{"action":"created","issue":{"url":"https://api.github.com/repos/chrovis/varity/issues/24","repository_url":"https://api.github.com/repos/chrovis/varity","labels_url":"https://api.github.com/repos/chrovis/varity/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/chrovis/varity/issues/24/comments","events_url":"https://api.github.com/repos/chrovis/varity/issues/24/events","html_url":"https://github.com/chrovis/varity/pull/24","id":388469097,"node_id":"MDExOlB1bGxSZXF1ZXN0MjM2NzI4MDc0","number":24,"title":"Fix pos of hgvs->vcf-variants for genes on reverse strand","user":{"login":"alumi","id":5086013,"node_id":"MDQ6VXNlcjUwODYwMTM=","avatar_url":"https://avatars3.githubusercontent.com/u/5086013?v=4","gravatar_id":"","url":"https://api.github.com/users/alumi","html_url":"https://github.com/alumi","followers_url":"https://api.github.com/users/alumi/followers","following_url":"https://api.github.com/users/alumi/following{/other_user}","gists_url":"https://api.github.com/users/alumi/gists{/gist_id}","starred_url":"https://api.github.com/users/alumi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alumi/subscriptions","organizations_url":"https://api.github.com/users/alumi/orgs","repos_url":"https://api.github.com/users/alumi/repos","events_url":"https://api.github.com/users/alumi/events{/privacy}","received_events_url":"https://api.github.com/users/alumi/received_events","type":"User","site_admin":false},"labels":[{"id":586233243,"node_id":"MDU6TGFiZWw1ODYyMzMyNDM=","url":"https://api.github.com/repos/chrovis/varity/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":{"login":"totakke","id":933940,"node_id":"MDQ6VXNlcjkzMzk0MA==","avatar_url":"https://avatars2.githubusercontent.com/u/933940?v=4","gravatar_id":"","url":"https://api.github.com/users/totakke","html_url":"https://github.com/totakke","followers_url":"https://api.github.com/users/totakke/followers","following_url":"https://api.github.com/users/totakke/following{/other_user}","gists_url":"https://api.github.com/users/totakke/gists{/gist_id}","starred_url":"https://api.github.com/users/totakke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/totakke/subscriptions","organizations_url":"https://api.github.com/users/totakke/orgs","repos_url":"https://api.github.com/users/totakke/repos","events_url":"https://api.github.com/users/totakke/events{/privacy}","received_events_url":"https://api.github.com/users/totakke/received_events","type":"User","site_admin":false},"assignees":[{"login":"totakke","id":933940,"node_id":"MDQ6VXNlcjkzMzk0MA==","avatar_url":"https://avatars2.githubusercontent.com/u/933940?v=4","gravatar_id":"","url":"https://api.github.com/users/totakke","html_url":"https://github.com/totakke","followers_url":"https://api.github.com/users/totakke/followers","following_url":"https://api.github.com/users/totakke/following{/other_user}","gists_url":"https://api.github.com/users/totakke/gists{/gist_id}","starred_url":"https://api.github.com/users/totakke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/totakke/subscriptions","organizations_url":"https://api.github.com/users/totakke/orgs","repos_url":"https://api.github.com/users/totakke/repos","events_url":"https://api.github.com/users/totakke/events{/privacy}","received_events_url":"https://api.github.com/users/totakke/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2018-12-07T01:33:11Z","updated_at":"2018-12-07T01:39:11Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/chrovis/varity/pulls/24","html_url":"https://github.com/chrovis/varity/pull/24","diff_url":"https://github.com/chrovis/varity/pull/24.diff","patch_url":"https://github.com/chrovis/varity/pull/24.patch"},"body":"### summary\r\nThis PR fixes a problem that hgvs->vcf converted `:pos` may be incorrect when the target gene is on the reverse strand.