[ADAM-595] Deleting the genotype- and variant- concordance classes.

ConcordanceTable and GenotypesSummary, as well as the concordance function from VariationRDDFunctions (in GenotypeRDDFunctions) are all being deleted, along with their tests. Also going are the GenotypeConcordance and SummarizeGenotypes commands from the CLI. All of this is being moved over to qc-metrics.
bigdatagenomics · Mar 1, 2015 · 4aa7af1 · 4aa7af1
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diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala
@@ -64,7 +64,6 @@ object ADAMMain extends Logging {
           VizReads,
           PrintTags,
           ListDict,
-          SummarizeGenotypes,
           AlleleCount,
           BuildInformation,
           View

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/GenotypeConcordance.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/GenotypeConcordance.scala
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/SummarizeGenotypes.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/SummarizeGenotypes.scala
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/ConcordanceTable.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/ConcordanceTable.scala