Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / open2c/pairtools issues and pull requests

#246 - What do "Uu" and "uU" mean in .pairs file?

Issue - State: open - Opened by jiehua1995 6 months ago

#245 - Support for lowercase SAM tags in pairtools parse2

Issue - State: open - Opened by LuJiansen 6 months ago

#244 - pairtools sort issue

Issue - State: open - Opened by ryvan1021 7 months ago - 2 comments

#243 - Extracting contact matrices from pairs file

Issue - State: open - Opened by arodel21 7 months ago - 2 comments

#242 - pairtools dedup: invalid value encountered in divide

Issue - State: open - Opened by gbdnorden 8 months ago - 1 comment

#239 - Fix scaling: take chromsizes from header

Pull Request - State: open - Opened by Phlya 9 months ago - 6 comments

#238 - Updating the ReadTheDocs

Issue - State: open - Opened by SaimMomin12 10 months ago

#237 - update the "publish" github action

Pull Request - State: closed - Opened by golobor 10 months ago

#236 - bump pairtools version and changes.md

Pull Request - State: closed - Opened by golobor 10 months ago

#234 - most likely due to a circular import

Issue - State: open - Opened by stephrom 10 months ago - 3 comments

#233 - Duplicate distance notebook

Pull Request - State: closed - Opened by Phlya 10 months ago - 1 comment

#232 - Wording in pairtools parse2 for --max-insert-size

Issue - State: open - Opened by bskubi 10 months ago

#231 - Update protocols_pipelines.rst

Pull Request - State: closed - Opened by golobor 11 months ago

#230 - Fixing sorting of numerical columns

Pull Request - State: closed - Opened by Phlya 11 months ago

#229 - Swap memory overconsumption & program failure during pairtools restrict

Issue - State: closed - Opened by bskubi 11 months ago - 1 comment

#228 - Memory overconsumption/leak (?) in pairtools restrict

Issue - State: open - Opened by bskubi 11 months ago

#226 - update docs

Pull Request - State: closed - Opened by golobor 11 months ago - 1 comment

#225 - Update docs

Pull Request - State: closed - Opened by golobor 11 months ago - 1 comment

#223 - Parse refactor

Pull Request - State: closed - Opened by golobor 11 months ago - 1 comment

#222 - stats: calculate the divergence point and corresponding read fractions

Pull Request - State: closed - Opened by golobor 11 months ago - 8 comments

#221 - All pairs are corrupt ("XX")

Issue - State: open - Opened by lu-r-lu 11 months ago - 6 comments

#219 - update docs

Pull Request - State: closed - Opened by golobor 11 months ago - 1 comment

#218 - update phase walkthrough

Pull Request - State: closed - Opened by golobor 11 months ago - 1 comment

#217 - Feature request - split parse from filters

Issue - State: closed - Opened by bskubi 11 months ago - 4 comments

#216 - stats redesign

Issue - State: open - Opened by golobor 11 months ago - 2 comments

#211 - pairtools dedup: turn mark-dups on by default

Pull Request - State: closed - Opened by golobor 11 months ago

#210 - Why reading using pipes rather than another method?

Issue - State: open - Opened by gdolsten 11 months ago - 1 comment

#209 - Added instructions on how to test pairtools

Pull Request - State: closed - Opened by Unique-Usman 12 months ago

#207 - pipe error with bwa-mem2.avx512bw (2.2.1)

Issue - State: open - Opened by pashapu43 12 months ago - 1 comment

#206 - What's the difference between "uu' and "UU" in .pairs file?

Issue - State: closed - Opened by YingChen94 about 1 year ago - 9 comments

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

Issue - State: open - Opened by CCCKW about 1 year ago - 9 comments

#204 - Gzip, BAM and CRAM support

Issue - State: closed - Opened by amvarani about 1 year ago - 5 comments

#201 - Fix dedup with empty pairs file

Pull Request - State: closed - Opened by Phlya about 1 year ago - 1 comment

#200 - quick fix bugs in stats

Pull Request - State: closed - Opened by sergpolly about 1 year ago
Labels: bug

#199 - bugs in stats

Issue - State: closed - Opened by sergpolly about 1 year ago - 2 comments
Labels: bug

#198 - dedup errors with empty pairs file

Issue - State: closed - Opened by Phlya about 1 year ago - 1 comment

#197 - 'xcats' positional argument error in coverage_by_chrom

Issue - State: open - Opened by laramiemckenna about 1 year ago - 4 comments

#196 - pairtools sort aborting with header error

Issue - State: closed - Opened by jctourtellotte about 1 year ago - 3 comments

#195 - make pairsio.py to read (and, in the future, write) .pairs files

Pull Request - State: closed - Opened by golobor about 1 year ago - 2 comments

#194 - Fix corrupt dedup output for inputs with quotes

Pull Request - State: closed - Opened by hkariti about 1 year ago - 2 comments

#193 - Parse2 clarification

Issue - State: open - Opened by NMaziak about 1 year ago

#192 - Dedup runs forever

Issue - State: closed - Opened by mcahn about 1 year ago - 31 comments

#191 - pairtools parse divide by zero encountered

Issue - State: closed - Opened by magspho over 1 year ago - 1 comment

#190 - pairtools parse dedup cpu issues

Issue - State: closed - Opened by jiangshan529 over 1 year ago - 3 comments

#189 - Update readthedocs.yml

Pull Request - State: closed - Opened by Phlya over 1 year ago - 1 comment

#188 - running pairtools merge sequentially produces circular dependencies

Issue - State: open - Opened by jiangshan529 over 1 year ago - 1 comment

#187 - Deduplication reporting update

Pull Request - State: open - Opened by agalitsyna over 1 year ago - 1 comment

#186 - Dedup with UMIs

Issue - State: closed - Opened by gdolsten over 1 year ago - 12 comments

#184 - Dedup dropping pairs

Issue - State: closed - Opened by nadabrovitxka over 1 year ago - 7 comments

#183 - Dedup parameters

Issue - State: closed - Opened by gdolsten over 1 year ago - 4 comments

#182 - pairtools split - float mapQ value

Issue - State: open - Opened by nservant over 1 year ago - 2 comments

#180 - parse - 90% of corrupt pair type

Issue - State: closed - Opened by nservant over 1 year ago - 2 comments

#179 - parse dedup getting killed by kernel.

