Compute raw activity profile #162
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@@ Coverage Diff @@
## master #162 +/- ##
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+ Coverage 96.39% 96.49% +0.09%
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Files 18 19 +1
Lines 749 798 +49
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+ Hits 722 770 +48
- Misses 27 28 +1
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This looks like you need a test for the new error message. I just reordered all the CLI tests: #164 maybe wait with adding the test for this PR? |
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Thanks! I'll wait for the pending PR and then update this one on Wednesday. |
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| * \brief Detect Single Nucleotide Polymorphisms (SNPs) and short deletions and insertions. | ||
| * \param reads_filename The file path where to find the sequenced reads. |
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| * \brief Detect Single Nucleotide Polymorphisms (SNPs) and short deletions and insertions. | |
| * \param reads_filename The file path where to find the sequenced reads. | |
| * \brief Detect Single Nucleotide Polymorphisms (SNPs) and short deletions and insertions (Indels). | |
| * \param[in] reads_filename - The file path where to find the sequenced reads. |
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Why do we put this hyphen? I don't find the meaning in the Doxygen manual for \param. I see it just ends up as the beginning of the description string.
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We once decided on this style, either we decide to change in general, or stay consistent. -> https://github.com/seqan/iGenVar/wiki/Coding-Guide
I find it clearer in the first image, but yes it looks a bit unnecessary in the second image. So if you think the change is important, then we should discuss it again and change it in a separate PR.
| "Start clustering...\n" | ||
| "Done with clustering. Found 0 junction clusters.\n" | ||
| "No refinement was selected.\n"; |
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Question for the next meeting: Do we have our own clustering method here or do we use the existing one? Do we need the refinement for SNPs at all?
Resolves #152: Scans a sam file and creates an activity vector per reference genome.
Solves also part of #151, as it introduces a parameter for a genome filename (the file is not yet read). If a genome file name is given, iGenVar switches to the SNP/Indel calling mode.
There are no tests yet for this functionality.