Register read, sequence, and slice schema records

adam-core/src/main/scala/org/bdgenomics/adam/projections/ReadField.scala

@@ -0,0 +1,28 @@
+/**
+ * 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.adam.projections
+
+import org.bdgenomics.formats.avro.Read
+
+/**
+ * Enumeration of Read field names for predicates and projections.
+ */
+object ReadField extends FieldEnumeration(Read.SCHEMA$) {
+
+  val name, description, alphabet, sequence, length, qualityScores, qualityScoreVariant = SchemaValue
+}

adam-core/src/main/scala/org/bdgenomics/adam/projections/SequenceField.scala

@@ -0,0 +1,28 @@
+/**
+ * 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.adam.projections
+
+import org.bdgenomics.formats.avro.Sequence
+
+/**
+ * Enumeration of Sequence field names for predicates and projections.
+ */
+object SequenceField extends FieldEnumeration(Sequence.SCHEMA$) {
+
+  val name, description, alphabet, sequence, length = SchemaValue
+}

adam-core/src/main/scala/org/bdgenomics/adam/projections/SliceField.scala

@@ -0,0 +1,28 @@
+/**
+ * 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.adam.projections
+
+import org.bdgenomics.formats.avro.Slice
+
+/**
+ * Enumeration of Slice field names for predicates and projections.
+ */
+object SliceField extends FieldEnumeration(Slice.SCHEMA$) {
+
+  val name, description, alphabet, sequence, start, end, strand, length = SchemaValue
+}

adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala

@@ -197,10 +197,16 @@ class ADAMKryoRegistrator extends KryoRegistrator {
       new AvroSerializer[org.bdgenomics.formats.avro.NucleotideContigFragment])
     kryo.register(classOf[org.bdgenomics.formats.avro.OntologyTerm],
       new AvroSerializer[org.bdgenomics.formats.avro.OntologyTerm])
+    kryo.register(classOf[org.bdgenomics.formats.avro.Read],
+      new AvroSerializer[org.bdgenomics.formats.avro.Read])
     kryo.register(classOf[org.bdgenomics.formats.avro.RecordGroupMetadata],
       new AvroSerializer[org.bdgenomics.formats.avro.RecordGroupMetadata])
     kryo.register(classOf[org.bdgenomics.formats.avro.Sample],
       new AvroSerializer[org.bdgenomics.formats.avro.Sample])
+    kryo.register(classOf[org.bdgenomics.formats.avro.Sequence],
+      new AvroSerializer[org.bdgenomics.formats.avro.Sequence])
+    kryo.register(classOf[org.bdgenomics.formats.avro.Slice],
+      new AvroSerializer[org.bdgenomics.formats.avro.Slice])
     kryo.register(classOf[org.bdgenomics.formats.avro.Strand])
     kryo.register(classOf[org.bdgenomics.formats.avro.TranscriptEffect],
       new AvroSerializer[org.bdgenomics.formats.avro.TranscriptEffect])
@@ -229,8 +235,11 @@ class ADAMKryoRegistrator extends KryoRegistrator {
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.GenotypeAllele]])
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.OntologyTerm]])
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.NucleotideContigFragment]])
+    kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.Read]])
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.RecordGroupMetadata]])
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.Sample]])
+    kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.Sequence]])
+    kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.Slice]])
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.TranscriptEffect]])
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.Variant]])
     kryo.register(classOf[scala.Array[org.bdgenomics.formats.avro.VariantAnnotation]])

