{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/5063","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5063/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5063/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5063/events","html_url":"https://github.com/broadinstitute/gatk/pull/5063","id":345278212,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA0NDcxNzAx","number":5063,"title":"Update references to old-style arguments","user":{"login":"anowlcalledjosh","id":9433472,"node_id":"MDQ6VXNlcjk0MzM0NzI=","avatar_url":"https://avatars1.githubusercontent.com/u/9433472?v=4","gravatar_id":"","url":"https://api.github.com/users/anowlcalledjosh","html_url":"https://github.com/anowlcalledjosh","followers_url":"https://api.github.com/users/anowlcalledjosh/followers","following_url":"https://api.github.com/users/anowlcalledjosh/following{/other_user}","gists_url":"https://api.github.com/users/anowlcalledjosh/gists{/gist_id}","starred_url":"https://api.github.com/users/anowlcalledjosh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/anowlcalledjosh/subscriptions","organizations_url":"https://api.github.com/users/anowlcalledjosh/orgs","repos_url":"https://api.github.com/users/anowlcalledjosh/repos","events_url":"https://api.github.com/users/anowlcalledjosh/events{/privacy}","received_events_url":"https://api.github.com/users/anowlcalledjosh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-27T15:52:23Z","updated_at":"2018-07-27T16:48:52Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/5063","html_url":"https://github.com/broadinstitute/gatk/pull/5063","diff_url":"https://github.com/broadinstitute/gatk/pull/5063.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/5063.patch"},"body":"Updating a few more old spellings of arguments.\r\n\r\nI also noticed some references to `-scatterTranches` and `-sampleEvery`, but as far as I can tell they're not currently valid arguments to anything, so I didn't touch the references to those."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/408476070","html_url":"https://github.com/broadinstitute/gatk/pull/5063#issuecomment-408476070","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/5063","id":408476070,"node_id":"MDEyOklzc3VlQ29tbWVudDQwODQ3NjA3MA==","user":{"login":"codecov-io","id":8655789,"node_id":"MDQ6VXNlcjg2NTU3ODk=","avatar_url":"https://avatars0.githubusercontent.com/u/8655789?v=4","gravatar_id":"","url":"https://api.github.com/users/codecov-io","html_url":"https://github.com/codecov-io","followers_url":"https://api.github.com/users/codecov-io/followers","following_url":"https://api.github.com/users/codecov-io/following{/other_user}","gists_url":"https://api.github.com/users/codecov-io/gists{/gist_id}","starred_url":"https://api.github.com/users/codecov-io/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codecov-io/subscriptions","organizations_url":"https://api.github.com/users/codecov-io/orgs","repos_url":"https://api.github.com/users/codecov-io/repos","events_url":"https://api.github.com/users/codecov-io/events{/privacy}","received_events_url":"https://api.github.com/users/codecov-io/received_events","type":"User","site_admin":false},"created_at":"2018-07-27T16:48:52Z","updated_at":"2018-07-27T16:48:52Z","author_association":"NONE","body":"# [Codecov](https://codecov.io/gh/broadinstitute/gatk/pull/5063?src=pr&el=h1) Report\n> Merging [#5063](https://codecov.io/gh/broadinstitute/gatk/pull/5063?src=pr&el=desc) into [master](https://codecov.io/gh/broadinstitute/gatk/commit/7a794724c58ca7258df116ba2a3af7df191ebc8a?src=pr&el=desc) will **decrease** coverage by `0.124%`.