{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/42157217","id":42157217,"diff_hunk":"@@ -0,0 +1,280 @@\n+package org.broadinstitute.hellbender.engine.dataflow.transforms.composite;\n+\n+import com.google.api.services.storage.Storage;\n+import com.google.cloud.dataflow.sdk.transforms.SerializableFunction;\n+import com.google.cloud.genomics.dataflow.readers.bam.BAMIO;\n+\n+import htsjdk.samtools.SAMRecord;\n+import htsjdk.samtools.SAMRecordIterator;\n+import htsjdk.samtools.SamReader;\n+import htsjdk.samtools.SamReaderFactory;\n+import htsjdk.samtools.ValidationStringency;\n+import org.apache.logging.log4j.Logger;\n+import org.apache.logging.log4j.LogManager;\n+import org.apache.spark.api.java.function.FlatMapFunction;\n+import org.broadinstitute.hellbender.engine.ReadContextData;\n+import org.broadinstitute.hellbender.engine.ContextShard;\n+import org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource;\n+import org.broadinstitute.hellbender.engine.filters.ReadFilter;\n+import org.broadinstitute.hellbender.engine.spark.AuthHolder;\n+import org.broadinstitute.hellbender.exceptions.GATKException;\n+import org.broadinstitute.hellbender.utils.IntervalUtils;\n+import org.broadinstitute.hellbender.utils.SimpleInterval;\n+import org.broadinstitute.hellbender.utils.collections.IntervalsSkipList;\n+import org.broadinstitute.hellbender.utils.gcs.BucketUtils;\n+import org.broadinstitute.hellbender.utils.read.GATKRead;\n+import org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter;\n+import org.broadinstitute.hellbender.utils.reference.ReferenceBases;\n+import org.broadinstitute.hellbender.utils.variant.Variant;\n+\n+\n+import java.io.File;\n+import java.io.IOException;\n+import java.io.Serializable;\n+import java.security.GeneralSecurityException;\n+import java.util.ArrayList;\n+import java.util.Iterator;\n+import java.util.List;\n+import java.util.NoSuchElementException;\n+\n+\n+public final class AddContextDataToReadOptimizedFn implements Serializable{\n+    private static final long serialVersionUID = 1L;\n+\n+    /**\n+     * Fill in reads that start in the given shard, and subshard the output to the requested size.\n+     * Signals an error if any read sticks out more than \"margin\" outside of the big shard.\n+     * Optionally filters the reads to only keep the ones that satisfy the given predicate.\n+     *\n+     * Hadoop paths aren't yet supported.\n+     *\n+     *   _   _  ____ _______ ______\n+     *  | \\ | |/ __ \\__   __|  ____|\n+     *  |  \\| | |  | | | |  | |__\n+     *  | . ` | |  | | | |  |  __|\n+     *  | |\\  | |__| | | |  | |____\n+     *  |_| \\_|\\____/  |_|  |______| (important):\n+     *\n+     * The reads are stored without the header.\n+     *\n+     * @param bam URL to the reads\n+     * @param outputShardSize subsharding size\n+     * @param margin throw an exception if any read sticks out beyond the margin\n+     * @param optFilter if specified, only reads that satisfy this will be included.\n+     * @return A DoFn that acts as described above.\n+     * @throws IOException\n+     */\n+    public static FlatMapFunction<ContextShard,ContextShard> subdivideAndFillReads(String bam, AuthHolder auth, int outputShardSize, int margin, final ReadFilter optFilter) throws IOException {\n+            return new FlatMapFunction<ContextShard, ContextShard>() {\n+                private static final long serialVersionUID = 1L;\n+                @Override\n+                public Iterable<ContextShard> call(ContextShard contextShard) throws Exception {\n+                    final SubdivideAndFillReadsIterator iterator = new SubdivideAndFillReadsIterator(bam, auth, outputShardSize, margin, optFilter, contextShard);\n+                    return new Iterable<ContextShard>() {\n+                        @Override\n+                        public Iterator<ContextShard> iterator() {\n+                            try {\n+                                return new SubdivideAndFillReadsIterator(bam, auth, outputShardSize, margin, optFilter, contextShard);\n+                            } catch (Exception x) {\n+                                throw new RuntimeException(x);\n+                            }\n+                        }\n+                    };\n+                }\n+            };\n+    }\n+\n+    /**\n+     * Given a shard that has reads and variants, query Google Genomics' Reference server and get reference info\n+     * (including an extra margin on either side), and fill that and the correct variants into readContext.