Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merge str harmonization update #153

Merged
merged 14 commits into from
Mar 24, 2022
Merged

Merge str harmonization update #153

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
ef84886
Added type annotations to mergeSTR.py
Kulivox Feb 5, 2022
f6a6c76
Added annotations that were revealed to be missing by mypy
Kulivox Feb 5, 2022
b108664
mergeSTR.py now uses harmonized position to figure out which records …
Kulivox Feb 5, 2022
a11ef6a
Merge branch 'develop' into mergeSTR_harmonization_update
Kulivox Feb 15, 2022
51885b4
fixed changes broken by merge
Kulivox Feb 15, 2022
3f21cc3
removed unnecessary variables
Kulivox Feb 17, 2022
cc7803b
updated types and added new function
Kulivox Feb 17, 2022
e77ef75
updated mergeSTR so it correctly merges hipstr records
Kulivox Feb 17, 2022
1424beb
updated tests to reflect changes
Kulivox Feb 17, 2022
9752bb1
remove string case change because it was unnecessary
Kulivox Feb 25, 2022
7427713
added case change for non harmonized values
Kulivox Feb 25, 2022
bf54073
created test confirming that merging now properly handles hipstr reco…
Kulivox Feb 25, 2022
418988d
added unreleased changes section and updated function docstring
Kulivox Mar 22, 2022
7aba69c
Merge branch 'develop' into mergeSTR_harmonization_update
LiterallyUniqueLogin Mar 24, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 8 additions & 1 deletion RELEASE_NOTES.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,18 @@
Unreleased changes
-----

CompareSTR and mergeutils changes:
Functionality Changes:

* MergeSTR: Decision on which records are able to be merged is now based on data from harmonized TRRecords,
and not from the records directly from VCF readers. Thanks to this, HipSTR records which have different starting positions,
but position of their repeat is at the same position are merged correctly. This difference is caused by flanking BP that are
included in the record. These flanking BPs are also removed during the merge, and merged HipSTR records no longer contain them

* CompareSTR: the tool now only compares records that start and end at the same position. If overlap in records is detected,
the program will output a warning to the user. This warning contains IDs of the records and their positions.

Misc:

* mergeutils: function GetMinHarmonizedRecords was transformed into GetRecordComparabilityAndIncrement, which allows the caller
to define custom predicate that decides whether records are comparable.

Expand Down
Loading