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seqan / iGenVar

The official repository for the iGenVar project.
BSD 3-Clause "New" or "Revised" License
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[FEATURE] Call inversions via split read method #210

Closed Irallia closed 2 years ago

Irallia commented 2 years ago

For reviewing look at the second commit ;)

This PR adds INVs to the iGenVar repertoir. An Inversion consists of two Breakpoints (start and end of the inv) which we merge into one Inversion junction. I decided also to add the inverted sequence to our junction struct. In the split read method we find the inversions via their different orientation. Later in the variant output, this is hidden, because we merged the two BNDs together. It now looks like a deletion with an inserted sequence.

codecov[bot] commented 2 years ago

Codecov Report

Merging #210 (86f4888) into master (c731471) will increase coverage by 0.04%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #210      +/-   ##
==========================================
+ Coverage   98.34%   98.38%   +0.04%     
==========================================
  Files          18       18              
  Lines         844      867      +23     
==========================================
+ Hits          830      853      +23     
  Misses         14       14
Impacted Files Coverage Δ
src/iGenVar.cpp 100.00% <ø> (ø)
...sv_detection_methods/analyze_split_read_method.cpp 97.34% <100.00%> (+0.50%) :arrow_up:
src/variant_detection/variant_output.cpp 100.00% <100.00%> (ø)

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