open2c pairtools issues

open2c / pairtools

Extract 3D contacts (.pairs) from sequencing alignments

MIT License

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issues

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convert pairtools result to dense matrix

#252 BenxiaHu opened 4 days ago
0
Fixing API incomplete functionality for read side detection

#251 agalitsyna opened 1 week ago
2
Python 3.13 removes pipes

#250 stefanor opened 3 weeks ago
1
Add option to save single mapped counts by side

#248 Phlya opened 4 weeks ago
0
single-end mode is broken in v1.1.0

#247 niederhuth opened 1 month ago
17
What do "Uu" and "uU" mean in .pairs file?

#246 jiehua1995 closed 3 weeks ago
1
Support for lowercase SAM tags in pairtools parse2

#245 LuJiansen opened 2 months ago
0
pairtools sort issue

#244 ryvan1021 closed 3 weeks ago
3
Extracting contact matrices from pairs file

#243 arodel21 opened 2 months ago
2
pairtools dedup: invalid value encountered in divide

#242 gbdnorden opened 3 months ago
1
pairtools parse used name sorted or coodinate sorted bam file as input

#241 SaimMomin12 closed 4 months ago
2
Scaling by pairs error

#240 DekkerBastiaan opened 4 months ago
1
Fix scaling: take chromsizes from header

#239 Phlya opened 5 months ago
6
Updating the ReadTheDocs

#238 SaimMomin12 opened 5 months ago
0
update the "publish" github action

#237 golobor closed 5 months ago
0
bump pairtools version and changes.md

#236 golobor closed 5 months ago
0
raise an error/warning if chromosome names in .chrom.sizes and bwa index differ too much

#235 golobor opened 5 months ago
0
most likely due to a circular import

#234 stephrom opened 5 months ago
5
Duplicate distance notebook

#233 Phlya closed 5 months ago
1
Wording in pairtools parse2 for --max-insert-size

#232 bskubi opened 6 months ago
0
Update protocols_pipelines.rst

#231 golobor closed 6 months ago
0
Fixing sorting of numerical columns

#230 Phlya closed 6 months ago
0
Swap memory overconsumption & program failure during pairtools restrict

#229 bskubi closed 6 months ago
1
Memory overconsumption/leak (?) in pairtools restrict

#228 bskubi opened 6 months ago
0
parse vs parse2 difference in default behavior for --flip?

#227 bskubi opened 6 months ago
0
update docs

#226 golobor closed 6 months ago
1
Update docs

#225 golobor closed 6 months ago
1
Cannot import name 'dedup_cython' from partially initialized module 'pairtools.lib' (most likely due to a circular import)

#224 narzouni closed 6 months ago
7
Parse refactor

#223 golobor closed 5 months ago
1
stats: calculate the divergence point and corresponding read fractions

#222 golobor closed 6 months ago
8
All pairs are corrupt ("XX")

#221 lu-r-lu opened 6 months ago
6
update docs

#219 golobor closed 6 months ago
1
update phase walkthrough

#218 golobor closed 6 months ago
1
Feature request - split parse from filters

#217 bskubi closed 6 months ago
4
stats redesign

#216 golobor opened 6 months ago
2
pairtools dedup: turn mark-dups on by default

#211 golobor closed 6 months ago
0
Why reading using pipes rather than another method?

#210 gdolsten opened 6 months ago
1
Added instructions on how to test pairtools

#209 Unique-Usman closed 6 months ago
0
There is no instruction on how to test the project.

#208 Unique-Usman opened 7 months ago
0
pipe error with bwa-mem2.avx512bw (2.2.1)

#207 pashapu43 opened 7 months ago
1
What's the difference between "uu' and "UU" in .pairs file?

#206 YingChen94 closed 8 months ago
9
warning [E::idx_find_and_load] Could not retrieve index file for

#205 CCCKW opened 8 months ago
9
Gzip, BAM and CRAM support

#204 amvarani closed 6 months ago
5
Fix dedup with empty pairs file

#201 Phlya closed 8 months ago
1
quick fix bugs in stats

#200 sergpolly closed 6 months ago
0
bugs in stats

#199 sergpolly closed 6 months ago
2
dedup errors with empty pairs file

#198 Phlya closed 8 months ago
1
'xcats' positional argument error in coverage_by_chrom

#197 laramiemckenna opened 9 months ago
4
pairtools sort aborting with header error

#196 jctourtellotte closed 9 months ago
3
make pairsio.py to read (and, in the future, write) .pairs files

#195 golobor closed 6 months ago
2