diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java index 7991e3432..ff69b9b11 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java @@ -39,6 +39,16 @@ public class GenotypeConcordance extends RodWalker evalSamples; List compSamples; + // todo -- integration test coverage + // todo -- deal with occurrences like: + // Eval: 20 4000 A C + // Eval: 20 4000 A AC + // Comp: 20 4000 A C + // currently this results in a warning and skipping + // todo -- extend to multiple eval, multiple comp + // todo -- table with "proportion of overlapping sites" (not just eval/comp margins) + + public ConcordanceMetrics reduceInit() { Map headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding)); VCFHeader evalHeader = headerMap.get(evalBinding.getName()); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java index 9a5b18735..50d71c532 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java @@ -34,6 +34,11 @@ import net.sf.picard.reference.ReferenceSequenceFile; public class ConcordanceMetricsUnitTest extends BaseTest { + // todo -- coverage for several sites (3,4) + // todo -- coverage for calculation of table margins + // todo -- coverage for site concordance + // todo -- coverage for disjoint and mostly-disjoint sample sets + private static ReferenceSequenceFile seq; private GenomeLocParser genomeLocParser;