diff --git a/.gitignore b/.gitignore
index 4970261..f3d830d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,3 +18,6 @@ project/plugins/project/
*.iml
.idea/
+
+*~
+*#*
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 9d21afe..3971085 100644
--- a/pom.xml
+++ b/pom.xml
@@ -27,7 +27,7 @@
2.2.0
0.99.2
- 0.16.0
+ 0.16.1-SNAPSHOT
0.1.2
diff --git a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/CompareADAM.scala b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/CompareADAM.scala
similarity index 97%
rename from qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/CompareADAM.scala
rename to qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/CompareADAM.scala
index ad8fd9d..f9b44af 100644
--- a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/CompareADAM.scala
+++ b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/CompareADAM.scala
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.cli
+package org.bdgenomics.qc.cli
import java.io.{ OutputStreamWriter, PrintWriter }
@@ -23,11 +23,12 @@ import org.apache.hadoop.fs.{ FileSystem, Path }
import org.apache.hadoop.mapreduce.Job
import org.apache.spark.SparkContext
import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.metrics.{ BucketComparisons, CombinedComparisons, DefaultComparisons }
+import org.bdgenomics.adam.cli._
import org.bdgenomics.adam.projections.AlignmentRecordField._
import org.bdgenomics.adam.projections.FieldValue
import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.comparisons.ComparisonTraversalEngine
+import org.bdgenomics.qc.metrics.{ BucketComparisons, CombinedComparisons, DefaultComparisons }
+import org.bdgenomics.qc.rdd.read.comparisons.ComparisonTraversalEngine
import org.bdgenomics.utils.metrics.aggregators.{ AggregatedCollection, CombinedAggregator, HistogramAggregator, Writable }
import org.bdgenomics.utils.metrics.{ Collection, Histogram }
import org.kohsuke.args4j.{ Argument, CmdLineParser, Option => Args4jOption }
@@ -251,4 +252,4 @@ class CompareADAM(protected val args: CompareADAMArgs) extends ADAMSparkCommand[
}
}
}
-}
\ No newline at end of file
+}
diff --git a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/FindReads.scala b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/FindReads.scala
similarity index 96%
rename from qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/FindReads.scala
rename to qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/FindReads.scala
index 7618de2..f0e35f4 100644
--- a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/FindReads.scala
+++ b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/FindReads.scala
@@ -15,19 +15,19 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.cli
+package org.bdgenomics.qc.cli
import java.io.OutputStreamWriter
import java.util.regex.Pattern
-
import org.apache.hadoop.fs.{ FileSystem, Path }
import org.apache.hadoop.mapreduce.Job
import org.apache.spark.SparkContext
import org.apache.spark.SparkContext._
import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.metrics.filters.{ CombinedFilter, GeneratorFilter }
-import org.bdgenomics.adam.metrics.{ BucketComparisons, DefaultComparisons }
+import org.bdgenomics.adam.cli._
import org.bdgenomics.adam.models.ReadBucket
+import org.bdgenomics.qc.metrics.filters.{ CombinedFilter, GeneratorFilter }
+import org.bdgenomics.qc.metrics.{ BucketComparisons, DefaultComparisons }
import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
import scala.collection.Seq
diff --git a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/GenotypeConcordance.scala b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/GenotypeConcordance.scala
similarity index 90%
rename from qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/GenotypeConcordance.scala
rename to qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/GenotypeConcordance.scala
index 07e037d..5c27e17 100644
--- a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/GenotypeConcordance.scala
+++ b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/GenotypeConcordance.scala
@@ -15,17 +15,19 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.cli
+package org.bdgenomics.qc.cli
import org.apache.hadoop.mapreduce.Job
import org.apache.spark.SparkContext._
import org.apache.spark.rdd.RDD
import org.apache.spark.{ Logging, SparkContext }
+import org.bdgenomics.adam.cli._
import org.bdgenomics.adam.predicates.GenotypeRecordPASSPredicate
import org.bdgenomics.adam.projections.GenotypeField
import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.variation.ConcordanceTable
import org.bdgenomics.formats.avro.Genotype
+import org.bdgenomics.qc.rdd.QCContext._
+import org.bdgenomics.qc.rdd.variation.ConcordanceTable
import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
object GenotypeConcordance extends ADAMCommandCompanion {
@@ -62,8 +64,8 @@ class GenotypeConcordance(protected val args: GenotypeConcordanceArgs) extends A
None
val projection = None //Some(Projection(project))
- val testGTs: RDD[Genotype] = sc.adamLoad(args.testGenotypesFile, predicate, projection)
- val truthGTs: RDD[Genotype] = sc.adamLoad(args.truthGenotypesFile, predicate, projection)
+ val testGTs: RDD[Genotype] = sc.loadGenotypes(args.testGenotypesFile, predicate, projection)
+ val truthGTs: RDD[Genotype] = sc.loadGenotypes(args.truthGenotypesFile, predicate, projection)
