{"action":"created","issue":{"url":"https://api.github.com/repos/HumanCellAtlas/sctools/issues/43","repository_url":"https://api.github.com/repos/HumanCellAtlas/sctools","labels_url":"https://api.github.com/repos/HumanCellAtlas/sctools/issues/43/labels{/name}","comments_url":"https://api.github.com/repos/HumanCellAtlas/sctools/issues/43/comments","events_url":"https://api.github.com/repos/HumanCellAtlas/sctools/issues/43/events","html_url":"https://github.com/HumanCellAtlas/sctools/pull/43","id":336386008,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk3ODUyNDg2","number":43,"title":"CountMatrix bugfix and new tests","user":{"login":"mbabadi","id":15305869,"node_id":"MDQ6VXNlcjE1MzA1ODY5","avatar_url":"https://avatars1.githubusercontent.com/u/15305869?v=4","gravatar_id":"","url":"https://api.github.com/users/mbabadi","html_url":"https://github.com/mbabadi","followers_url":"https://api.github.com/users/mbabadi/followers","following_url":"https://api.github.com/users/mbabadi/following{/other_user}","gists_url":"https://api.github.com/users/mbabadi/gists{/gist_id}","starred_url":"https://api.github.com/users/mbabadi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mbabadi/subscriptions","organizations_url":"https://api.github.com/users/mbabadi/orgs","repos_url":"https://api.github.com/users/mbabadi/repos","events_url":"https://api.github.com/users/mbabadi/events{/privacy}","received_events_url":"https://api.github.com/users/mbabadi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-27T21:01:35Z","updated_at":"2018-06-27T21:05:44Z","closed_at":null,"author_association":"NONE","pull_request":{"url":"https://api.github.com/repos/HumanCellAtlas/sctools/pulls/43","html_url":"https://github.com/HumanCellAtlas/sctools/pull/43","diff_url":"https://github.com/HumanCellAtlas/sctools/pull/43.diff","patch_url":"https://github.com/HumanCellAtlas/sctools/pull/43.patch"},"body":"This PR fixes some algorithmic issues in the `CountMatrix` class. It also improves related unit tests. The current counting algorithm implemented in `CountMatrix.from_sorted_tagged_bam` is expected to be functionally similar to CellRanger methods.\r\n\r\nCloses #42."},"comment":{"url":"https://api.github.com/repos/HumanCellAtlas/sctools/issues/comments/400828877","html_url":"https://github.com/HumanCellAtlas/sctools/pull/43#issuecomment-400828877","issue_url":"https://api.github.com/repos/HumanCellAtlas/sctools/issues/43","id":400828877,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMDgyODg3Nw==","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":"2018-06-27T21:05:44Z","updated_at":"2018-06-27T21:05:44Z","author_association":"NONE","body":"# [Codecov](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43?src=pr&el=h1) Report\n> Merging [#43](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43?src=pr&el=desc) into [master](https://codecov.io/gh/HumanCellAtlas/sctools/commit/24ed25f95b861e4438233e832fec56c6b65153eb?src=pr&el=desc) will **increase** coverage by `0.23%`.\n> The diff coverage is `97.53%`.\n\n[![Impacted file tree graph](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43/graphs/tree.svg?width=650&token=bfAz5mte7Z&height=150&src=pr)](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43?src=pr&el=tree)\n\n```diff\n@@            Coverage Diff            @@\n##           master     #43      +/-   ##\n=========================================\n+ Coverage   94.67%   94.9%   +0.23%     \n=========================================\n  Files          24      24              \n  Lines        1727    1982     +255     \n=========================================\n+ Hits         1635    1881     +246     \n- Misses         92     101       +9\n```\n\n\n| [Impacted Files](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43?src=pr&el=tree) | Coverage Δ | |\n|---|---|---|\n| [src/sctools/platform.py](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43/diff?src=pr&el=tree#diff-c3JjL3NjdG9vbHMvcGxhdGZvcm0ucHk=) | `81.96% <0%> (-0.15%)` | :arrow_down: |\n| [src/sctools/test/test\\_metrics.py](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43/diff?src=pr&el=tree#diff-c3JjL3NjdG9vbHMvdGVzdC90ZXN0X21ldHJpY3MucHk=) | `100% <100%> (ø)` | :arrow_up: |\n| [src/sctools/gtf.py](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43/diff?src=pr&el=tree#diff-c3JjL3NjdG9vbHMvZ3RmLnB5) | `88.88% <94.11%> (+1.08%)` | :arrow_up: |\n| [src/sctools/count.py](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43/diff?src=pr&el=tree#diff-c3JjL3NjdG9vbHMvY291bnQucHk=) | `88.49% <95.83%> (-2.42%)` | :arrow_down: |\n| [src/sctools/test/test\\_count.py](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43/diff?src=pr&el=tree#diff-c3JjL3NjdG9vbHMvdGVzdC90ZXN0X2NvdW50LnB5) | `98.71% <98.69%> (-1.29%)` | :arrow_down: |\n\n------\n\n[Continue to review full report at Codecov](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43?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/HumanCellAtlas/sctools/pull/43?src=pr&el=footer). Last update [24ed25f...e736196](https://codecov.io/gh/HumanCellAtlas/sctools/pull/43?src=pr&el=lastupdated). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).\n"}}
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