{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/guacamole/issues/590","repository_url":"https://api.github.com/repos/hammerlab/guacamole","labels_url":"https://api.github.com/repos/hammerlab/guacamole/issues/590/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/guacamole/issues/590/comments","events_url":"https://api.github.com/repos/hammerlab/guacamole/issues/590/events","html_url":"https://github.com/hammerlab/guacamole/pull/590","id":179938010,"number":590,"title":"rm broken .array call","user":{"login":"ryan-williams","id":465045,"avatar_url":"https://avatars.githubusercontent.com/u/465045?v=3","gravatar_id":"","url":"https://api.github.com/users/ryan-williams","html_url":"https://github.com/ryan-williams","followers_url":"https://api.github.com/users/ryan-williams/followers","following_url":"https://api.github.com/users/ryan-williams/following{/other_user}","gists_url":"https://api.github.com/users/ryan-williams/gists{/gist_id}","starred_url":"https://api.github.com/users/ryan-williams/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryan-williams/subscriptions","organizations_url":"https://api.github.com/users/ryan-williams/orgs","repos_url":"https://api.github.com/users/ryan-williams/repos","events_url":"https://api.github.com/users/ryan-williams/events{/privacy}","received_events_url":"https://api.github.com/users/ryan-williams/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"arahuja","id":455755,"avatar_url":"https://avatars.githubusercontent.com/u/455755?v=3","gravatar_id":"","url":"https://api.github.com/users/arahuja","html_url":"https://github.com/arahuja","followers_url":"https://api.github.com/users/arahuja/followers","following_url":"https://api.github.com/users/arahuja/following{/other_user}","gists_url":"https://api.github.com/users/arahuja/gists{/gist_id}","starred_url":"https://api.github.com/users/arahuja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arahuja/subscriptions","organizations_url":"https://api.github.com/users/arahuja/orgs","repos_url":"https://api.github.com/users/arahuja/repos","events_url":"https://api.github.com/users/arahuja/events{/privacy}","received_events_url":"https://api.github.com/users/arahuja/received_events","type":"User","site_admin":false},"assignees":[{"login":"arahuja","id":455755,"avatar_url":"https://avatars.githubusercontent.com/u/455755?v=3","gravatar_id":"","url":"https://api.github.com/users/arahuja","html_url":"https://github.com/arahuja","followers_url":"https://api.github.com/users/arahuja/followers","following_url":"https://api.github.com/users/arahuja/following{/other_user}","gists_url":"https://api.github.com/users/arahuja/gists{/gist_id}","starred_url":"https://api.github.com/users/arahuja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arahuja/subscriptions","organizations_url":"https://api.github.com/users/arahuja/orgs","repos_url":"https://api.github.com/users/arahuja/repos","events_url":"https://api.github.com/users/arahuja/events{/privacy}","received_events_url":"https://api.github.com/users/arahuja/received_events","type":"User","site_admin":false}],"milestone":null,"comments":4,"created_at":"2016-09-29T02:30:12Z","updated_at":"2016-09-29T19:32:47Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/hammerlab/guacamole/pulls/590","html_url":"https://github.com/hammerlab/guacamole/pull/590","diff_url":"https://github.com/hammerlab/guacamole/pull/590.diff","patch_url":"https://github.com/hammerlab/guacamole/pull/590.patch"},"body":"I was seeing task (then stage) failures in `Likelihood` due to the `.array` call I removed here:\r\n\r\n```\r\njava.lang.ClassCastException: [Ljava.lang.Object; cannot be cast to [Lorg.hammerlab.guacamole.variants.Allele;\r\n        at org.hammerlab.guacamole.likelihood.Likelihood$.likelihoodsOfGenotypes(Likelihood.scala:137)\r\n        at org.hammerlab.guacamole.likelihood.Likelihood$.likelihoodsOfAllPossibleGenotypesFromPileup(Likelihood.scala:78)\r\n        at org.hammerlab.guacamole.commands.SomaticStandard$Caller$.findPotentialVariantAtLocus(SomaticStandardCaller.scala:166)\r\n        at org.hammerlab.guacamole.commands.SomaticStandard$Caller$$anonfun$1.apply(SomaticStandardCaller.scala:80)\r\n        at org.hammerlab.guacamole.commands.SomaticStandard$Caller$$anonfun$1.apply(SomaticStandardCaller.scala:79)\r\n        at org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapTwoSamples$1.apply(PileupFlatMapUtils.scala:95)\r\n        at org.hammerlab.guacamole.distributed.PileupFlatMapUtils$$anonfun$pileupFlatMapTwoSamples$1.apply(PileupFlatMapUtils.scala:90)\r\n        at org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$windowFlatMapWithState$1$$anonfun$apply$1.apply(WindowFlatMapUtils.scala:65)\r\n        at org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$windowFlatMapWithState$1$$anonfun$apply$1.apply(WindowFlatMapUtils.scala:55)\r\n        at org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply(WindowFlatMapUtils.scala:141)\r\n        at org.hammerlab.guacamole.distributed.WindowFlatMapUtils$$anonfun$splitPartitionByContigAndMap$2.apply(WindowFlatMapUtils.scala:131)\r\n        at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)\r\n        at org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:284)\r\n        at org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171)\r\n        at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78)\r\n        at org.apache.spark.rdd.RDD.iterator(RDD.scala:268)\r\n        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)\r\n        at org.apache.spark.scheduler.Task.run(Task.scala:89)\r\n        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)\r\n        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n        at java.lang.Thread.run(Thread.java:745)\r\n```\r\n\r\nIs there a reason it was needed? Any ideas why it would lead to this crashing?"},"comment":{"url":"https://api.github.com/repos/hammerlab/guacamole/issues/comments/250567995","html_url":"https://github.com/hammerlab/guacamole/pull/590#issuecomment-250567995","issue_url":"https://api.github.com/repos/hammerlab/guacamole/issues/590","id":250567995,"user":{"login":"ryan-williams","id":465045,"avatar_url":"https://avatars.githubusercontent.com/u/465045?v=3","gravatar_id":"","url":"https://api.github.com/users/ryan-williams","html_url":"https://github.com/ryan-williams","followers_url":"https://api.github.com/users/ryan-williams/followers","following_url":"https://api.github.com/users/ryan-williams/following{/other_user}","gists_url":"https://api.github.com/users/ryan-williams/gists{/gist_id}","starred_url":"https://api.github.com/users/ryan-williams/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ryan-williams/subscriptions","organizations_url":"https://api.github.com/users/ryan-williams/orgs","repos_url":"https://api.github.com/users/ryan-williams/repos","events_url":"https://api.github.com/users/ryan-williams/events{/privacy}","received_events_url":"https://api.github.com/users/ryan-williams/received_events","type":"User","site_admin":false},"created_at":"2016-09-29T19:32:47Z","updated_at":"2016-09-29T19:32:47Z","body":"As an aside: if it's abnormal or unintended that we'd ever have that `alleles` array be empty, that could be worth digging into further; lmk if you think that's the case!"}}
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