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updated, reports more stuff now, including stats for external consistency checks 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@789 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-21 22:28:18 +00:00
parent 30c63daf89
commit 7afc10fd6f
1 changed files with 37 additions and 7 deletions
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44
java/src/org/broadinstitute/sting/playground/utils/GenotypingCallStats.java
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@ -10,12 +10,17 @@ import org.broadinstitute.sting.utils.Utils;
*
*/
public class GenotypingCallStats {
public long covered = 0; // number of loci covered in all 3 individuals (not necessarily confidently called)
public long assessed = 0; // number of loci with all 3 genotypes available at or above the specified cutoff
public long ref = 0; // number of assessed loci, where all 3 people have homogeneous reference allele
public long covered = 0; // number of loci covered in an individual (not necessarily confidently called)
public long assessed = 0; // number of loci with confident calls
public long ref = 0; // number of assessed loci where the reference is called
public int variant = 0; // number of assessed loci where a variant is observed in the individual
// NOTE: consistent_ref + inconsistent_ref is the total number of ref calls assessed for consistency (by some external application).
// this number does not have to be equal to 'ref' ( total number of ref calls in this individual - we migh be unable to assess
// the consistency for all of them!); same applies to (in)consistent_variant.
public int consistent_variant = 0; // variants that are consistent in any (application-specific) sense, e.g. variant matches variants in other members of the family trio
public int consistent_ref = 0; // reference calls that are consistent in any (app-specific) sense, e.g. consistent with other members of the family trio
public int inconsistent_variant = 0; // variants that are inconsistent in any (application-specific) sense, e.g. variant does not match variants in other members of the family trio
public int inconsistent_ref = 0; // reference calls that are inconsistent in any (app-specific) sense, e.g. inconsistent with other members of the family trio
public int non_biallelic_variant = 0; // number of variant calls that are not biallelic
public GenotypingCallStats add(GenotypingCallStats other) {
@ -25,6 +30,8 @@ public class GenotypingCallStats {
this.variant += other.variant;
this.consistent_variant += other.consistent_variant;
this.consistent_ref += other.consistent_ref;
this.inconsistent_variant += other.consistent_variant;
this.inconsistent_ref += other.consistent_ref;
this.non_biallelic_variant += other.non_biallelic_variant;
return this;
}
@ -35,13 +42,36 @@ public class GenotypingCallStats {
StringBuilder b = new StringBuilder();
b.append( String.format(" covered: %d%n assessed: %d (%3.2f%%)%n ref: %d (%3.2f%%)%n variants: %d (%3.2f%%)%n multiallelic: %d (%3.2f%%)%n",
covered, assessed, Utils.percentage(assessed, covered),
ref, Utils.percentage(ref,assessed),
variant, Utils.percentage(variant,assessed),
b.append( String.format(" covered: %d%n assessed: %d (%3.2f%% covered)%n",
covered, assessed, Utils.percentage(assessed, covered) )
);
b.append( String.format(" ref: %d (%3.2f%% assessed)%n",
ref, Utils.percentage(ref,assessed))
);
int z = consistent_ref+inconsistent_ref;
b.append( String.format(" ref assessed for consistency: %d (%3.2f%% ref)%n",
z, Utils.percentage(z, ref) )
);
b.append( String.format(" consistent ref: %d (%3.2f%% consistency-assessed ref)%n",
consistent_ref, Utils.percentage(consistent_ref,z) )
);
b.append( String.format(" variants: %d (%3.2f%% assessed)%n",
variant, Utils.percentage(variant,assessed))
);
b.append( String.format(" multiallelic: %d (%3.2f%% variants)%n",
non_biallelic_variant, Utils.percentage(non_biallelic_variant, variant))
);
z = consistent_variant+inconsistent_variant;
b.append( String.format(" variants assessed for consistency: %d (%3.2f%% variants)%n",
z, Utils.percentage(z, variant) )
);
b.append( String.format(" consistent variants: %d (%3.2f%% consistency-assessed variants)%n",
consistent_ref, Utils.percentage(consistent_variant,z) )
);
return b.toString();
}
}