drivenbyentropy

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Size difference in per read statistics file when running `tombo detect_modifications model_sample_compare` with different `multiprocess-region-size` values

That's what I suspected, thank you for confirming.

Details regarding modified fraction calculation from per-read statistic files

Thank you @Chris-Kimmel for this. You are correct, I did not apply the pseudo-counts in my initial description. Based on your formula, *n* corresponds to the total number of reads...

Koloboke Fails to Compile on Java 9

I second this. Do you have plans to support JDK 9 in the future? Thanks for this great project btw!

Koloboke Fails to Compile on Java 9

Thanks for the update. For now, I have worked around the issue with the following hack. I used Koloboke Compile to generate an implementation for my data structure. I then...

Counter and control selection parameters

A counter selection refers to any cycle in which the aptamers were incubated with molecules that are not the target and where those sequences that did not bind where kept...

Crashes when Importing Data

Hi, It is possible that your are running into memory issues and that AptaSuite is crashing because you are running out of memory. Please refer to the following [wiki article](github.com/drivenbyentropy/aptasuite/wiki/Frequent-issues)...

Add support for FASTA format

Good idea, I will add a note to the manual that the 3' primer is always to be provided in 5' to 3' orientation of the forward run. Thanks for...

```get_io_reads()``` fails with ```Move table discordant with signal``` on some reads

@marcus1487 Could you please link to the changes in the code for this issue and if you have the time, elaborate on what caused this and how it was solved?...

```get_io_reads()``` fails with ```Move table discordant with signal``` on some reads

I can confirm that this issue is solved with v3.2. On a dataset of 60000 reads mapping onto a plasmid, prior versions failed on 50000 of them. Now, all are...

DataCorruption error when loading previously parsed data

Hi, Thank you for reporting this. This is the first time I am hearing about such an issue. Are you by any chance storing your projects on a network drive?