pairtools
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open2c
Extract 3D contacts (.pairs) from sequencing alignments
Hi, While running scaling by pairs I ran into the following error. > File ~/miniconda3/envs/tools/lib/python3.10/site-packages/pairtools/lib/scaling.py:54, in (.0) def assign_regs(chroms, pos, regs): gb_regs = regs.sort_values(["chrom", "start", "end"]).groupby(["chrom"]) regs_dict = { --->...
Dear, I systematically get the following error: ImportError: cannot import name 'dedup_cython' from partially initialized module 'pairtools.lib' (most likely due to a circular import) (/shared/clssoft/apps/x86_64/pairtools/1.0.3/lib/python3.8/site-pack could one advice, please Best...
Scaling without a view was broken! Docs said it would use the chromsizes from the header, but there was no code that was doing it...
Hi, Thanks for rolling out a new release of `pairtools` v1.1.0. Upon reviewing the changelog provided for this release (https://github.com/open2c/pairtools/releases/tag/v1.1.0/)), I noticed alterations to the behavior and default settings of...
Added `--count-dups` reporting mode for scipy and scikit-learn backends that report the number of duplicates (a little bit unfair, though, as the parent is counted there as well - it...
it'd be also important to propagate this error to distiller
For the --max-insert-size parameter of pairtools parse2, the documentation says: > When searching for overlapping ends of left and right read (R1 and R2), this sets the minimal distance when...
I'm using pairtools restrict to label restriction fragments. When I include this step in my pipeline, I notice mounting consumption of swap memory that grows past the amount available on...
Until recently, I'd been using pairtools parse. Recently I switched to parse2. In testing my parse2-based pipeline, I started running into issues with sorting where, for example, I'd have a...
Hello, A colleague and myself are stuck trying to figure out why are we getting the dreaded XX quality indicator for all our pairs when we try to run: samtools...
