{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/39581506","id":39581506,"diff_hunk":"@@ -8,26 +8,37 @@\n import org.apache.hadoop.conf.Configuration;\n import org.apache.hadoop.fs.Path;\n import org.apache.hadoop.io.LongWritable;\n+import org.apache.hadoop.mapreduce.Job;\n+import org.apache.parquet.avro.AvroParquetInputFormat;\n import org.apache.spark.api.java.JavaPairRDD;\n import org.apache.spark.api.java.JavaRDD;\n import org.apache.spark.api.java.JavaSparkContext;\n+import org.apache.spark.api.java.function.Function;\n+import org.apache.spark.broadcast.Broadcast;\n+import org.bdgenomics.adam.models.SAMFileHeaderWritable;\n+import org.bdgenomics.formats.avro.AlignmentRecord;\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.read.BDGAlignmentRecordToGATKReadAdapter;\n import org.broadinstitute.hellbender.utils.read.GATKRead;\n import org.broadinstitute.hellbender.utils.read.GoogleGenomicsReadToGATKReadAdapter;\n import org.seqdoop.hadoop_bam.AnySAMInputFormat;\n import org.seqdoop.hadoop_bam.SAMRecordWritable;\n import org.seqdoop.hadoop_bam.util.SAMHeaderReader;\n+import scala.Tuple2;\n \n import java.io.IOException;\n+import java.io.Serializable;\n import java.util.List;\n \n /** Loads the reads from disk either serially (using samReaderFactory) or in parallel using Hadoop-BAM.\n  * The parallel code is a modified version of the example writing code from Hadoop-BAM.\n  */\n-public class ReadsSparkSource {\n-    private final JavaSparkContext ctx;\n+public class ReadsSparkSource implements Serializable 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is adding Serializable necessary?","created_at":"2015-09-16T00:08:38Z","updated_at":"2015-09-16T00:08:38Z","html_url":"https://github.com/broadinstitute/hellbender/pull/888#discussion_r39581506","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/888","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/39581506"},"html":{"href":"https://github.com/broadinstitute/hellbender/pull/888#discussion_r39581506"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/888"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/888","id":44737066,"html_url":"https://github.com/broadinstitute/hellbender/pull/888","diff_url":"https://github.com/broadinstitute/hellbender/pull/888.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/888.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/888","number":888,"state":"open","locked":false,"title":"Initial ADAM Parquet I/O support","user":{"login":"laserson","id":118141,"avatar_url":"https://avatars.githubusercontent.com/u/118141?v=3","gravatar_id":"","url":"https://api.github.com/users/laserson","html_url":"https://github.com/laserson","followers_url":"https://api.github.com/users/laserson/followers","following_url":"https://api.github.com/users/laserson/following{/other_user}","gists_url":"https://api.github.com/users/laserson/gists{/gist_id}","starred_url":"https://api.github.com/users/laserson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/laserson/subscriptions","organizations_url":"https://api.github.com/users/laserson/orgs","repos_url":"https://api.github.com/users/laserson/repos","events_url":"https://api.github.com/users/laserson/events{/privacy}","received_events_url":"https://api.github.com/users/laserson/received_events","type":"User","site_admin":false},"body":"Add support for reading/writing Parquet via ADAM/BDG `AlignmentRecord` type.\r\n\r\nNot 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merge.","created_at":"2015-09-11T01:06:20Z","updated_at":"2015-09-16T00:08:38Z","closed_at":null,"merged_at":null,"merge_commit_sha":"82b369ad7d5cbf1a8fefa55d85873271514b5e71","assignee":{"login":"davidadamsphd","id":12084283,"avatar_url":"https://avatars.githubusercontent.com/u/12084283?v=3","gravatar_id":"","url":"https://api.github.com/users/davidadamsphd","html_url":"https://github.com/davidadamsphd","followers_url":"https://api.github.com/users/davidadamsphd/followers","following_url":"https://api.github.com/users/davidadamsphd/following{/other_user}","gists_url":"https://api.github.com/users/davidadamsphd/gists{/gist_id}","starred_url":"https://api.github.com/users/davidadamsphd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidadamsphd/subscriptions","organizations_url":"https://api.github.com/users/davidadamsphd/orgs","repos_url":"https://api.github.com/users/davidadamsphd/repos","events_url":"https://api.github.com/users/davidadamsphd/events{/privacy}","received_events_url":"https://api.github.com/users/davidadamsphd/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/888/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/888/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/888/comments","statuses_url":"https://api.github.com/repos/broadinstitute/hellbender/statuses/55b7f59d4cbc04968ef6ee1d606cf35ff3a46ac3","head":{"label":"broadinstitute:ul_parquet_io","ref":"ul_parquet_io","sha":"55b7f59d4cbc04968ef6ee1d606cf35ff3a46ac3","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":"hellbender","full_name":"broadinstitute/hellbender","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/hellbender","description":"GATK4 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