Ecosyste.ms: Issues

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GitHub / open2c/pairtools issues and pull requests

#114 - pairtools phase critical update

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

#113 - ImportError: cannot import name 'Mapping' from 'collections'

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

#112 - total_single_sided_mapped contains Pair types

Issue - State: open - Opened by wbszhu almost 3 years ago
Labels: help wanted

#111 - format pairtools stats output as YAML

Issue - State: closed - Opened by golobor about 3 years ago - 1 comment

#110 - Pysam backend update

Pull Request - State: closed - Opened by agalitsyna about 3 years ago

#109 - Parse2 update (#99)

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

#108 - Python3.10 Support

Pull Request - State: closed - Opened by stefanor about 3 years ago - 1 comment

#107 - Chunked dedup

Pull Request - State: closed - Opened by Phlya over 3 years ago - 12 comments

#106 - detecting optical duplicates

Issue - State: closed - Opened by golobor over 3 years ago - 5 comments
Labels: enhancement

#105 - Add summaries

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

#104 - type of UU (unique-unique) is close to each other

Issue - State: open - Opened by wbszhu over 3 years ago
Labels: help wanted

#103 - pairtools sort fails, but no error messages

Issue - State: closed - Opened by MyBiscuit over 3 years ago - 1 comment

#102 - Coordinate Sorted vs Read Sorted BAM files give drastically different results

Issue - State: closed - Opened by aakashsur over 3 years ago - 1 comment

#101 - Error: failed to open file "mapped.PT.bam"

Issue - State: closed - Opened by jiangshan529 over 3 years ago - 1 comment
Labels: help wanted

#100 - NaNs in the feature table for snipping

Issue - State: closed - Opened by agalitsyna almost 4 years ago

#99 - Parse2 update

Pull Request - State: closed - Opened by agalitsyna almost 4 years ago - 1 comment

#98 - sort command processing time

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

#97 - pip install via wheel fails

Issue - State: closed - Opened by aakashsur almost 4 years ago - 1 comment
Labels: help wanted

#96 - Parse2: created

Pull Request - State: closed - Opened by agalitsyna almost 4 years ago - 3 comments

#95 - modify the pairtools-dedup to select the best MAPQ alignment as output of deduplication

Pull Request - State: closed - Opened by frankyan almost 4 years ago - 2 comments

#94 - Use GH actions for testing and publishing to PyPI

Pull Request - State: closed - Opened by Phlya almost 4 years ago

#93 - Junction index update

Pull Request - State: closed - Opened by agalitsyna almost 4 years ago

#92 - how to use "phase" function?

Issue - State: closed - Opened by yx-xiang about 4 years ago - 1 comment
Labels: help wanted, question

#90 - update formats to make pair types more visible

Pull Request - State: closed - Opened by gfudenberg about 4 years ago

#88 - pairtools parse keyError

Issue - State: closed - Opened by sckinta over 4 years ago - 5 comments

#87 - Pairtools sort issue

Issue - State: closed - Opened by marco91sol over 4 years ago - 2 comments

#86 - Walks policy "parse all"

Pull Request - State: closed - Opened by agalitsyna over 4 years ago - 1 comment

#85 - binary file format for pairs

Issue - State: closed - Opened by golobor over 4 years ago - 8 comments
Labels: enhancement

#84 - PairTools sort failure on merged data

Issue - State: closed - Opened by dowenlab over 4 years ago - 9 comments

#83 - add chromsizes into pairtools stats output

Issue - State: closed - Opened by sergpolly almost 5 years ago - 1 comment

#81 - improve distance binning for FR,RR,FR,RF pairs "scalings" in stats output

Issue - State: closed - Opened by sergpolly almost 5 years ago - 10 comments
Labels: enhancement

#80 - collect mapq stats in the pairs-stats if possible

Issue - State: closed - Opened by sergpolly about 5 years ago - 6 comments
Labels: enhancement

#79 - should we store stats as YAML (or json)

Issue - State: closed - Opened by sergpolly about 5 years ago - 4 comments
Labels: enhancement, question

#78 - Make a module for multi-qc

Issue - State: closed - Opened by sergpolly about 5 years ago - 15 comments
Labels: enhancement

#76 - restrict can't handle '!' chromosome

Issue - State: closed - Opened by zhqu1148980644 over 5 years ago - 1 comment

#73 - Assignment of fragment in restrict passed the first fragment.

Issue - State: closed - Opened by zhqu1148980644 over 5 years ago - 3 comments

#72 - pairtools sort not parallelizing

Issue - State: closed - Opened by SooLee almost 6 years ago - 2 comments
Labels: help wanted, question

#71 - VisibleDeprecationWarning

Issue - State: closed - Opened by zhqu1148980644 about 6 years ago - 3 comments

#68 - Fragment-level analysis

Issue - State: open - Opened by Phlya over 6 years ago - 41 comments
Labels: enhancement

#66 - pairsamtools subsampling [new tool, enhancement]

Issue - State: closed - Opened by sergpolly over 6 years ago - 5 comments

#65 - throw an readable error message upon encountering an unpaired sam entry

Issue - State: open - Opened by golobor almost 7 years ago - 2 comments
Labels: enhancement

#64 - semantic confusion in stats

Issue - State: open - Opened by sergpolly about 7 years ago - 2 comments
Labels: question

#61 - merge without arguments

Issue - State: closed - Opened by hakanozadam about 7 years ago - 1 comment

#59 - optical dedup stats

Issue - State: closed - Opened by sergpolly about 7 years ago - 20 comments
Labels: enhancement

#56 - calculate Pc(s) in stats

Issue - State: closed - Opened by golobor about 7 years ago - 4 comments

#54 - add non-additive stat summaries to dedup/stats: complexity estimation, cis/total, ...

Issue - State: closed - Opened by golobor over 7 years ago - 5 comments
Labels: enhancement

#51 - add tests for compression/decompression

Issue - State: open - Opened by golobor over 7 years ago - 2 comments
Labels: enhancement

#48 - make auto_open default to stdin/stdout when path evaluates to False

Issue - State: closed - Opened by golobor over 7 years ago - 1 comment

#35 - add a test for the example_pipeline

Issue - State: open - Opened by golobor over 7 years ago - 1 comment
Labels: enhancement

#34 - default to bgzip if pbgzip is absent

Issue - State: closed - Opened by golobor over 7 years ago

#18 - in merge, add an option to take a header from the first file and ignore other headers

Issue - State: closed - Opened by golobor almost 8 years ago - 2 comments

#16 - add restriction tool

Issue - State: closed - Opened by golobor almost 8 years ago - 4 comments

#6 - make pairsamtools conda-installable

Issue - State: closed - Opened by golobor almost 8 years ago - 4 comments
Labels: enhancement

#5 - tests for dedup

Issue - State: closed - Opened by golobor almost 8 years ago - 4 comments
Labels: enhancement