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Add in some todo items

This commit is contained in:
Chris Hartl 2013-01-09 13:16:06 -05:00
parent 8d126161e2
commit c1de92b511
2 changed files with 15 additions and 0 deletions
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10
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
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@ -39,6 +39,16 @@ public class GenotypeConcordance extends RodWalker<Pair<VariantContext,VariantCo
List<String> evalSamples; List<String> evalSamples;
List<String> compSamples; List<String> 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() { public ConcordanceMetrics reduceInit() {
Map<String,VCFHeader> headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding)); Map<String,VCFHeader> headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding));
VCFHeader evalHeader = headerMap.get(evalBinding.getName()); VCFHeader evalHeader = headerMap.get(evalBinding.getName());

5
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
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@ -34,6 +34,11 @@ import net.sf.picard.reference.ReferenceSequenceFile;
public class ConcordanceMetricsUnitTest extends BaseTest { 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 static ReferenceSequenceFile seq;
private GenomeLocParser genomeLocParser; private GenomeLocParser genomeLocParser;