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Hello John,
When I was reporting another issue (fixed rev-comp problem with unitig-caller), I've realized unitig-counter seems to make erroneous calls if a contig in particular isolate starts with…
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I had only inserted "#include " at the head of the gatb-core example file debruijn1.cpp, and type the following commands:
> cmake -DGATB_CORE_INCLUDE_EXAMPLES=True -DCMAKE_BUILD_TYPE=Debug ..…
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The *de novo* discovery routine can be multi-threaded by first loading up all GATB de Bruijn graphs (this cannot be done multi-threaded) and attaching them to their respective `CandidateRegion`. Then …
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I.e. can it be set in the `config.yaml` and if so, what key is needed?
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Hello,
There seem to be no clear instruction on how to install this program. Can it be made simpler?
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Hello,
I am packaging simka as a debian package[1].
Cloning and compiling directly from source completes successfully. However, with regards to debian policy, gatb-core is already available as a…
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For some cases, the output edge representation of Bcalm2 is hard to work with. I will describe another natural representation below, and this "issue" is a feature request to add a flag to support this…
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I created a file with fasta sequence of all Kmers of length 4 (Kmer and its reverse complement -> 256).
When I count this file with dsk (-abundance-min 1 -kmer-size 4), I obtain 136 "kmers_nb_distinc…
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I keep getting an error after the installation:
2 warnings and 10 errors generated.
make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.c…
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- Compile DSK
- Run on one or more genomes