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Initial Spark dataflow commit, basic skeleton with some tests.
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86 changes: 86 additions & 0 deletions
86
src/main/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSpark.java
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| package org.broadinstitute.hellbender.engine.spark; | ||
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| import com.google.common.collect.Iterables; | ||
| import com.google.common.collect.Lists; | ||
| import org.apache.spark.api.java.JavaPairRDD; | ||
| import org.apache.spark.api.java.JavaRDD; | ||
| import org.broadinstitute.hellbender.engine.dataflow.datasources.ReadContextData; | ||
| import org.broadinstitute.hellbender.engine.dataflow.datasources.ReferenceDataflowSource; | ||
| import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
| import org.broadinstitute.hellbender.utils.reference.ReferenceBases; | ||
| import org.broadinstitute.hellbender.utils.variant.Variant; | ||
| import scala.Tuple2; | ||
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| import java.util.List; | ||
| import java.util.Map; | ||
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| /** | ||
| * AddContextDataToRead pairs reference bases and overlapping variants with each GATKRead in the PCollection input. | ||
| * The variants are obtained from a local file (later a GCS Bucket). The reference bases come from the Google Genomics API. | ||
| * | ||
| * This transform is intended for direct use in pipelines. | ||
| * | ||
| * The reference bases paired with each read can be customized by passing in a reference window function | ||
| * inside the {@link ReferenceDataflowSource} argument to {@link #add}. See | ||
| * {@link org.broadinstitute.hellbender.engine.dataflow.datasources.RefWindowFunctions} for examples. | ||
| */ | ||
| public class AddContextDataToReadSpark { | ||
| public static JavaPairRDD<GATKRead, ReadContextData> add( | ||
| final JavaRDD<GATKRead> reads, final ReferenceDataflowSource referenceDataflowSource, | ||
| final JavaRDD<Variant> variants) { | ||
| // Join Reads and Variants, Reads and ReferenceBases | ||
| JavaPairRDD<GATKRead, Iterable<Variant>> readiVariants = JoinReadsWithVariants.join(reads, variants); | ||
| JavaPairRDD<GATKRead, ReferenceBases> readRefBases = JoinReadsWithRefBases.addBases(referenceDataflowSource, reads); | ||
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| // For testing we want to know that the reads from the KVs coming back from JoinReadsWithVariants.Join | ||
| // and JoinReadsWithRefBases.Pair are the same reads from "reads". | ||
| boolean assertsEnabled = false; | ||
| assert assertsEnabled = true; // Intentional side-effect!!! | ||
| // Now assertsEnabled is set to the correct value | ||
| if (assertsEnabled) { | ||
| assertSameReads(reads, readRefBases, readiVariants); | ||
| } | ||
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| JavaPairRDD<GATKRead, Tuple2<Iterable<Iterable<Variant>>, Iterable<ReferenceBases>>> cogroup = readiVariants.cogroup(readRefBases); | ||
| return cogroup.mapToPair(in -> { | ||
| List<Iterable<Variant>> liVariants = Lists.newArrayList(in._2()._1()); | ||
| List<Variant> lVariants = Lists.newArrayList(); | ||
| if (!liVariants.isEmpty()) { | ||
| final Iterable<Variant> iVariant = Iterables.getOnlyElement(in._2()._1()); | ||
| // It's possible for the iVariant to contain only a null variant, we don't | ||
| // want to add that to the ReadContextData. | ||
| final Variant next = iVariant.iterator().next(); | ||
| if (next != null) { | ||
| lVariants = Lists.newArrayList(iVariant); | ||
| } | ||
| } | ||
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| ReferenceBases refBases = Iterables.getOnlyElement(in._2()._2()); | ||
| ReadContextData readContextData = new ReadContextData(refBases, lVariants); | ||
| return new Tuple2<>(in._1(), readContextData); | ||
| }); | ||
| } | ||
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| private static void assertSameReads(final JavaRDD<GATKRead> reads, | ||
| final JavaPairRDD<GATKRead, ReferenceBases> readRefBases, | ||
| final JavaPairRDD<GATKRead, Iterable<Variant>> readiVariants) { | ||
| List<GATKRead> vReads = reads.collect(); | ||
| Map<GATKRead, ReferenceBases> vReadRef = readRefBases.collectAsMap(); | ||
| Map<GATKRead, Iterable<Variant>> vReadVariant = readiVariants.collectAsMap(); | ||
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| // This assumes all rdds doesn't have any duplicates. | ||
| JavaRDD<GATKRead> refBasesReads = readRefBases.keys(); | ||
| JavaRDD<GATKRead> variantsReads = readiVariants.keys(); | ||
| JavaRDD<GATKRead> distinctReads = reads.intersection(refBasesReads).intersection(variantsReads); | ||
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| long counts = reads.count(); | ||
| assert counts == distinctReads.count(); | ||
| assert counts == refBasesReads.count(); | ||
| assert counts == variantsReads.count(); | ||
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| assert vReadRef.size() == vReads.size(); | ||
| assert vReadVariant.size() == vReads.size(); | ||
| } | ||
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| } | ||
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27
src/main/java/org/broadinstitute/hellbender/engine/spark/GATKRegistrator.java
