Option flank is never used in merge_bed.py

[ghost]

I was wondering that the fuzzy search in merge_bed.py gives me the same results as without the fuzzy search.
I looked into merge_bed.py and saw that this option is never used. Is there any reason to call the function read_to_hash with parameter flank always with 0 in line 49?
inputs = [read_to_hash(a,flank=0) for a in args]
Will it work if I replace the zero with options.flank?
inputs = [read_to_hash(a,flank=options.flank) for a in args]

[marvin-jens]

Hi raistlin91, well spotted. No, I think you can give it a try. It should work (tm). However, I have not used the fuzzy search in many years. If you could run some tests to make sure it works as expected, I'd be happy to pull a patch from you. Best regards, - Marvin

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On Monday, March 27, 2017 11:33:23 AM EDT raistlin91 wrote: I was wondering that the fuzzy search in merge_bed.py gives me the same results as without the fuzzy search. I looked into merge_bed.py and saw that this option is never used. Is there any reason to call the function `read_to_hash` with parameter flank always with 0 in line 49? `inputs = [read_to_hash(a,flank=0) for a in args]` Will it work if I replace the zero with options.flank? `inputs = [read_to_hash(a,flank=options.flank) for a in args]`

[mschilli87]

Hi @raistlin91

Thanks for the feedback.
Just in case you didn't know, the main repository of find_circ moved.
So future issues might have higher visibility (also for other users) when opened there.

Also, feel free to ask for features over at ciRcus as we plan to implement (some of) the merge_bed.py functionality there and we need user feedback to prioritize these according to what is actually used.