From 9027cfaf0693d0413591363cce2de9c82c849c89 Mon Sep 17 00:00:00 2001 From: Frank Austin Nothaft Date: Fri, 6 Mar 2015 17:50:07 -0800 Subject: [PATCH] [QC-METRICS-2] Cleaned up package names. --- .gitignore | 3 +++ pom.xml | 2 +- .../{adam => qc}/cli/CompareADAM.scala | 9 ++++--- .../{adam => qc}/cli/FindReads.scala | 8 +++--- .../cli/GenotypeConcordance.scala | 10 ++++--- .../bdgenomics/{adam => qc}/cli/QCMain.scala | 4 +-- .../{adam => qc}/cli/SummarizeGenotypes.scala | 7 ++--- .../metrics/AvailableComparisons.scala | 2 +- .../{adam => qc}/metrics/Comparisons.scala | 4 +-- .../metrics/filters/GeneratorFilter.scala | 4 +-- .../org/bdgenomics/qc/rdd/QCContext.scala | 26 +++++++++++++++++++ .../ComparisonTraversalEngine.scala | 6 ++--- .../rdd/variation/ConcordanceTable.scala | 4 +-- .../GenotypeConcordanceRDDFunctions.scala | 2 +- .../rdd/variation/GenotypesSummary.scala | 7 +++-- .../adam/metrics/ComparisonsSuite.scala | 2 +- .../filters/GeneratorFilterSuite.scala | 2 +- .../ComparisonTraversalEngineSuite.scala | 4 +-- ...GenotypeConcordanceRDDFunctionsSuite.scala | 15 ++++++----- .../rdd/variation/GenotypesSummarySuite.scala | 4 +-- 20 files changed, 79 insertions(+), 46 deletions(-) rename qc-metrics-cli/src/main/scala/org/bdgenomics/{adam => qc}/cli/CompareADAM.scala (97%) rename qc-metrics-cli/src/main/scala/org/bdgenomics/{adam => qc}/cli/FindReads.scala (96%) rename qc-metrics-cli/src/main/scala/org/bdgenomics/{adam => qc}/cli/GenotypeConcordance.scala (90%) rename qc-metrics-cli/src/main/scala/org/bdgenomics/{adam => qc}/cli/QCMain.scala (98%) rename qc-metrics-cli/src/main/scala/org/bdgenomics/{adam => qc}/cli/SummarizeGenotypes.scala (92%) rename qc-metrics-core/src/main/scala/org/bdgenomics/{adam => qc}/metrics/AvailableComparisons.scala (99%) rename qc-metrics-core/src/main/scala/org/bdgenomics/{adam => qc}/metrics/Comparisons.scala (98%) rename qc-metrics-core/src/main/scala/org/bdgenomics/{adam => qc}/metrics/filters/GeneratorFilter.scala (95%) create mode 100644 qc-metrics-core/src/main/scala/org/bdgenomics/qc/rdd/QCContext.scala rename qc-metrics-core/src/main/scala/org/bdgenomics/{adam => qc}/rdd/read/comparisons/ComparisonTraversalEngine.scala (95%) rename qc-metrics-core/src/main/scala/org/bdgenomics/{adam => qc}/rdd/variation/ConcordanceTable.scala (97%) rename qc-metrics-core/src/main/scala/org/bdgenomics/{adam => qc}/rdd/variation/GenotypeConcordanceRDDFunctions.scala (98%) rename qc-metrics-core/src/main/scala/org/bdgenomics/{adam => qc}/rdd/variation/GenotypesSummary.scala (98%) 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 {