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| package org.broadinstitute.hellbender.engine.spark; | ||
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| import com.esotericsoftware.kryo.Kryo; | ||
| import com.google.api.services.genomics.model.Read; | ||
| import de.javakaffee.kryoserializers.UnmodifiableCollectionsSerializer; | ||
| import org.apache.spark.serializer.KryoRegistrator; | ||
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| import java.util.Collections; | ||
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| /** | ||
| * GATKRegistrator registers Serializers for our project. We need a JsonSerializer for the Google Genomics classes | ||
| * and UnmodifiableCollectionsSerializer from a bug in the version of Kryo we're on. | ||
| */ | ||
| public class GATKRegistrator implements KryoRegistrator { | ||
| @SuppressWarnings("unchecked") | ||
| @Override | ||
| public void registerClasses(Kryo kryo) { | ||
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| // JsonSerializer is needed for the Google Genomics classes like Read and Reference. | ||
| kryo.register(Read.class, new JsonSerializer<Read>()); | ||
| // htsjdk.variant.variantcontext.CommonInfo has a Map<String, Object> that defaults to | ||
| // a Collections.unmodifiableMap. This can't be handled by the version of kryo used in Spark, it's fixed | ||
| // in newer versions, but we can't use those because of incompatibility with Spark. We just include the fix | ||
| // here. | ||
| kryo.register(Collections.unmodifiableMap(Collections.EMPTY_MAP).getClass(), new UnmodifiableCollectionsSerializer()); | ||
| } | ||
| } |
74 changes: 74 additions & 0 deletions
74
src/main/java/org/broadinstitute/hellbender/engine/spark/JoinReadsWithRefBases.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| package org.broadinstitute.hellbender.engine.spark; | ||
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| import com.google.common.collect.Lists; | ||
| import org.apache.spark.api.java.JavaPairRDD; | ||
| import org.apache.spark.api.java.JavaRDD; | ||
| import org.broadinstitute.hellbender.engine.dataflow.datasources.ReferenceDataflowSource; | ||
| import org.broadinstitute.hellbender.engine.dataflow.datasources.ReferenceShard; | ||
| import org.broadinstitute.hellbender.utils.SimpleInterval; | ||
| import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
| import org.broadinstitute.hellbender.utils.reference.ReferenceBases; | ||
| import scala.Tuple2; | ||
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| import java.util.List; | ||
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| /** | ||
| * RefBasesForReads queries the Google Genomics API for reference bases overlapping all of the reads. | ||
| * | ||
| * step 1: key reads by reference shards | ||
| * | ||
| * |--------- shard 0 ----------|---------- shard 1 ----------|--------- shard 2 ----------|--------- shard 3 ----------| | ||
| * |------ read a -----| |-- read b --| |---- read c ----| | ||
| * | ||
| * step 2: group reads by the shard they start in | ||
| * | ||
| * |--------- shard 0 ----------| | ||
| * |------ read a -----| | ||
| * | ||
| * | ||
| * |--------- shard 2 ----------| | ||
| * |-- read b --| |---- read c ----| | ||
| * | ||
| * step 3: query the Google Genomics API for all bases needed for each shard | ||
| * | ||
| * |--- ref bases 1 ---| |--------- ref bases 2 -----------| | ||
| * |------ read a -----| |-- read b --| |---- read c ----| | ||
| * | ||
| * step 4: pair the ref bases needed for each read with the read | ||
| * | ||
| * |------ read a -----| |-- read b --| |---- read c ----| | ||
| * |-- ref bases 1a ---| |ref bases 2b| |- ref bases 2c -| | ||
| * | ||
| * or in code, | ||
| * KV<read a, ref bases 1a> | ||
| * KV<read b, ref bases 2b> | ||
| * KV<read c, ref bases 2c> | ||
| * | ||
| * The reference bases paired with each read can be customized by passing in a reference window function | ||
| * inside the {@link ReferenceDataflowSource} argument to {@link #addBases}. See {@link org.broadinstitute.hellbender.engine.dataflow.datasources.RefWindowFunctions} for examples. | ||
| */ | ||
| public class JoinReadsWithRefBases { | ||
| public static JavaPairRDD<GATKRead, ReferenceBases> addBases(final ReferenceDataflowSource referenceDataflowSource, | ||
| final JavaRDD<GATKRead> reads) { | ||
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| JavaPairRDD<ReferenceShard, GATKRead> shardRead = reads.mapToPair(gatkRead -> { | ||
| ReferenceShard shard = ReferenceShard.getShardNumberFromInterval(gatkRead); | ||
| return new Tuple2<>(shard, gatkRead); | ||
| }); | ||
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| JavaPairRDD<ReferenceShard, Iterable<GATKRead>> shardiRead = shardRead.groupByKey(); | ||
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| return shardiRead.flatMapToPair(in -> { | ||
| List<Tuple2<GATKRead, ReferenceBases>> out = Lists.newArrayList(); | ||
| Iterable<GATKRead> iReads = in._2(); | ||
| SimpleInterval interval = SimpleInterval.getSpanningInterval(iReads); | ||
| ReferenceBases bases = referenceDataflowSource.getReferenceBases(null, interval); | ||
| for (GATKRead r : iReads) { | ||
| final ReferenceBases subset = bases.getSubset(new SimpleInterval(r)); | ||
| out.add(new Tuple2<>(r, subset)); | ||
| } | ||
| return out; | ||
| }); | ||
| } | ||
| } |
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