pairtools

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stats redesign

2

stats are getting out of control. A non-comprehensive list of issues: 1. We have several stats, each generated by a different tool during their runtime (parse/stats, dedup, filterbycov). This is...

golobor

warning [E::idx_find_and_load] Could not retrieve index file for

9

pairtools parse /cluster/home/Kangwen/Hic/data_new/snHic_index/XY5/snHic_SRR0_tmp/SRR0.qc.bam -c /cluster/home/Kangwen/common/hg38/hg38.fa.chrom.sizes --drop-sam --drop-seq --output-stats SRR0.stats --assembly hg38 --no-flip --add-columns mapq --walks-policy all -o SRR0.pairs.gz --nproc-in 60 --nproc-out 60 [E::idx_find_and_load] Could not retrieve index file for '/cluster/home/Kangwen/Hic/data_new/snHic_index/XY5/snHic_SRR0_tmp/SRR0.qc.bam'...

CCCKW

pairtools split - float mapQ value

2

Hi, I'm using `pairtools split` to transform a pairsam into a pairs.gz file, and then apply `pairtools select` on the output with ``` pairtools select "(mapq1>10 and mapq2>10)" -o selected.pairs.gz...

nservant

running pairtools merge sequentially produces circular dependencies

2

Hi, I am merging two .pairs.gz files, but met this problem: $ pairtools merge --max-nmerge 7 --nproc 8 --memory 100G --tmpdir ./ --output ./merge_KO.pairs.gz ./*.gz Traceback (most recent call last):...

jiangshan529

pipe error with bwa-mem2.avx512bw (2.2.1)

1

Hi, I am trying to align paired-end HI-C data with bwa-mem2 but it seems there is an issue with header. Here is the command i used: bwa-mem2.avx512bw mem -5SP -T0...

pashapu43

Why reading using pipes rather than another method?

1

Hi, I'm just curious why the io is using pipes for e.g. lz4 files instead of using the python package lz4. Curious to learn more. Thanks!

gdolsten

Problem Statement Different projects may have slight variations in their testing procedures. As a result, contributing developers may find it challenging to understand how to run tests effectively. Proposed Solution...

Unique-Usman

'xcats' positional argument error in coverage_by_chrom

4

Hi there, I recently came across pairtools and I am super excited to start implementing it in our workflows. I tried to visualize the stats file via multiqc, but encountered...

laramiemckenna

Hello, Thank you so much for creating such useful tools! I'm currently doing analysis on Micro-C data and had some questions on the parse2 options `--report-orientation` and `--report-position`. Just for...

NMaziak

python API docs

1

We should create them... From highest priority to lowest: - [ ] io/header: https://github.com/open2c/pairtools/blob/master/pairtools/lib/headerops.py - [ ] scaling: https://github.com/open2c/pairtools/blob/master/pairtools/lib/scaling.py - [ ] stats: https://github.com/open2c/pairtools/blob/master/pairtools/lib/stats.py

Phlya