Closed Irallia closed 2 years ago
Merging #208 (91ec8dc) into master (71ad200) will decrease coverage by
0.00%
. The diff coverage is100.00%
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@@ Coverage Diff @@
## master #208 +/- ##
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- Coverage 98.35% 98.34% -0.01%
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Files 18 18
Lines 850 848 -2
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- Hits 836 834 -2
Misses 14 14
Impacted Files | Coverage Δ | |
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src/iGenVar.cpp | 100.00% <ø> (ø) |
|
...sv_detection_methods/analyze_split_read_method.cpp | 96.84% <100.00%> (+0.03%) |
:arrow_up: |
src/variant_detection/variant_output.cpp | 100.00% <100.00%> (ø) |
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To discuss: What is the length of a tandem duplication.
I had a quick look at the specification (source) and I found that SVLEN = Difference in length between REF and ALT alleles Therefore, I would change the length to 27 in your example.
However, it feels a bit redundant to me that SVLEN is always END-POS, because it doesn't add information.
Yes, but the SVLEN is not used everywhere, I found a discussion about INVs here. Maybe we just introduce a second INFO value beside the SVLEN. I will adjust the PR.
This PR adds the duplicated sequence to the output. To discuss: What is the length of a tandem duplication. In this PR I decided to use the length of the duplicated sequence. For example:
Than the duplication goes from (5, 23], its duplicated sequence is AAACCCGGG and the SVLEN is 9.