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Allow user to set min confidence score for comp tracks too 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3222 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-21 05:09:09 +00:00
parent 3db73e0791
commit 114819d980
1 changed files with 4 additions and 6 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -55,8 +55,6 @@ import java.util.*;
// todo -- evalations should support comment lines // todo -- evalations should support comment lines
// todo -- add Mendelian variable explanations (nDeNovo and nMissingTransmissions) // todo -- add Mendelian variable explanations (nDeNovo and nMissingTransmissions)
// todo -- write a simple column table system and have the evaluators return this instead of the list<list<string>> objects
// todo -- site frequency spectrum eval (freq. of variants in eval as a function of their AC and AN numbers) // todo -- site frequency spectrum eval (freq. of variants in eval as a function of their AC and AN numbers)
// todo -- clustered SNP counter // todo -- clustered SNP counter
// todo -- HWEs // todo -- HWEs
@ -64,7 +62,6 @@ import java.util.*;
// todo -- synonymous / non-synonmous ratio, or really just comparison of observed vs. expected biological annotation values // todo -- synonymous / non-synonmous ratio, or really just comparison of observed vs. expected biological annotation values
// todo -- Performance: // todo -- Performance:
// todo -- create JEXL context implementing object that simply looks up values for JEXL evaluations. Throws error for unknown fields
// todo -- deal with performance issues with variant contexts // todo -- deal with performance issues with variant contexts
// todo -- port over SNP density walker: // todo -- port over SNP density walker:
@ -78,9 +75,6 @@ import java.util.*;
// todo -- useful general capability. Right now you need to add arguments to VariantEval2 to handle new // todo -- useful general capability. Right now you need to add arguments to VariantEval2 to handle new
// todo -- evaluation arguments (which is better than passing a string!) // todo -- evaluation arguments (which is better than passing a string!)
// todo -- write or find a simple way to organize the table like output of variant eval 2. A generic table of strings?
// todo -- these really should be implemented as default select expression // todo -- these really should be implemented as default select expression
// todo Extend VariantEval, our general-purpose tool for SNP evaluation, to differentiate Ti/Tv at CpG islands and also // todo Extend VariantEval, our general-purpose tool for SNP evaluation, to differentiate Ti/Tv at CpG islands and also
// todo classify (and count) variants into coding, non-coding, synonomous/non-symonomous, 2/4 fold degenerate sites, etc. // todo classify (and count) variants into coding, non-coding, synonomous/non-symonomous, 2/4 fold degenerate sites, etc.
@ -154,6 +148,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
private static double NO_MIN_QUAL_SCORE = -1.0; private static double NO_MIN_QUAL_SCORE = -1.0;
@Argument(shortName = "Q", fullName="minPhredConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false) @Argument(shortName = "Q", fullName="minPhredConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
public double minQualScore = NO_MIN_QUAL_SCORE; public double minQualScore = NO_MIN_QUAL_SCORE;
@Argument(shortName = "Qcomp", fullName="minPhredConfidenceScoreForComp", doc="Minimum confidence score to consider a comp SNP a variant", required=false)
public double minCompQualScore = NO_MIN_QUAL_SCORE;
// Right now we will only be looking at SNPS // Right now we will only be looking at SNPS
EnumSet<VariantContext.Type> ALLOW_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION); EnumSet<VariantContext.Type> ALLOW_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION);
@ -469,6 +465,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
break; break;
case 2: case 2:
VariantContext comp = vcs.get(group.compTrackName); VariantContext comp = vcs.get(group.compTrackName);
if ( comp != null && minCompQualScore != NO_MIN_QUAL_SCORE && comp.getNegLog10PError() < (minCompQualScore / 10.0))
comp = null;
String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context ); String interesting = evaluation.update2( evalWantsVC ? vc : null, comp, tracker, ref, context );
if ( interesting != null ) interestingReasons.add(interesting); if ( interesting != null ) interestingReasons.add(interesting);
break; break;