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changed IS_GERMLINE to SV_STATUS #11

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changed IS_GERMLINE to SV_STATUS #11

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Fix # (see https://help.github.com/en/articles/closing-issues-using-keywords)

Describe changes proposed in this pull request:

  • a
  • b

Checks

  • Runs on heroku
  • Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
  • The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
  • Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

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mandawilson and others added 2 commits January 11, 2022 11:59
@mandawilson @averyniceday
@sheridancbio @kalletlak
Remove support for FUSION datatype.
3baf7c2 
Co-authored-by: Avery Wang <[email protected]>
Co-authored-by: Manda Wilson <[email protected]>
Co-authored-by: Robert Sheridan <[email protected]>
Co-authored-by: Karthik Kalletla <[email protected]>
@mandawilson
- unit test for structural variant
4ed00e2 
- bug fix in TabDelimitedFileUtil.java parseInt was using Float.parseFloat and the casting to int and losing precision (string "138536968" was converted to int 138536960)
@mandawilson mandawilson force-pushed the add-germline-flag-to-sv branch from 32cbbb9 to e253dfb Compare February 8, 2022 17:55
@averyniceday
update mybatis xml (#24)
c19f199 
- fix sv gene counts (now using unique identifier instead of stable id)
- prevent double counting of sv records where SITE1 and SITE2 genes are the same

Co-authored-by: Avery Wang <[email protected]>
@mandawilson mandawilson force-pushed the add-germline-flag-to-sv branch 10 times, most recently from 4fe21b3 to 9ae33b4 Compare February 9, 2022 16:47
@mandawilson mandawilson force-pushed the add-germline-flag-to-sv branch 3 times, most recently from a8d5b65 to 7d1ec79 Compare February 9, 2022 21:02
@mandawilson mandawilson force-pushed the add-germline-flag-to-sv branch from 7d1ec79 to 453a022 Compare February 9, 2022 21:32
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5 participants
@mandawilson @averyniceday @yichaoS @inodb @sheridancbio