{"action":"opened","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1247","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1247/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1247/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1247/events","html_url":"https://github.com/broadinstitute/gatk/issues/1247","id":120323675,"number":1247,"title":"Hadoop-bam 7.3.0 incompatible with htsjdk 2.0.0 (?) Breaks on CRAM","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-12-04T03:20:26Z","updated_at":"2015-12-04T03:20:26Z","closed_at":null,"body":"I get this on my branch `ak_spark_cram` when trying to read a cram file on spark - see `ReadsSparkSourceUnitTest`\r\n\r\nIt seems that the constructor that Hadoop-bam was using is now gone and so it fails with `NoSuchMethodError`\r\n\r\n```\r\njava.lang.NoSuchMethodError: htsjdk.samtools.CRAMIterator.<init>(Lhtsjdk/samtools/seekablestream/SeekableStream;Lhtsjdk/samtools/cram/ref/ReferenceSource;[J)V\r\n\tat org.seqdoop.hadoop_bam.CRAMRecordReader.initialize(CRAMRecordReader.java:51)\r\n\tat org.seqdoop.hadoop_bam.CRAMInputFormat.createRecordReader(CRAMInputFormat.java:83)\r\n\tat org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:131)\r\n\tat org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:104)\r\n\r\n```\r\n\r\n@cmnbroad can you help?"}}