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Rename org.bdgenomics.adam.rdd.features package to o.b.a.rdd.feature #1256

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Nov 10, 2016
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Rename org.bdgenomics.adam.rdd.features package to o.b.a.rdd.feature #1256

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2 changes: 1 addition & 1 deletion adam-apis/src/main/scala/org/bdgenomics/adam/apis/java/JavaADAMContext.scala
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Expand Up @@ -23,7 +23,7 @@ import org.bdgenomics.adam.models.{ RecordGroupDictionary, SequenceDictionary }
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.ADAMContext
import org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDD
import org.bdgenomics.adam.rdd.features.FeatureRDD
import org.bdgenomics.adam.rdd.feature.FeatureRDD
import org.bdgenomics.adam.rdd.fragment.FragmentRDD
import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
import org.bdgenomics.adam.rdd.variation.{
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2 changes: 1 addition & 1 deletion adam-apis/src/test/java/org/bdgenomics/adam/apis/java/JavaADAMFeatureConduit.java
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Expand Up @@ -25,7 +25,7 @@
import org.bdgenomics.adam.models.RecordGroupDictionary;
import org.bdgenomics.adam.models.SequenceDictionary;
import org.bdgenomics.adam.rdd.ADAMContext;
import org.bdgenomics.adam.rdd.features.FeatureRDD;
import org.bdgenomics.adam.rdd.feature.FeatureRDD;
import org.bdgenomics.formats.avro.AlignmentRecord;

/**
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2 changes: 1 addition & 1 deletion adam-cli/src/main/scala/org/bdgenomics/adam/cli/Reads2Coverage.scala
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Expand Up @@ -21,7 +21,7 @@ import org.apache.spark.SparkContext
import org.bdgenomics.adam.projections.AlignmentRecordField._
import org.bdgenomics.adam.projections.Projection
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.features.CoverageRDD
import org.bdgenomics.adam.rdd.feature.CoverageRDD
import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD }
import org.bdgenomics.utils.cli._
import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
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2 changes: 1 addition & 1 deletion adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
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Expand Up @@ -47,7 +47,7 @@ import org.bdgenomics.adam.projections.{
Projection
}
import org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDD
import org.bdgenomics.adam.rdd.features._
import org.bdgenomics.adam.rdd.feature._
import org.bdgenomics.adam.rdd.fragment.FragmentRDD
import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD, UnalignedReadRDD }
import org.bdgenomics.adam.rdd.variation._
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2 changes: 1 addition & 1 deletion ...omics/adam/rdd/features/CoverageRDD.scala → ...nomics/adam/rdd/feature/CoverageRDD.scala
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Expand Up @@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.rdd.features
package org.bdgenomics.adam.rdd.feature

import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.models.{
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2 changes: 1 addition & 1 deletion ...ics/adam/rdd/features/FeatureParser.scala → ...mics/adam/rdd/feature/FeatureParser.scala
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Expand Up @@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.rdd.features
package org.bdgenomics.adam.rdd.feature

import htsjdk.samtools.ValidationStringency
import java.io.File
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4 changes: 2 additions & 2 deletions ...nomics/adam/rdd/features/FeatureRDD.scala → ...enomics/adam/rdd/feature/FeatureRDD.scala
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Expand Up @@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.rdd.features
package org.bdgenomics.adam.rdd.feature

import com.google.common.collect.ComparisonChain
import java.util.Comparator
Expand Down Expand Up @@ -107,7 +107,7 @@ object FeatureRDD {
* @param feature Feature to convert to GTF format.
* @return Returns this feature as a GTF line.
*/
private[features] def toGtf(feature: Feature): String = {
private[feature] def toGtf(feature: Feature): String = {
def escape(entry: (Any, Any)): String = {
entry._1 + " \"" + entry._2 + "\""
}
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4 changes: 2 additions & 2 deletions ...genomics/adam/rdd/features/Features.scala → ...dgenomics/adam/rdd/feature/Features.scala
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Expand Up @@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.rdd.features
package org.bdgenomics.adam.rdd.feature

import org.bdgenomics.formats.avro.{ Dbxref, Feature, OntologyTerm, Strand }
import scala.collection.JavaConversions._
Expand All @@ -24,7 +24,7 @@ import scala.collection.mutable.{ ArrayBuffer, HashMap, MutableList }
/**
* Utility methods on features and related classes.
*/
private[features] object Features {
private[feature] object Features {

/**
* Parse a strand from the specified string.
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2 changes: 1 addition & 1 deletion adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala
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Expand Up @@ -52,7 +52,7 @@ import org.bdgenomics.adam.rdd.{
SAMHeaderWriter,
Unaligned
}
import org.bdgenomics.adam.rdd.features.CoverageRDD
import org.bdgenomics.adam.rdd.feature.CoverageRDD
import org.bdgenomics.adam.rdd.read.realignment.RealignIndels
import org.bdgenomics.adam.rdd.read.recalibration.BaseQualityRecalibration
import org.bdgenomics.adam.rdd.fragment.FragmentRDD
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2 changes: 1 addition & 1 deletion .../adam/rdd/features/CoverageRDDSuite.scala → ...s/adam/rdd/feature/CoverageRDDSuite.scala
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Expand Up @@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.rdd.features
package org.bdgenomics.adam.rdd.feature

import org.apache.parquet.filter2.dsl.Dsl._
import org.bdgenomics.adam.models.{
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2 changes: 1 addition & 1 deletion ...s/adam/rdd/features/FeatureRDDSuite.scala → ...cs/adam/rdd/feature/FeatureRDDSuite.scala
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Expand Up @@ -15,7 +15,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.rdd.features
package org.bdgenomics.adam.rdd.feature

import com.google.common.collect.ImmutableMap
import java.io.File
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2 changes: 1 addition & 1 deletion adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala
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Expand Up @@ -28,7 +28,7 @@ import org.bdgenomics.adam.models.{
}
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.TestSaveArgs
import org.bdgenomics.adam.rdd.features.CoverageRDD
import org.bdgenomics.adam.rdd.feature.CoverageRDD
import org.bdgenomics.adam.rdd.variation.{
VariantContextRDD,
VCFOutFormatter
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