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[TEST] Add more test cases to mini example: #146

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merged 1 commit into from
Aug 4, 2021
Merged

[TEST] Add more test cases to mini example: #146

merged 1 commit into from
Aug 4, 2021

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Irallia
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@Irallia Irallia commented Aug 3, 2021 •
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Resolves first part of #144.
More test cases in mini example: Translocation and Duplications
plus the new IGV view:
single_end_IGV_View

@Irallia Irallia self-assigned this Aug 3, 2021
@Irallia Irallia linked an issue Aug 3, 2021 that may be closed by this pull request
iGenVar - Call Duplications #144
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@Irallia Irallia requested review from a team and eaasna and removed request for a team August 3, 2021 16:26
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codecov bot commented Aug 3, 2021 •
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Codecov Report

Merging #146 (9804321) into master (8b1569b) will not change coverage.
The diff coverage is n/a.

❗ Current head 9804321 differs from pull request most recent head 13f240a. Consider uploading reports for the commit 13f240a to get more accurate results
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@@           Coverage Diff           @@
##           master     #146   +/-   ##
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  Coverage   94.73%   94.73%           
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  Files          18       18           
  Lines         703      703           
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  Hits          666      666           
  Misses         37       37

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eaasna
eaasna approved these changes Aug 4, 2021
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Looks good. It's a nice idea to have the explanation.fasta file

As I understand the output_err.txt is what's printed to standard output and output_res.txt is the output file?

test/data/mini_example/explanation.fasta Outdated
ATATTTCTGCGGGGCT TCGGCTAACGGTT AGAG CGCCCCTCCGCGATTA C <- Translocation ref: (266, 267, 232, 233, 236, 237, 249)
oder ref: [267, 286] deleted
ATATTTCTGCGGGGCT TCGGCTAACGGTT AGAG CGCCCCTCCGCGATTA C <- Double Translocation ref: (266, 267, 232, 233, 236, 237, 249)
oder ref: [267, 286] deleted
ACCCATGCGGATTATAAACGGG ATATTAAGGGCTTT <- Duplication in der Referenz
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Here's some Denglish in case you want to avoid that 😉

@Irallia Irallia requested a review from joergi-w August 4, 2021 08:21
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joergi-w approved these changes Aug 4, 2021
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Looks good! I marked two places where there could be a possible mistake with the boundaries. Please double-check :)

test/data/mini_example/explanation.fasta Outdated
ATCGGGGGGCCCCCATTTTAAACGG CCCCGGGGCCAATTT GGATCTTGACTCTGGAAAACTTTTA <- Insertion ref: after 125 something inserted
ACGCCGGGAATCGGTAGTCCTTTCGCGGGG ATATATTT ATATATTT TACGGGATATAA <- Duplication ref: (180 or 189) something inserted
CGCCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCG breakpoints:
GCGGCAT ATACATAAGGGGCTCATCGATCGATTTCGG <- Deletion ref: (57, 70] deleted
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Attention: equivalent to the previous would be (56 here, so I guess it was mistaken before?

test/data/mini_example/explanation.fasta Outdated
CGCCCATGCAACTAGCGATGCTAGCTAGCTAGCTTACGACTGGCCATGCG breakpoints:
GCGGCAT ATACATAAGGGGCTCATCGATCGATTTCGG <- Deletion ref: (57, 70] deleted
ATCGGGGGGCCCCCATTTTAAACGG CCCCGGGGCCAATTT GGATCTTGACTCTGGAAAACTTTTA <- Insertion ref: after 125
ACGCCGGGAATCGGTAGTCCTTTCGCGGGG ATATATTT ATATATTT TACGGGATATAA <- Tandem Duplication ref: [180, 188] duplicated
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the same here, now 180 is included, before it wasn't

@Irallia Irallia merged commit 863297c into seqan:master Aug 4, 2021
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iGenVar - Call Duplications
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