{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/883","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/883/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/883/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/883/events","html_url":"https://github.com/broadinstitute/hellbender/issues/883","id":105630116,"number":883,"title":"Dataflow BQSR Direct Runner fails with --knownSites","user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/Dataflow","name":"Dataflow","color":"fbca04"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/DataflowPreprocessingPipeline","name":"DataflowPreprocessingPipeline","color":"5319e7"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-09-09T16:11:45Z","updated_at":"2015-10-07T00:44:43Z","closed_at":null,"body":"From @tomwhite:\r\n\r\nI noticed that the test with \"-knownSites\" from BaseRecalibratorIntegrationTest (i.e. the non-dataflow version) fails with both the Direct and Spark runners. I had a look at the file output and there are a few discrepancies (see diff below). \r\n\r\n```\r\ndiff /var/folders/d1/8f5_j4hx04z72w6wgqxkb2l40000gn/T/walktest.tmp_param.02172067147450353519.tmp src/test/resources/org/broadinstitute/hellbender/tools/BQSR/expected.NA12878.chr17_69k_70k.2inputs.txt\r\n60c60\r\n<           34   3051              34\r\n---\r\n>           34   3050              34\r\n71c71\r\n<           45  46942              45\r\n---\r\n>           45  46940              45\r\n124,126c124,126\r\n< 809R9ABXX101220.5  D                   45.0000             45.0000         23471    0.00\r\n< 809R9ABXX101220.5  I                   45.0000             45.0000         23471    0.00\r\n< 809R9ABXX101220.5  M                   27.0000             27.0494         23471   49.13\r\n---\r\n> 809R9ABXX101220.5  D                   45.0000             45.0000         23470    0.00\r\n> 809R9ABXX101220.5  I                   45.0000             45.0000         23470    0.00\r\n> 809R9ABXX101220.5  M                   27.0000             27.0493         23470   49.13\r\n155c155\r\n< 809R9ABXX101220.5            34  M                   34.0000          3051    2.96\r\n---\r\n> 809R9ABXX101220.5            34  M                   34.0000          3050    2.96\r\n161,162c161,162\r\n< 809R9ABXX101220.5            45  D                   45.0000         23471    0.00\r\n< 809R9ABXX101220.5            45  I                   45.0000         23471    0.00\r\n---\r\n> 809R9ABXX101220.5            45  D                   45.0000         23470    0.00\r\n> 809R9ABXX101220.5            45  I                   45.0000         23470    0.00\r\n2714c2714\r\n< 809R9ABXX101220.5            34  29              Cycle          M                   34.0000            20    0.00\r\n---\r\n> 809R9ABXX101220.5            34  29              Cycle          M                   34.0000            19    0.00\r\n2773c2773\r\n< 809R9ABXX101220.5            34  CA              Context        M                   34.0000           506    0.00\r\n---\r\n> 809R9ABXX101220.5            34  CA              Context        M                   34.0000           505    0.00\r\n3464,3465c3464,3465\r\n< 809R9ABXX101220.5            45  29              Cycle          D                   45.0000           180    0.00\r\n< 809R9ABXX101220.5            45  29              Cycle          I                   45.0000           180    0.00\r\n---\r\n> 809R9ABXX101220.5            45  29              Cycle          D                   45.0000           179    0.00\r\n> 809R9ABXX101220.5            45  29              Cycle          I                   45.0000           179    0.00\r\n3634,3635c3634,3635\r\n< 809R9ABXX101220.5            45  GCA             Context        D                   45.0000           278    0.00\r\n< 809R9ABXX101220.5            45  GCA             Context        I                   45.0000           278    0.00\r\n---\r\n> 809R9ABXX101220.5            45  GCA             Context        D                   45.0000           277    0.00\r\n> 809R9ABXX101220.5            45  GCA             Context        I                   45.0000           277    0.00\r\n```\r\n\r\nThe relevant test is this one from `BaseRecalibratorDataflowIntegrationTest`\r\n\r\n```\r\n new BQSRTest(hg18Reference, HiSeqBam, dbSNPb37, \"-knownSites \" + moreSites, getResourceDir() + \"expected.NA12878.chr17_69k_70k.2inputs.txt\")\r\n```"},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments/146045223","html_url":"https://github.com/broadinstitute/hellbender/issues/883#issuecomment-146045223","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/883","id":146045223,"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},"created_at":"2015-10-07T00:44:42Z","updated_at":"2015-10-07T00:44:42Z","body":"This issue was moved to broadinstitute/hellbender-dataflow#15"}}