val tables = testGTs.concordanceWith(truthGTs)
diff --git a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/QCMain.scala b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/QCMain.scala
similarity index 98%
rename from qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/QCMain.scala
rename to qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/QCMain.scala
index 908f0ef..939f479 100644
--- a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/QCMain.scala
+++ b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/QCMain.scala
@@ -15,11 +15,11 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.cli
+package org.bdgenomics.qc.cli
import java.util.logging.Level._
-
import org.apache.spark.Logging
+import org.bdgenomics.adam.cli._
import org.bdgenomics.adam.util.ParquetLogger
object QCMain extends Logging {
diff --git a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/SummarizeGenotypes.scala b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/SummarizeGenotypes.scala
similarity index 92%
rename from qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/SummarizeGenotypes.scala
rename to qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/SummarizeGenotypes.scala
index 4eb3f09..9003133 100644
--- a/qc-metrics-cli/src/main/scala/org/bdgenomics/adam/cli/SummarizeGenotypes.scala
+++ b/qc-metrics-cli/src/main/scala/org/bdgenomics/qc/cli/SummarizeGenotypes.scala
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.cli
+package org.bdgenomics.qc.cli
import java.io.{ BufferedWriter, OutputStreamWriter }
@@ -24,9 +24,10 @@ import org.apache.hadoop.fs.{ FileSystem, Path }
import org.apache.hadoop.mapreduce.Job
import org.apache.spark.rdd.RDD
import org.apache.spark.{ Logging, SparkContext }
+import org.bdgenomics.adam.cli._
import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.variation.{ GenotypesSummary, GenotypesSummaryFormatting }
import org.bdgenomics.formats.avro.Genotype
+import org.bdgenomics.qc.rdd.variation.{ GenotypesSummary, GenotypesSummaryFormatting }
import org.kohsuke.args4j
object SummarizeGenotypes extends ADAMCommandCompanion {
@@ -54,7 +55,7 @@ class SummarizeGenotypes(val args: SummarizeGenotypesArgs) extends ADAMSparkComm
val companion = SummarizeGenotypes
def run(sc: SparkContext, job: Job) {
- val adamGTs: RDD[Genotype] = sc.adamLoad(args.adamFile)
+ val adamGTs: RDD[Genotype] = sc.loadGenotypes(args.adamFile)
val stats = GenotypesSummary(adamGTs)
val result = args.format match {
case "human" => GenotypesSummaryFormatting.format_human_readable(stats)
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/AvailableComparisons.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/AvailableComparisons.scala
similarity index 99%
rename from qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/AvailableComparisons.scala
rename to qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/AvailableComparisons.scala
index a3c43a1..75aaa7d 100644
--- a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/AvailableComparisons.scala
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/AvailableComparisons.scala
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.metrics
+package org.bdgenomics.qc.metrics
import org.bdgenomics.formats.avro.AlignmentRecord
import org.bdgenomics.adam.projections.FieldValue
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/Comparisons.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/Comparisons.scala
similarity index 98%
rename from qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/Comparisons.scala
rename to qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/Comparisons.scala
index 273fc61..1aa5a9e 100644
--- a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/Comparisons.scala
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/Comparisons.scala
@@ -15,12 +15,12 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.metrics
+package org.bdgenomics.qc.metrics
import java.util.regex.Pattern
-import org.bdgenomics.adam.metrics.filters.ComparisonsFilter
import org.bdgenomics.adam.models.ReadBucket
import org.bdgenomics.adam.projections.FieldValue
+import org.bdgenomics.qc.metrics.filters.ComparisonsFilter
import org.bdgenomics.utils.metrics.Collection
trait BucketComparisons[+T] {
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/filters/GeneratorFilter.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/filters/GeneratorFilter.scala
similarity index 95%
rename from qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/filters/GeneratorFilter.scala
rename to qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/filters/GeneratorFilter.scala
index f82b189..1064921 100644
--- a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/metrics/filters/GeneratorFilter.scala
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/metrics/filters/GeneratorFilter.scala
@@ -15,9 +15,9 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.metrics.filters
+package org.bdgenomics.qc.metrics.filters
-import org.bdgenomics.adam.metrics.{ CombinedComparisons, BucketComparisons }
+import org.bdgenomics.qc.metrics.{ CombinedComparisons, BucketComparisons }
import org.bdgenomics.utils.metrics.{ Collection => BDGCollection }
/**
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/QCContext.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/QCContext.scala
