Marcel Martin

Hi, there was a question by @brentp in issue #18 about how to retrieve the extent of an alignment: >> Also, is there an efficient way for this to get...

Since odopoi looks good and is already close to what I need, I'm trying to use it as a basis for my own project. Thanks for making the sources available!...

Optimized parameters for multi-context seeds

6

Branch: mcs-optimized-parameters (commit 7fe07b498e274567050cfe888bb91d1752e961c9). The same command as in #407 was used: ``` ./search.py -c ${commit} -x --accuracy-slack 0.1 --mapping-rate-slack 1 -r ${read_length} ``` ## Suggested changes Using parameters from...

Decompress with ISA-L

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This is a continuation of #269 where I fixed the things I commented on. I will need to re-measure memory usage. At some point, it was higher than previously, but...

Experiment: Asymmetric randstrobe hashes

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I’ve written about this by e-mail, but thought I’d show the code as well and a table that shows a comparison of accuracies. This PR includes two commits. The first...

Optimize parameters (again)

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Here are suggested new indexing parameters for all read lengths. This supersedes #397. I ran the optimization script for both v0.12.0 (commit 6fd4c5d) and multi-context seeds (commit c4a7f61). Differences to...

Make Python scripts compatible with Python 3

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Following up on the discussin about the Conda recipe at #7, I found that these commands are sufficient to make the `ms2chromosomes.py` script be compatible with Python 3: ``` sed...

Updated dependencies of a PyPI package not recognized

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An autobump PR bioconda/bioconda-recipes#18310 was merged without updating the dependencies. It appears as if the bot has some functionality to detect updated dependencies, but this doesn’t seem work for PyPI...

sga index output unexpectedly placed in working directory

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When running ``` sga index --no-reverse directory/file.fastq ``` I would have expected the index files that are created to be `directory/file.bwt` and `directory/file.sai`, but they are actually put into the...

Cutadapt is used quite often to trim primer sequences, in which case it is expected that the "adapter" (primer) is not preceded/followed by a random nucleotide, but a specific one....