\r\n\r\n### problem\r\nFor example, [KRAS p.Q61K](https://www.ncbi.nlm.nih.gov/clinvar/variation/177777/) is reported to be located at chr12:25227343 (hg38)\r\n\r\n#### reference sequence\r\n\r\n```clojure\r\n(cseq/read-sequence seq-rdr {:chr \"chr12\", :start 25227340, :end 25227350})\r\n;; => \"CTTGACCTGCT\"\r\n;;     01234567890\r\n```\r\n- 25227341 `T`\r\n- 25227343 `G`\r\n\r\n#### master\r\n\r\n```clojure\r\n(h2v/hgvs->vcf-variants (hgvs/parse \"p.Q61K\") \"KRAS\" seq-rdr rg-idx)\r\n;; => ({:chr \"chr12\", :pos 25227341, :ref \"G\", :alt \"T\"})\r\n```\r\n\r\n### cause\r\n\r\nThis was caused by aligning reverse-complement nucleotide sequences and ascending genomic coordinate sequences. Reversing the genomic coordinates will fix the problem.\r\n\r\n#### PR\r\n\r\n```clojure\r\n(h2v/hgvs->vcf-variants (hgvs/parse \"p.Q61K\") \"KRAS\" seq-rdr rg-idx)\r\n;; => ({:chr \"chr12\", :pos 25227343, :ref \"G\", :alt \"T\"})\r\n```\r\n\r\n### checks\r\n- `lein test :all` :ok:\r\n- `lein check` :ok:\r\n- `lein eastwood` :ok:\r\n- `lein cljfmt check` :ok:\r\n- `lein bikeshed` :ok:"},"comment":{"url":"https://api.github.com/repos/chrovis/varity/issues/comments/445092764","html_url":"https://github.com/chrovis/varity/pull/24#issuecomment-445092764","issue_url":"https://api.github.com/repos/chrovis/varity/issues/24","id":445092764,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NTA5Mjc2NA==","user":{"login":"codecov[bot]","id":22429695,"node_id":"MDM6Qm90MjI0Mjk2OTU=","avatar_url":"https://avatars2.githubusercontent.com/in/254?v=4","gravatar_id":"","url":"https://api.github.com/users/codecov%5Bbot%5D","html_url":"https://github.com/apps/codecov","followers_url":"https://api.github.com/users/codecov%5Bbot%5D/followers","following_url":"https://api.github.com/users/codecov%5Bbot%5D/following{/other_user}","gists_url":"https://api.github.com/users/codecov%5Bbot%5D/gists{/gist_id}","starred_url":"https://api.github.com/users/codecov%5Bbot%5D/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/codecov%5Bbot%5D/subscriptions","organizations_url":"https://api.github.com/users/codecov%5Bbot%5D/orgs","repos_url":"https://api.github.com/users/codecov%5Bbot%5D/repos","events_url":"https://api.github.com/users/codecov%5Bbot%5D/events{/privacy}","received_events_url":"https://api.github.com/users/codecov%5Bbot%5D/received_events","type":"Bot","site_admin":false},"created_at":"2018-12-07T01:39:11Z","updated_at":"2018-12-07T01:39:11Z","author_association":"NONE","body":"# [Codecov](https://codecov.io/gh/chrovis/varity/pull/24?src=pr&el=h1) Report\n> Merging [#24](https://codecov.io/gh/chrovis/varity/pull/24?src=pr&el=desc) into [master](https://codecov.io/gh/chrovis/varity/commit/d3c9073dca133b1cfbddb3d7c7904349c184d11f?src=pr&el=desc) will **decrease** coverage by `0.02%`.\n> The diff coverage is `0%`.\n\n[![Impacted file tree graph](https://codecov.io/gh/chrovis/varity/pull/24/graphs/tree.svg?width=650&token=cfxZjb12kk&height=150&src=pr)](https://codecov.io/gh/chrovis/varity/pull/24?src=pr&el=tree)\n\n```diff\n@@            Coverage Diff             @@\n##           master      #24      +/-   ##\n==========================================\n- Coverage    39.1%   39.08%   -0.03%     \n==========================================\n  Files          13       13              \n  Lines        1460     1461       +1     \n  Branches       31       31              \n==========================================\n  Hits          571      571              \n- Misses        858      859       +1     \n  Partials       31       31\n```\n\n\n| [Impacted Files](https://codecov.io/gh/chrovis/varity/pull/24?src=pr&el=tree) | Coverage Δ | |\n|---|---|---|\n| [src/varity/hgvs\\_to\\_vcf/protein.clj](https://codecov.io/gh/chrovis/varity/pull/24/diff?src=pr&el=tree#diff-c3JjL3Zhcml0eS9oZ3ZzX3RvX3ZjZi9wcm90ZWluLmNsag==) | `10% <0%> (-0.15%)` | :arrow_down: |\n\n------\n\n[Continue to review full report at Codecov](https://codecov.io/gh/chrovis/varity/pull/24?src=pr&el=continue).\n> **Legend** - [Click here to learn more](https://docs.codecov.io/docs/codecov-delta)\n> `Δ = absolute <relative> (impact)`, `ø = not affected`, `? = missing data`\n> Powered by [Codecov](https://codecov.io/gh/chrovis/varity/pull/24?src=pr&el=footer). Last update [d3c9073...d21df86](https://codecov.io/gh/chrovis/varity/pull/24?src=pr&el=lastupdated). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).\n"}}
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