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open2c
/
pairtools
Extract 3D contacts (.pairs) from sequencing alignments
MIT License
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32
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stats: missing CLI docstring for --with-chromsizes
#136
golobor
closed
2 years ago
4
Column with annotated mismatched in parse/parse2
#134
agalitsyna
closed
2 years ago
3
Combinatorial expansion for pairs in the same read
#133
agalitsyna
closed
2 years ago
0
[WIP] Stats split by filters
#132
Phlya
closed
2 years ago
8
Pre0.4.0
#131
Phlya
closed
2 years ago
1
high percentage of **total_single_sided_mapped**
#122
wbszhu
closed
8 months ago
9
Header CLI
#121
agalitsyna
closed
2 years ago
1
CLI to add header
#119
Phlya
closed
2 years ago
3
pairtools 1.0.0 updates
#117
agalitsyna
closed
2 years ago
1
pairtools v1.0.0 roadmap
#116
agalitsyna
closed
2 years ago
2
pairtools phase critical update
#114
agalitsyna
closed
2 years ago
0
ImportError: cannot import name 'Mapping' from 'collections'
#113
Phlya
closed
2 years ago
3
total_single_sided_mapped contains Pair types
#112
wbszhu
opened
2 years ago
0
format pairtools stats output as YAML
#111
golobor
closed
2 years ago
1
Pysam backend update
#110
agalitsyna
closed
2 years ago
0
Parse2 update (#99)
#109
agalitsyna
closed
2 years ago
1
Python3.10 Support
#108
stefanor
closed
2 years ago
1
Chunked dedup
#107
Phlya
closed
2 years ago
12
detecting optical duplicates
#106
golobor
closed
2 years ago
5
Add summaries
#105
Phlya
closed
2 years ago
2
type of UU (unique-unique) is close to each other
#104
wbszhu
opened
3 years ago
0
pairtools sort fails, but no error messages
#103
aminakur
closed
3 years ago
1
Coordinate Sorted vs Read Sorted BAM files give drastically different results
#102
aakashsur
closed
2 years ago
1
Error: failed to open file "mapped.PT.bam"
#101
jiangshan529
closed
2 years ago
1
NaNs in the feature table for snipping
#100
agalitsyna
closed
2 years ago
0
Parse2 update
#99
agalitsyna
closed
2 years ago
1
sort command processing time
#98
andyjslee
closed
2 years ago
2
pip install via wheel fails
#97
aakashsur
closed
2 years ago
1
Parse2: created
#96
agalitsyna
closed
3 years ago
3
modify the pairtools-dedup to select the best MAPQ alignment as output of deduplication
#95
frankyan
closed
2 years ago
2
Use GH actions for testing and publishing to PyPI
#94
Phlya
closed
3 years ago
0
Junction index update
#93
agalitsyna
closed
3 years ago
0
how to use "phase" function?
#92
yxian9
closed
2 years ago
1
standalone flip fails when "reduced.chrom.sizes" provided, should go lexicographical
#91
sergpolly
closed
2 years ago
1
update formats to make pair types more visible
#90
gfudenberg
closed
3 years ago
0
pairtools._headerops.extract_chromsizes fails due to wrong namespace usage and missing pandas import
#89
dmalzl
closed
4 years ago
1
pairtools parse keyError
#88
sckinta
closed
4 years ago
5
Pairtools sort issue
#87
marco91sol
closed
4 years ago
2
Walks policy "parse all"
#86
agalitsyna
closed
4 years ago
1
binary file format for pairs
#85
golobor
closed
8 months ago
8
PairTools sort failure on merged data
#84
dowenlab
closed
2 years ago
9
add chromsizes into pairtools stats output
#83
sergpolly
closed
2 years ago
1
Readid transform
#82
golobor
closed
4 years ago
6
improve distance binning for FR,RR,FR,RF pairs "scalings" in stats output
#81
sergpolly
closed
2 years ago
10
collect mapq stats in the pairs-stats if possible
#80
sergpolly
closed
2 years ago
6
should we store stats as YAML (or json)
#79
sergpolly
closed
2 years ago
4
Make a module for multi-qc
#78
sergpolly
closed
2 years ago
15
list index out of range error on line 574 of pairtools_parse.py
#77
nkschaefer
closed
5 years ago
2
restrict can't handle '!' chromosome
#76
zhqu1148980644
closed
2 years ago
1
Provide conda installation for version 0.3.0
#75
dawnmy
closed
5 years ago
1
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