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I just tried the fasta parsing feature of pyGATB, and I find surprizing results. See the following ipython3 session:
```
In [1]: from gatb import Bank
In [2]: sum(len(seq.sequence) for seq in B…
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FYI Guillaume, latest gatb-core master branch (not the one currently linked to this repository) crashes with -kmer-size multiple of 4 on any input file.. (not a high priority)
```
[DSK: Pass 1/1, …
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Hello,
When giving a file of files (fof) to create a graph with gatb::core::debruijn::impl::Graph::create() (-in parameter), I ran into several problems regarding relative paths. I am using the lat…
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On OSX, I did:
```bash
cd
git clone https://github.com/GATB/pyGATB.git
mkdir build ; cd build;
cmake -DCMAKE_BUILD_TYPE=Release ..
```
While checking at the CMale working trace, I saw this:
…
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I'd like to optimize the `-abundance` parameter, and to that end it would be nice to separate the `dsk` stage from the `bcalm` stage so that the `-abundance` parameter can be optimized without having …
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Hi K!
I'm trying to run besst on chr14 data, 35 kbp insert jumping libs. It crashes because it couldn't estimate a "cov" parameter. Yielded that bug:
the error message:
```
Creating contig graph w…
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~~SPCC736.09c tfx1 TRAX~~ NOT
~~SPCC1682.08c mcp2 pumilio family RNA-binding protein Mcp2~~ (meiotic cell cycle)
- [x] SPAC139.01c ath2 Ath1 complex protein Ath2 nuclease, XP-G family (predicted)
…
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Dear Developers,
I am facing an ImportError: No module named kover.dataset.create while trying to run the following command:
bashs@promec1-vm:~/kover$ bin/kover dataset create from-reads --geno…
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The following errors during I compile example in mac (version 10.11.6 ):
In file included from examples/debruijn/debruijn1.cpp:4:
In file included from include/gatb/gatb_core.hpp:78:
include/gatb…
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Hi,
Any plans to implement paired-end read support? Have you ever tried [Flash](http://scottmyourstone.blogspot.com.au/2013/10/merging-overlapping-paired-end-reads.html) or
shuffleReadsfasta.pl from…