\n+     */\n+    public static ContextShard fillContext(ReferenceMultiSource refSource, ContextShard shard) {\n+        if (null==shard) return null;\n+        // use the function to make sure we get the exact correct amount of reference bases\n+        int start = Integer.MAX_VALUE;\n+        int end = Integer.MIN_VALUE;\n+        SerializableFunction<GATKRead, SimpleInterval> referenceWindowFunction = refSource.getReferenceWindowFunction();\n+        for (GATKRead r : shard.reads) {\n+            SimpleInterval readRefs = referenceWindowFunction.apply(r);\n+            start = Math.min(readRefs.getStart(), start);\n+            end = Math.max(readRefs.getEnd(), end);\n+        }\n+\n+        if (start==Integer.MAX_VALUE) {\n+            // there are no reads in this shard, so we're going to remove it\n+            return null;\n+        }\n+\n+        SimpleInterval refInterval = new SimpleInterval(shard.interval.getContig(), start, end);\n+        ReferenceBases refBases;\n+        try {\n+            refBases = refSource.getReferenceBases(null, refInterval);\n+        } catch (IOException x) {\n+            throw new GATKException(\"Unable to read the reference\");\n+        }\n+\n+        ArrayList<ReadContextData> readContext = new ArrayList<>();\n+        for (GATKRead r : shard.reads) {\n+            SimpleInterval readInterval = new SimpleInterval(r);\n+            ArrayList<Variant> variantsOverlappingThisRead = shard.variantsOverlapping(readInterval);\n+            // we pass all the bases. That's better because this way it's just a shared\n+            // pointer instead of being an array copy. Downstream processing is fine with having\n+            // extra bases (it expects a few, actually).\n+            readContext.add(new ReadContextData(refBases, variantsOverlappingThisRead));\n+        }\n+        return shard.withReadContext(readContext);\n+    }\n+\n+    protected static final class SubdivideAndFillReadsIterator implements Iterator<ContextShard>, Serializable {\n+        private static final long serialVersionUID = 1L;\n+        private static final Logger log = LogManager.getLogger(SubdivideAndFillReadsIterator.class);\n+        private final transient SamReader reader;\n+        private final transient SAMRecordIterator query;\n+        private final ContextShard shard;\n+        private final String bam;\n+        private final ReadFilter optFilter;\n+        private final int lastValidPos;\n+        private final int firstValidPos;\n+        private final List<SimpleInterval> subshards;\n+        private int currentSubShardIndex;\n+        private ArrayList<GATKRead> readsSoFar = new ArrayList<>();\n+        private Storage.Objects storageClient = null;\n+        private SimpleInterval currentSubShard;\n+        private ContextShard nextOutput = null;\n+        private boolean readerClosed = false;\n+        private int outputCount;\n+\n+        public SubdivideAndFillReadsIterator(String bam, AuthHolder auth, int outputShardSize, int margin, final ReadFilter optFilter, ContextShard shard) throws IOException, GeneralSecurityException, ClassNotFoundException {\n+            this.bam = bam;\n+            this.shard = shard;\n+            this.optFilter = optFilter;\n+            lastValidPos = shard.interval.getEnd() + margin;\n+            firstValidPos = shard.interval.getStart() - margin;\n+            ArrayList<SimpleInterval> ints =new ArrayList<>();\n+            ints.add(shard.interval);\n+            subshards = IntervalUtils.cutToShards(ints, outputShardSize);\n+            currentSubShardIndex = 