{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/140924875","pull_request_review_id":65065351,"id":140924875,"diff_hunk":"@@ -95,10 +95,12 @@ jacocoTestReport {\n \n //NOTE: we ignore contracts for now\n compileJava {\n-  options.compilerArgs = ['-proc:none', '-Xlint:all','-Werror', '-Xdiags:verbose']\n+  // removing -Werror temporarily","path":"build.gradle","position":14,"original_position":14,"commit_id":"6def5a7395eba9b84055e382e57d32a28836c21d","original_commit_id":"6def5a7395eba9b84055e382e57d32a28836c21d","user":{"login":"jean-philippe-martin","id":10458949,"avatar_url":"https://avatars3.githubusercontent.com/u/10458949?v=4","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":"I put -Werr back in, it works. Thanks!","created_at":"2017-09-25T23:26:45Z","updated_at":"2017-09-25T23:26:45Z","html_url":"https://github.com/broadinstitute/gatk/pull/2558#discussion_r140924875","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2558","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/140924875"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/2558#discussion_r140924875"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/2558"}},"in_reply_to_id":140903248},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2558","id":113731908,"html_url":"https://github.com/broadinstitute/gatk/pull/2558","diff_url":"https://github.com/broadinstitute/gatk/pull/2558.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/2558.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2558","number":2558,"state":"open","locked":false,"title":"NIO output support for PrintReads","user":{"login":"jean-philippe-martin","id":10458949,"avatar_url":"https://avatars3.githubusercontent.com/u/10458949?v=4","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":"Add a version of `createSAMWriter` that takes in a `Path` so we can work with NIO for output. This allows PrintReads to write its output to a cloud bucket.\r\n\r\nTested like this:\r\n```\r\n$ ./gatk-launch PrintReads -I gs://$MYBUCKET/CEUTrio.HiSeq.WEx.b37.NA12892.bam -L 10:1000000-2000000  -O gs://$MYBUCKET/pr.bam\r\n$ gsutil cp gs//$MYBUCKET/pr.bam .\r\n$ samtools view pr.bam | md5sum\r\nc7f41be91031bea6d28d59d40b54f304  -\r\n```\r\n\r\nThis MD5 matches the expected output for this command.\r\n\r\nOnce we agree this is the correct way forward, I should go ahead and change all of the other tools similarly.\r\n\r\nThis PR is part of addressing 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