codecov[bot]
commented
2 years ago Codecov Report
Merging #227 (63d9733) into master (23112df) will increase coverage by
0.01%. The diff coverage is97.17%.
@@ Coverage Diff @@
## master #227 +/- ##
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+ Coverage 98.47% 98.48% +0.01%
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Files 20 20
Lines 985 1124 +139
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+ Hits 970 1107 +137
- Misses 15 17 +2 | Impacted Files | Coverage Δ | |
|---|---|---|
| src/variant_detection/method_enums.cpp | 100.00% <ø> (ø) |
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| src/variant_detection/variant_detection.cpp | 95.12% <50.00%> (-1.52%) |
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| src/variant_detection/snp_indel_detection.cpp | 97.56% <97.72%> (-0.86%) |
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| include/structures/junction.hpp | 96.66% <100.00%> (+0.83%) |
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| src/iGenVar.cpp | 100.00% <100.00%> (ø) |
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| src/structures/junction.cpp | 100.00% <100.00%> (+8.00%) |
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| src/variant_detection/variant_output.cpp | 100.00% <100.00%> (ø) |
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| src/structures/debruijn_graph.cpp | 100.00% <0.00%> (+0.92%) |
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joergi-w
The first commit extends the junction class by two members: (1) The "deleted sequence" contains the part of the reference sequence that is deleted in the reads. (2) The "quality" is a float value to be passed to the vcf file and represents how well a SNP or Indel is represented in the read data. I implemented a new constructor with the new members next to the existing one, because it is a less invasive change than editing all the existing constructor calls.
The second commit adds the
snp_indelmethod to iGenVar. It is enabled by default and used if a genome file and short reads are provided. We use the de Bruijn graph to compute haplotype sequences from the reads in a high-activity region. The haplotypes are in turn aligned against the reference, and SNPs and indels are extracted from the alignment and printed with the vcf writer. Currently, they are appended to the end of the existing vcf file; however, we can think about a different way in the future.