new file mode 100644
index 0000000..c69f0a7
--- /dev/null
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/QCContext.scala
@@ -0,0 +1,26 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.qc.rdd
+
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.formats.avro.Genotype
+import org.bdgenomics.qc.rdd.variation.GenotypeConcordanceRDDFunctions
+
+object QCContext {
+ implicit def rddToGenotypeConcordanceRDD(rdd: RDD[Genotype]) = new GenotypeConcordanceRDDFunctions(rdd)
+}
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/read/comparisons/ComparisonTraversalEngine.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/read/comparisons/ComparisonTraversalEngine.scala
similarity index 95%
rename from qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/read/comparisons/ComparisonTraversalEngine.scala
rename to qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/read/comparisons/ComparisonTraversalEngine.scala
index 28bdb8f..08ae71d 100644
--- a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/read/comparisons/ComparisonTraversalEngine.scala
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/read/comparisons/ComparisonTraversalEngine.scala
@@ -15,18 +15,18 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.rdd.read.comparisons
+package org.bdgenomics.qc.rdd.read.comparisons
import org.apache.hadoop.fs.Path
import org.apache.spark.SparkContext
import org.apache.spark.SparkContext._
import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.metrics.BucketComparisons
-import org.bdgenomics.adam.metrics.filters.GeneratorFilter
import org.bdgenomics.adam.models.ReadBucket
import org.bdgenomics.adam.projections.{ FieldValue, Projection }
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.formats.avro.AlignmentRecord
+import org.bdgenomics.qc.metrics.BucketComparisons
+import org.bdgenomics.qc.metrics.filters.GeneratorFilter
import org.bdgenomics.utils.metrics.aggregators.{ Aggregated, Aggregator }
import scala.reflect.ClassTag
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/ConcordanceTable.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/ConcordanceTable.scala
similarity index 97%
rename from qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/ConcordanceTable.scala
rename to qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/ConcordanceTable.scala
index 9549352..2ba2148 100644
--- a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/ConcordanceTable.scala
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/ConcordanceTable.scala
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.rdd.variation
+package org.bdgenomics.qc.rdd.variation
import java.util.EnumSet
@@ -45,7 +45,7 @@ object ConcordanceTable {
* to "truth" genotypes.
*/
class ConcordanceTable {
- import org.bdgenomics.adam.rdd.variation.ConcordanceTable._
+ import org.bdgenomics.qc.rdd.variation.ConcordanceTable._
private val table_ = Array.fill[Long](GenotypeType.values.length, GenotypeType.values.length)(0L)
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/GenotypeConcordanceRDDFunctions.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/GenotypeConcordanceRDDFunctions.scala
similarity index 98%
rename from qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/GenotypeConcordanceRDDFunctions.scala
rename to qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/GenotypeConcordanceRDDFunctions.scala
index c4378e7..dd63221 100644
--- a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/GenotypeConcordanceRDDFunctions.scala
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/GenotypeConcordanceRDDFunctions.scala
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.rdd.variation
+package org.bdgenomics.qc.rdd.variation
import org.apache.hadoop.io.LongWritable
import org.apache.spark.SparkContext._
diff --git a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/GenotypesSummary.scala b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/GenotypesSummary.scala
similarity index 98%
rename from qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/GenotypesSummary.scala
rename to qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/GenotypesSummary.scala
index 46160dd..f19f110 100644
--- a/qc-metrics-core/src/main/scala/org/bdgenomics/adam/rdd/variation/GenotypesSummary.scala
+++ b/qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/variation/GenotypesSummary.scala
@@ -15,14 +15,13 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.rdd.variation
+package org.bdgenomics.qc.rdd.variation
import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.rdd.variation.GenotypesSummary.StatisticsMap
-import org.bdgenomics.adam.rdd.variation.GenotypesSummaryCounts.ReferenceAndAlternate
import org.bdgenomics.adam.rich.RichVariant._
import org.bdgenomics.formats.avro.{ Genotype, GenotypeAllele }
-
+import org.bdgenomics.qc.rdd.variation.GenotypesSummary.StatisticsMap
+import org.bdgenomics.qc.rdd.variation.GenotypesSummaryCounts.ReferenceAndAlternate
import scala.collection.JavaConverters._
import scala.collection.immutable.Map
import scala.collection.mutable
diff --git a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/ComparisonsSuite.scala b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/ComparisonsSuite.scala
index e4509f9..57c445b 100644
--- a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/ComparisonsSuite.scala