\n> The diff coverage is `n/a`.\n\n\n```diff\n@@              Coverage Diff               @@\n##             master     #5063       +/-   ##\n==============================================\n- Coverage     86.35%   86.225%   -0.124%     \n+ Complexity    28824     28775       -49     \n==============================================\n  Files          1791      1791               \n  Lines        133601    133601               \n  Branches      14920     14920               \n==============================================\n- Hits         115364    115198      -166     \n- Misses        12834     13007      +173     \n+ Partials       5403      5396        -7\n```\n\n\n\n\n| [Impacted Files](https://codecov.io/gh/broadinstitute/gatk/pull/5063?src=pr&el=tree) | Coverage Δ | Complexity Δ | |\n|---|---|---|---|\n| [...ender/tools/walkers/filters/VariantFiltration.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy93YWxrZXJzL2ZpbHRlcnMvVmFyaWFudEZpbHRyYXRpb24uamF2YQ==) | `89.076% <ø> (ø)` | `41 <0> (ø)` | :arrow_down: |\n| [...otypecaller/HaplotypeCallerArgumentCollection.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy93YWxrZXJzL2hhcGxvdHlwZWNhbGxlci9IYXBsb3R5cGVDYWxsZXJBcmd1bWVudENvbGxlY3Rpb24uamF2YQ==) | `100% <ø> (ø)` | `2 <0> (ø)` | :arrow_down: |\n| [...idation/AnnotateVcfWithExpectedAlleleFraction.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy93YWxrZXJzL3ZhbGlkYXRpb24vQW5ub3RhdGVWY2ZXaXRoRXhwZWN0ZWRBbGxlbGVGcmFjdGlvbi5qYXZh) | `96.429% <ø> (ø)` | `7 <0> (ø)` | :arrow_down: |\n| [...bender/tools/walkers/vqsr/VariantRecalibrator.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy93YWxrZXJzL3Zxc3IvVmFyaWFudFJlY2FsaWJyYXRvci5qYXZh) | `59.223% <ø> (ø)` | `58 <0> (ø)` | :arrow_down: |\n| [...ller/ReadThreadingAssemblerArgumentCollection.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy93YWxrZXJzL2hhcGxvdHlwZWNhbGxlci9SZWFkVGhyZWFkaW5nQXNzZW1ibGVyQXJndW1lbnRDb2xsZWN0aW9uLmphdmE=) | `100% <ø> (ø)` | `1 <0> (ø)` | :arrow_down: |\n| [...notyper/GenotypeCalculationArgumentCollection.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy93YWxrZXJzL2dlbm90eXBlci9HZW5vdHlwZUNhbGN1bGF0aW9uQXJndW1lbnRDb2xsZWN0aW9uLmphdmE=) | `100% <ø> (ø)` | `2 <0> (ø)` | :arrow_down: |\n| [...itute/hellbender/tools/walkers/vqsr/ApplyVQSR.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy93YWxrZXJzL3Zxc3IvQXBwbHlWUVNSLmphdmE=) | `75% <ø> (ø)` | `55 <0> (ø)` | :arrow_down: |\n| [...s/spark/ParallelCopyGCSDirectoryIntoHDFSSpark.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy9zcGFyay9QYXJhbGxlbENvcHlHQ1NEaXJlY3RvcnlJbnRvSERGU1NwYXJrLmphdmE=) | `0% <0%> (-74.257%)` | `0% <0%> (-17%)` | |\n| [...nder/tools/spark/pipelines/PrintVariantsSpark.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci90b29scy9zcGFyay9waXBlbGluZXMvUHJpbnRWYXJpYW50c1NwYXJrLmphdmE=) | `0% <0%> (-66.667%)` | `0% <0%> (-2%)` | |\n| [...oadinstitute/hellbender/utils/test/XorWrapper.java](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree#diff-c3JjL21haW4vamF2YS9vcmcvYnJvYWRpbnN0aXR1dGUvaGVsbGJlbmRlci91dGlscy90ZXN0L1hvcldyYXBwZXIuamF2YQ==) | `13.043% <0%> (-65.217%)` | `2% <0%> (-7%)` | |\n| ... and [12 more](https://codecov.io/gh/broadinstitute/gatk/pull/5063/diff?src=pr&el=tree-more) | |\n"}}
{"actor":{"display_login":"codecov-io"}}