zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

minor update in report printout format 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@790 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-22 13:56:09 +00:00
parent 7afc10fd6f
commit 63caca31bf
1 changed files with 15 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

27
java/src/org/broadinstitute/sting/playground/utils/GenotypingCallStats.java
View File

@ -18,9 +18,9 @@ public class GenotypingCallStats {
// 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 long 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 long 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) {
@ -30,14 +30,17 @@ 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.inconsistent_variant += other.inconsistent_variant;
this.inconsistent_ref += other.inconsistent_ref;
this.non_biallelic_variant += other.non_biallelic_variant;
return this;
}
// public int totalVariants() { return consistent_variant + inconsistent_variant + non_biallelic_variant; }
public long assessedForConsistencyRef() { return consistent_ref + inconsistent_ref; }
public int assessedForConsistencyVariant() { return consistent_variant + inconsistent_variant; }
public String toString() {
StringBuilder b = new StringBuilder();
@ -50,27 +53,27 @@ public class GenotypingCallStats {
ref, Utils.percentage(ref,assessed))
);
int z = consistent_ref+inconsistent_ref;
long zr = assessedForConsistencyRef();
b.append( String.format(" ref assessed for consistency: %d (%3.2f%% ref)%n",
z, Utils.percentage(z, ref) )
zr, Utils.percentage(zr, ref) )
);
b.append( String.format(" consistent ref: %d (%3.2f%% consistency-assessed ref)%n",
consistent_ref, Utils.percentage(consistent_ref,z) )
consistent_ref, Utils.percentage(consistent_ref,zr) )
);
b.append( String.format(" variants: %d (%3.2f%% assessed)%n",
variant, Utils.percentage(variant,assessed))
b.append( String.format(" variants: %d (%3.2f%% assessed, or 1 per %3.2f kB)%n",
variant, Utils.percentage(variant,assessed), ((double)assessed/variant)/1000.0 )
);
b.append( String.format(" multiallelic: %d (%3.2f%% variants)%n",
non_biallelic_variant, Utils.percentage(non_biallelic_variant, variant))
);
z = consistent_variant+inconsistent_variant;
int zv = assessedForConsistencyVariant();
b.append( String.format(" variants assessed for consistency: %d (%3.2f%% variants)%n",
z, Utils.percentage(z, variant) )
zv, Utils.percentage(zv, variant) )
);
b.append( String.format(" consistent variants: %d (%3.2f%% consistency-assessed variants)%n",
consistent_ref, Utils.percentage(consistent_variant,z) )
consistent_variant, Utils.percentage(consistent_variant,zv) )
);
return b.toString();
}