{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/791","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/791/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/791/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/791/events","html_url":"https://github.com/broadinstitute/hellbender/issues/791","id":99695487,"number":791,"title":"Fix java.lang.VerifyError: Bad type on operand stack","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},"labels":[{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/BestPracticesPipeline","name":"BestPracticesPipeline","color":"006b75"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/broadinstitute/hellbender/milestones/5","html_url":"https://github.com/broadinstitute/hellbender/milestones/alpha","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/milestones/5/labels","id":1220227,"number":5,"title":"alpha","description":"","creator":{"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},"open_issues":83,"closed_issues":20,"state":"open","created_at":"2015-07-22T13:37:37Z","updated_at":"2015-08-07T18:21:20Z","due_on":"2015-10-31T04:00:00Z","closed_at":null},"comments":2,"created_at":"2015-08-07T17:44:40Z","updated_at":"2015-08-07T19:34:38Z","closed_at":null,"body":"When [ReadsDataflowSource.getReadPCollection](https://github.com/broadinstitute/hellbender/blob/master/src/main/java/org/broadinstitute/hellbender/engine/dataflow/datasources/ReadsDataflowSource.java#L129) calls Google Dataflow's [ReadBAMTransform.getReadsFromBAMFilesSharded](https://github.com/googlegenomics/dataflow-java/blob/master/src/main/java/com/google/cloud/genomics/dataflow/readers/bam/ReadBAMTransform.java#L104) we get a **java.lang.VerifyError**. The full error looks like this:\r\n\r\n````\r\nException in thread \"main\" java.lang.VerifyError: Bad type on operand stack\r\nException Details:\r\n  Location:\r\n    com/google/cloud/genomics/dataflow/readers/bam/ReadBAMTransform.getReadsFromBAMFilesSharded(Lcom/google/cloud/dataflow/sdk/Pipeline;Lcom/google/cloud/genomics/utils/GenomicsFactory$OfflineAuth;Ljava/lang/Iterable;Lcom/google/cloud/genomics/dataflow/readers/bam/ReaderOptions;Ljava/util/List;)Lcom/google/cloud/dataflow/sdk/values/PCollection; @25: invokevirtual\r\n  Reason:\r\n    Type 'com/google/cloud/dataflow/sdk/transforms/Create' (current frame, stack[2]) is not assignable to 'com/google/cloud/dataflow/sdk/transforms/PTransform'\r\n  Current Frame:\r\n    bci: @25\r\n    flags: { }\r\n    locals: { 'com/google/cloud/dataflow/sdk/Pipeline', 'com/google/cloud/genomics/utils/GenomicsFactory$OfflineAuth', 'java/lang/Iterable', 'com/google/cloud/genomics/dataflow/readers/bam/ReaderOptions', 'java/util/List', 'com/google/cloud/genomics/dataflow/readers/bam/ReadBAMTransform' }\r\n    stack: { 'com/google/cloud/dataflow/sdk/values/TupleTag', 'com/google/cloud/dataflow/sdk/Pipeline', 'com/google/cloud/dataflow/sdk/transforms/Create' }\r\n  Bytecode:\r\n    0x0000000: bb00 0159 2db7 0002 3a05 1905 2bb6 0003\r\n    0x0000010: b200 042a 1904 b800 05b6 0006 c000 07b8\r\n    0x0000020: 0008 b600 09b8 000a b200 0b2a 2cb8 0005\r\n    0x0000030: b600 06c0 0007 120c b800 0db6 0009 b600\r\n    0x0000040: 0e3a 0619 0519 06b6 000f b0            \r\n\r\n\tat org.broadinstitute.hellbender.engine.dataflow.datasources.ReadsDataflowSource.getReadPCollection(ReadsDataflowSource.java:130)\r\n\tat org.broadinstitute.hellbender.dev.tools.walkers.bqsr.BadTypeRepro.ingestReadsAndGrabHeader(BadTypeRepro.java:100)\r\n\tat org.broadinstitute.hellbender.dev.tools.walkers.bqsr.BadTypeRepro.setupPipeline(BadTypeRepro.java:74)\r\n````\r\n\r\nThis is the same error I saw when upgrading to google-cloud-dataflow-java-sdk-all:0.4.150710 (#754), so perhaps this is caused by a version mismatch somewhere.\r\n\r\nI wrote a small bug-reproducing class, [BadTypeRepro](https://github.com/broadinstitute/hellbender/blob/jp_badtype_repro/src/main/java/org/broadinstitute/hellbender/dev/tools/walkers/bqsr/BadTypeRepro.java), in its eponymous branch."},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments/128804629","html_url":"https://github.com/broadinstitute/hellbender/issues/791#issuecomment-128804629","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/791","id":128804629,"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},"created_at":"2015-08-07T19:34:38Z","updated_at":"2015-08-07T19:34:38Z","body":"Sure, I can look into it."}}