0;\n+            currentSubShard = subshards.get(currentSubShardIndex);\n+\n+            if (BucketUtils.isCloudStorageUrl(bam)) {\n+                storageClient = auth.makeStorageClient();\n+                reader = BAMIO.openBAM(storageClient, bam, ValidationStringency.SILENT);\n+            } else if (BucketUtils.isHadoopUrl(bam)) {\n+                throw new RuntimeException(\"Sorry, Hadoop paths aren't yet supported\");","path":"src/main/java/org/broadinstitute/hellbender/engine/dataflow/transforms/composite/AddContextDataToReadOptimizedFn.java","position":163,"original_position":163,"commit_id":"83deaa7a5f2bac45869060395707b0bd6f5c4f32","original_commit_id":"83deaa7a5f2bac45869060395707b0bd6f5c4f32","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"body":"Ouch! This is the cost we pay for bypassing `ReadsSparkSource`...but ok for now.","created_at":"2015-10-15T17:54:21Z","updated_at":"2015-10-15T17:54:21Z","html_url":"https://github.com/broadinstitute/gatk/pull/987#discussion_r42157217","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/987","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/42157217"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/987#discussion_r42157217"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/987"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/987","id":47217863,"html_url":"https://github.com/broadinstitute/gatk/pull/987","diff_url":"https://github.com/broadinstitute/gatk/pull/987.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/987.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/987","number":987,"state":"open","locked":false,"title":"Spark Optimized BaseRecalibrator","user":{"login":"jean-philippe-martin","id":10458949,"avatar_url":"https://avatars.githubusercontent.com/u/10458949?v=3","gravatar_id":"","url":"https://api.github.com/users/jean-philippe-martin","html_url":"https://github.com/jean-philippe-martin","followers_url":"https://api.github.com/users/jean-philippe-martin/followers","following_url":"https://api.github.com/users/jean-philippe-martin/following{/other_user}","gists_url":"https://api.github.com/users/jean-philippe-martin/gists{/gist_id}","starred_url":"https://api.github.com/users/jean-philippe-martin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jean-philippe-martin/subscriptions","organizations_url":"https://api.github.com/users/jean-philippe-martin/orgs","repos_url":"https://api.github.com/users/jean-philippe-martin/repos","events_url":"https://api.github.com/users/jean-philippe-martin/events{/privacy}","received_events_url":"https://api.github.com/users/jean-philippe-martin/received_events","type":"User","site_admin":false},"body":"This code (building off of Louis' fixes) adds the following:\r\n\r\n * AuthHolder, a replacement for the PipelineOptions. It stores the authentication info we need for GCS and supports both API_KEY and client-secrets.json. I adapted a few classes to accept an AuthHolder.\r\n\r\n * BaseRecalibratorOptimizedSpark, a port of the \"shard\" approach I first did on the Dataflow side. Note that currently this code only performs reasonably for small inputs if you specify -L on the command line (for large inputs it doesn't matter).\r\n\r\n","created_at":"2015-10-08T23:10:13Z","updated_at":"2015-10-15T17:54:21Z","closed_at":null,"merged_at":null,"merge_commit_sha":"209aec48d88ee310c5b50a4129339eb98111356c","assignee":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/987/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/987/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/987/comments","statuses_url":"https://api.github.com/repos/broadinstitute/gatk/statuses/83deaa7a5f2bac45869060395707b0bd6f5c4f32","head":{"label":"broadinstitute:jp_spark_br","ref":"jp_spark_br","sha":"83deaa7a5f2bac45869060395707b0bd6f5c4f32","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":27452807,"name":"gatk","full_name":"broadinstitute/gatk","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/gatk","description":"GATK4 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