Having only one region in toml caused issue

[jennieli421]

Having only one region in toml caused issue

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[Adoni5]

max_chunks has to be greater than min_chunks, and should not be set to 1.
You also don't seem to have set any targets?

[jennieli421]

We have been using max_chunks=1 for a very long time and the results were fine. Here I am only providing targeted region's reference, so I don't need to specify targets

[mattloose]

Here I am only providing targeted region's reference, so I don't need to specify targets

I'm not quite sure what you are trying to do here. If you do not give any targets then you will not get any unblocking activity. An empty

targets = []
will mean that no targets are checked and so the later logic of on or off target will not be evaluated.

An example toml enriching for two chromosomes from a reference is available here:
https://github.com/LooseLab/readfish/blob/main/docs/_static/example_tomls/human_chr_selection.toml

In short, you must have something in the targets = [] for any unblocking activity to occur.

[jennieli421]

I have been using this setting (with split region) for a long time and it is working as expected. The design for not having targets can be traced back to this conversation:
#242 (comment)

Basically I have provided references of only the desired sequences, so everything mapped to the reference is accepted.
Thus, the problem I want to fix is why this setting does not work when I only have one region.

[mattloose]

Hmmm

I indeed stand corrected.

Let me check this further and come back to you.

[mattloose]

Hi, Could you pleaase confrim your readfish version and also share your readfish log with us - the log should be called the <run_id>.tsv

Thanks

Matt

[jennieli421]

tested_one_or_more_regions_ef170d0f.zip

Unfortunately, I was testing different region settings during the run, so this run had multiple settings. I hope this is fine.

[Adoni5]

Hi @jennieli421 - do these logs contain an example of it working, with a region of control=true, where you see unblocking?

And can I just check the version of readfish you were using?

readfish --version

Final question, what is the mean read length of the library you are testing?

[jennieli421]

readfish --version
readfish 2023.1.1

Both should contain multiple trials where I see unblocking, as long as there is a region of control=True.

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