Issue - State: closed - Opened by nikhilp11 over 1 year ago - 32 comments

#178 - most pairs are classified as corrupt (XX)

Issue - State: closed - Opened by sahlenlab over 1 year ago - 5 comments

#177 - Pairtools dedup ValueError or incompatible reads?

Issue - State: closed - Opened by ddepierre almost 2 years ago - 4 comments

#175 - Pairtools for OmniC pipeline no longer working

Issue - State: closed - Opened by gdaviduu almost 2 years ago - 5 comments

#174 - multiqc section of walkthrough

Issue - State: open - Opened by gfudenberg almost 2 years ago - 1 comment
Labels: enhancement

#173 - Update mock.4flip.pairs

Pull Request - State: open - Opened by muffato almost 2 years ago

#172 - pairtools cov CLI

Issue - State: open - Opened by agalitsyna almost 2 years ago

#171 - Stats docs

Pull Request - State: closed - Opened by agalitsyna about 2 years ago - 4 comments

#170 - Upper bound on numpy version

Issue - State: closed - Opened by eharr about 2 years ago - 3 comments
Labels: bug

#169 - Don't save index in scaling?

Issue - State: closed - Opened by Phlya about 2 years ago - 1 comment
Labels: enhancement

#167 - Question about pairtools parse strand information

Issue - State: closed - Opened by jiangshan529 about 2 years ago - 1 comment

#164 - P(s) convergence point in stats

Issue - State: open - Opened by Phlya about 2 years ago

#163 - python API docs

Issue - State: open - Opened by Phlya about 2 years ago - 1 comment
Labels: enhancement

#162 - Allow column names in all dedup backends, and allow sorting by arbitrary columns

Pull Request - State: closed - Opened by Phlya about 2 years ago - 44 comments

#161 - Allow arbitrary columns in dedup

Issue - State: closed - Opened by Phlya about 2 years ago - 1 comment

#160 - Crashes on pairtools merge with latest version

Issue - State: closed - Opened by mblanche about 2 years ago - 4 comments

#159 - IndexError: pop index out of range for pairtools split

Issue - State: closed - Opened by KunFang93 about 2 years ago - 3 comments

#156 - pairtools parsing engine abstraction

Issue - State: open - Opened by agalitsyna about 2 years ago - 1 comment

#151 - OSX support

Issue - State: open - Opened by agalitsyna over 2 years ago - 2 comments

#150 - Error when computing scalings using a narrow distance range

Issue - State: closed - Opened by itsameerkat over 2 years ago - 1 comment
Labels: bug

#149 - Fix hardcoded full path for pysam libs.

Pull Request - State: open - Opened by ccoulombe over 2 years ago - 2 comments

#148 - Important fixes of splitting schema

Pull Request - State: closed - Opened by agalitsyna over 2 years ago - 1 comment

#147 - Error with pairtools 1.0.1

Issue - State: closed - Opened by mblanche over 2 years ago - 8 comments

#145 - IndexError in pairtools split

Issue - State: closed - Opened by MyBiscuit over 2 years ago - 8 comments

#144 - Change query to indexing

Pull Request - State: closed - Opened by Phlya over 2 years ago - 2 comments

#143 - Extension dtypes (e.g. pd.Int64) break .eval() and .query()

Issue - State: closed - Opened by Phlya over 2 years ago - 1 comment

#142 - Fix reading and summing files with chromsizes

Pull Request - State: closed - Opened by Phlya over 2 years ago

#139 - post-v1.0.0 proposals and issues (header post)

Issue - State: open - Opened by agalitsyna over 2 years ago

#137 - stats: merge broken with yaml input

Issue - State: closed - Opened by Phlya over 2 years ago - 3 comments

#136 - stats: missing CLI docstring for --with-chromsizes

Issue - State: closed - Opened by golobor over 2 years ago - 4 comments

#134 - Column with annotated mismatched in parse/parse2

Pull Request - State: closed - Opened by agalitsyna over 2 years ago - 3 comments

#133 - Combinatorial expansion for pairs in the same read

Pull Request - State: closed - Opened by agalitsyna over 2 years ago

#132 - [WIP] Stats split by filters

Pull Request - State: closed - Opened by Phlya almost 3 years ago - 8 comments

#131 - Pre0.4.0

Pull Request - State: closed - Opened by Phlya almost 3 years ago - 1 comment

#122 - high percentage of **total_single_sided_mapped**

Issue - State: closed - Opened by wbszhu almost 3 years ago - 9 comments
Labels: help wanted

#121 - Header CLI

Pull Request - State: closed - Opened by agalitsyna almost 3 years ago - 1 comment

#119 - CLI to add header

Issue - State: closed - Opened by Phlya almost 3 years ago - 3 comments

#117 - pairtools 1.0.0 updates

Pull Request - State: closed - Opened by agalitsyna almost 3 years ago - 1 comment

#116 - pairtools v1.0.0 roadmap

Issue - State: closed - Opened by agalitsyna almost 3 years ago - 2 comments