adam-core/src/test/scala/org/bdgenomics/adam/projections/ReadFieldSuite.scala

@@ -0,0 +1,66 @@
+/**
+ * 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.adam.projections
+
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.adam.projections.ReadField._
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.adam.rdd.TestSaveArgs
+import org.bdgenomics.adam.util.ADAMFunSuite
+import org.bdgenomics.formats.avro.{
+  Alphabet,
+  QualityScoreVariant,
+  Read
+}
+
+class ReadFieldSuite extends ADAMFunSuite {
+
+  sparkTest("Use projection when reading parquet reads") {
+    val path = tmpFile("reads.parquet")
+    val rdd = sc.parallelize(Seq(Read.newBuilder()
+      .setName("read 1")
+      .setDescription("read 1")
+      .setAlphabet(Alphabet.DNA)
+      .setSequence("ACTG")
+      .setLength(4)
+      .setQualityScores("0123")
+      .setQualityScoreVariant(QualityScoreVariant.FASTQ_SANGER)
+      .build()))
+    rdd.saveAsParquet(TestSaveArgs(path))
+
+    val projection = Projection(
+      name,
+      description,
+      alphabet,
+      sequence,
+      length,
+      qualityScores,
+      qualityScoreVariant
+    )
+
+    val reads: RDD[Read] = sc.loadParquet(path, projection = Some(projection))
+    assert(reads.count() === 1)
+    assert(reads.first.getName === "read 1")
+    assert(reads.first.getDescription === "read 1")
+    assert(reads.first.getAlphabet === Alphabet.DNA)
+    assert(reads.first.getSequence === "ACTG")
+    assert(reads.first.getLength === 4)
+    assert(reads.first.getQualityScores === "0123")
+    assert(reads.first.getQualityScoreVariant === QualityScoreVariant.FASTQ_SANGER)
+  }
+}

adam-core/src/test/scala/org/bdgenomics/adam/projections/SequenceFieldSuite.scala

@@ -0,0 +1,56 @@
+/**
+ * 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.adam.projections
+
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.adam.projections.SequenceField._
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.adam.rdd.TestSaveArgs
+import org.bdgenomics.adam.util.ADAMFunSuite
+import org.bdgenomics.formats.avro.{ Alphabet, Sequence }
+
+class SequenceFieldSuite extends ADAMFunSuite {
+
+  sparkTest("Use projection when reading parquet sequences") {
+    val path = tmpFile("sequences.parquet")
+    val rdd = sc.parallelize(Seq(Sequence.newBuilder()
+      .setName("6")
+      .setDescription("Chromosome 6")
+      .setAlphabet(Alphabet.DNA)
+      .setSequence("ACTG")
+      .setLength(4)
+      .build()))
+    rdd.saveAsParquet(TestSaveArgs(path))
+
+    val projection = Projection(
+      name,
+      description,
+      alphabet,
+      sequence,
+      length
+    )
+
+    val sequences: RDD[Sequence] = sc.loadParquet(path, projection = Some(projection));
+    assert(sequences.count() === 1)
+    assert(sequences.first.getName === "6")
+    assert(sequences.first.getDescription === "Chromosome 6")
+    assert(sequences.first.getAlphabet === Alphabet.DNA)
+    assert(sequences.first.getSequence === "ACTG")
+    assert(sequences.first.getLength === 4)
+  }
+}

adam-core/src/test/scala/org/bdgenomics/adam/projections/SliceFieldSuite.scala

@@ -0,0 +1,69 @@
+/**
+ * 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.adam.projections
+
+import org.apache.spark.rdd.RDD
+import org.bdgenomics.adam.projections.SliceField._
+import org.bdgenomics.adam.rdd.ADAMContext._
+import org.bdgenomics.adam.rdd.TestSaveArgs
+import org.bdgenomics.adam.util.ADAMFunSuite
+import org.bdgenomics.formats.avro.{
+  Alphabet,
+  Slice,
+  Strand
+}
+
+class SliceFieldSuite extends ADAMFunSuite {
+
+  sparkTest("Use projection when reading parquet slices") {
+    val path = tmpFile("slices.parquet")
+    val rdd = sc.parallelize(Seq(Slice.newBuilder()
+      .setName("6")
+      .setDescription("Chromosome 6")
+      .setAlphabet(Alphabet.DNA)
+      .setSequence("ACTG")
+      .setStart(0)
+      .setEnd(4)
+      .setStrand(Strand.FORWARD)
+      .setLength(4)
+      .build()))
+    rdd.saveAsParquet(TestSaveArgs(path))
+
+    val projection = Projection(
+      name,
+      description,
+      alphabet,
+      sequence,
+      start,
+      end,
+      strand,
+      length
+    )
+
+    val slices: RDD[Slice] = sc.loadParquet(path, projection = Some(projection));
+    assert(slices.count() === 1)
+    assert(slices.first.getName === "6")
+    assert(slices.first.getDescription === "Chromosome 6")
+    assert(slices.first.getAlphabet === Alphabet.DNA)
+    assert(slices.first.getSequence === "ACTG")
+    assert(slices.first.getStart === 0)
+    assert(slices.first.getEnd === 4)
+    assert(slices.first.getStrand === Strand.FORWARD)
+    assert(slices.first.getLength === 4)
+  }
+}