+++ b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/ComparisonsSuite.scala
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.metrics
+package org.bdgenomics.qc.metrics
import org.bdgenomics.adam.models.SingleReadBucket
import org.bdgenomics.adam.util.ADAMFunSuite
diff --git a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/filters/GeneratorFilterSuite.scala b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/filters/GeneratorFilterSuite.scala
index 855fbe1..fa81dbb 100644
--- a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/filters/GeneratorFilterSuite.scala
+++ b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/metrics/filters/GeneratorFilterSuite.scala
@@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.metrics.filters
+package org.bdgenomics.qc.metrics.filters
import org.bdgenomics.utils.metrics.{ Collection => BDGCollection }
import org.scalatest._
diff --git a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/read/comparisons/ComparisonTraversalEngineSuite.scala b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/read/comparisons/ComparisonTraversalEngineSuite.scala
index e892dd5..507dd61 100644
--- a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/read/comparisons/ComparisonTraversalEngineSuite.scala
+++ b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/read/comparisons/ComparisonTraversalEngineSuite.scala
@@ -15,13 +15,13 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.rdd.read.comparisons
+package org.bdgenomics.qc.rdd.read.comparisons
import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.metrics.MappedPosition
import org.bdgenomics.adam.projections.AlignmentRecordField
import org.bdgenomics.adam.util.ADAMFunSuite
import org.bdgenomics.formats.avro.{ AlignmentRecord, Contig }
+import org.bdgenomics.qc.metrics.MappedPosition
import org.bdgenomics.utils.metrics.Histogram
import org.bdgenomics.utils.metrics.aggregators.HistogramAggregator
diff --git a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypeConcordanceRDDFunctionsSuite.scala b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypeConcordanceRDDFunctionsSuite.scala
index f38b1a8..343aff8 100644
--- a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypeConcordanceRDDFunctionsSuite.scala
+++ b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypeConcordanceRDDFunctionsSuite.scala
@@ -15,13 +15,14 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.rdd.variation
+package org.bdgenomics.qc.rdd.variation
import org.apache.spark.SparkContext._
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.util.ADAMFunSuite
import org.bdgenomics.formats.avro._
+import org.bdgenomics.qc.rdd.QCContext._
class GenotypeConcordanceRDDFunctionsSuite extends ADAMFunSuite {
def v0 = Variant.newBuilder
@@ -38,16 +39,16 @@ class GenotypeConcordanceRDDFunctionsSuite extends ADAMFunSuite {
val g0 = gb.build
val g1 = gb.build
- val tables0 = sc.parallelize(Seq(g0)).concordanceWith(sc.parallelize(Seq(g1))).collectAsMap
+ val tables0: scala.collection.Map[String, ConcordanceTable] = sc.parallelize(Seq(g0)).concordanceWith(sc.parallelize(Seq(g1))).collectAsMap
assert(tables0.size === 1)
- val table0 = tables0.getOrElse("NA12878", ConcordanceTable())
+ val table0: ConcordanceTable = tables0.getOrElse("NA12878", ConcordanceTable())
assert(table0.total === 1)
assert(table0.get(GenotypeType.HET, GenotypeType.HET) === 1)
val g2 = gb.setAlleles(List(GenotypeAllele.Ref, GenotypeAllele.Ref)).build
- val table1 = sc.parallelize(Seq(g0))
+ val tables1: scala.collection.Map[String, ConcordanceTable] = sc.parallelize(Seq(g0))
.concordanceWith(sc.parallelize(Seq(g2))).collectAsMap()
- .getOrElse("NA12878", ConcordanceTable())
+ val table1: ConcordanceTable = tables1.getOrElse("NA12878", ConcordanceTable())
assert(table1.total === 1)
assert(table1.get(GenotypeType.HET, GenotypeType.HOM_REF) === 1)
}
@@ -58,10 +59,10 @@ class GenotypeConcordanceRDDFunctionsSuite extends ADAMFunSuite {
val gts: RDD[Genotype] = sc.loadGenotypes(path)
assert(gts.filter(_.getSampleId == "NA12878").count === 5)
- val tables = gts.concordanceWith(gts).collectAsMap
+ val tables: scala.collection.Map[String, ConcordanceTable] = gts.concordanceWith(gts).collectAsMap
assert(tables.size === 3L)
- val table0 = tables.getOrElse("NA12878", ConcordanceTable())
+ val table0: ConcordanceTable = tables.getOrElse("NA12878", ConcordanceTable())
assert(table0.total === 5L)
assert(table0.concordance === 1.0)
}
diff --git a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypesSummarySuite.scala b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypesSummarySuite.scala
index 5a07519..68bc80a 100644
--- a/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypesSummarySuite.scala
+++ b/qc-metrics-core/src/test/scala/org/bdgenomics/adam/rdd/variation/GenotypesSummarySuite.scala
@@ -15,11 +15,11 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.bdgenomics.adam.rdd.variation
+package org.bdgenomics.qc.rdd.variation
import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.variation.GenotypesSummaryCounts.ReferenceAndAlternate
import org.bdgenomics.adam.util.ADAMFunSuite
+import org.bdgenomics.qc.rdd.variation.GenotypesSummaryCounts.ReferenceAndAlternate
import org.bdgenomics.formats.avro._
class GenotypesSummarySuite extends ADAMFunSuite {