n reference: %d (%3.2f%%)%n", assessed_loci, consistent_ref, Utils.percentage(consistent_ref,assessed_loci )) );
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b.append(String.format(" total snp sites: %d%n consistent snp: %d (%3.2f%%)%n multiallelic snp: %d (%3.2f%%)%n inconsistent snp: %d (%3.2f%%)%n",
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totalSNP(), consistent_snp, Utils.percentage(consistent_snp,totalSNP() ), non_biallelic_snp, Utils.percentage(non_biallelic_snp,totalSNP()),
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inconsistent_snp, Utils.percentage(inconsistent_snp, totalSNP()) ) );
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b.append(String.format(" total indel sites: %d%n consistent indel: %d (%3.2f%%)%n multiallelic indel: %d (%3.2f%%)%n inconsistent indels: %d (%3.2f%%)%n missing from daughter: %d (%3.2f%%)%n missing from both parents: %d (%3.2f%%)%n",
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totalIndels(), consistent_indels, Utils.percentage(consistent_indels,totalIndels()),
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non_biallelic_indel, Utils.percentage(non_biallelic_indel, totalIndels()),
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inconsistent_indels, Utils.percentage(inconsistent_indels, totalIndels()),
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missing_indels_in_kid, Utils.percentage(missing_indels_in_kid, inconsistent_indels),
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missing_indels_in_parents, Utils.percentage(missing_indels_in_parents, inconsistent_indels)
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));
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b.append(String.format("%ncovered in trio: %d%n", trio.covered ) );
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b.append(String.format(" unclassified (snp+indel): %d%n", unclassified_events));
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b.append(String.format("assessed in trio: %d (%3.2f%% covered)%n",
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trio.assessed, Utils.percentage(trio.assessed,trio.covered )) );
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b.append( String.format("per trio individual:%n mother:%n assessed: %d%n ref: %d%n snps: %d%n indels: %d%n", mom_assessed, mom_ref, mom_snp,mom_indel) );
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b.append( String.format(" father:%n assessed: %d%n ref: %d%n snps: %d%n indels: %d%n", dad_assessed, dad_ref, dad_snp,dad_indel) );
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b.append( String.format(" daughter:%n assessed: %d%n ref: %d%n snps: %d%n indels: %d%n", kid_assessed, kid_ref, kid_snp,kid_indel) );
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b.append(String.format(" reference in all samples: %d (%3.2f%% assessed)%n",
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trio.ref, Utils.percentage(trio.ref,trio.assessed )) );
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b.append(String.format(" variant sites: %d (%3.2f%% assessed, or 1 per %3.2f kB)%n",
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totalVariants(), Utils.percentage(totalVariants(), trio.assessed), ((double)trio.assessed/totalVariants())/1000.0
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));
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b.append(String.format(" consistent variants: %d (%3.2f%% variants)%n",
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trio.consistent_variant, Utils.percentage(trio.consistent_variant,totalVariants())
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));
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// b.append(String.format(" passed (in daughter and parent(s)): %d%n lost (in parent(s) but not in daughter): %d%n",
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// consistent_variant_passed, consistent_variant - consistent_variant_passed));
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b.append(String.format(" multiallelic variant: %d (%3.2f%% variants)%n",
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trio.non_biallelic_variant, Utils.percentage(trio.non_biallelic_variant, totalVariants())
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));
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b.append(String.format(" inconsistent variant: %d (%3.2f%% variants)%n",
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trio.inconsistent_variant, Utils.percentage(trio.inconsistent_variant, totalVariants())
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));
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b.append(String.format(" missing from daughter: %d (%3.2f%% inconsistent variants)%n",
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missing_variant_in_kid, Utils.percentage(missing_variant_in_kid, trio.inconsistent_variant)
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));
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b.append(String.format(" missing from both parents: %d (%3.2f%% inconsistent variants)%n",
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missing_variant_in_parents, Utils.percentage(missing_variant_in_parents, trio.inconsistent_variant)
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));
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b.append(String.format(" non-matching in daughter: %d (%3.2f%% inconsistent variants)%n",
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nonmatching_variant_in_kid, Utils.percentage(nonmatching_variant_in_kid, trio.inconsistent_variant)
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));
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b.append("per trio individual:\n");
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b.append(" mother:\n");
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b.append(mom.toString());
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b.append(" father:\n");
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b.append(dad.toString());
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b.append(" daughter:\n");
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b.append(kid.toString());
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return b.toString();
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}
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