jdidion atropos issues - Githubissues

jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Other

118 stars 14 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

cython is required at build time but not install time

#138 tillea closed 7 months ago
1
Fix compatibility issues with Python 3.10-3.12

#137 jdidion closed 7 months ago
0
Replace SafeConfigParser with ConfigParser

#136 vpa1977 closed 7 months ago
0
Python 3.12 build errors due to SafeConfigParser removal

#135 vpa1977 closed 7 months ago
2
Move CI to github actions

#134 jdidion opened 1 year ago
0
Test python 3.10 compatibility

#133 jdidion closed 7 months ago
0
Install Error

#132 JChristopherEllis opened 1 year ago
1
Make code compatible with Python 3.10

#131 jmarshall closed 1 year ago
0
defaults not listed in cli docs

#130 nick-youngblut opened 2 years ago
0
detect: --max-reads default

#129 nick-youngblut opened 2 years ago
1
Can atropos remove 5' adapter variants that are incomplete from the tail?

#128 lokapal opened 2 years ago
5
error while running the detect command

#127 manasakaringula opened 3 years ago
2
Empty gz

#126 jdidion closed 3 years ago
0
Use xopen when opening `force_create` files

#125 jdidion closed 3 years ago
0
Atropos generated empty gzip files are not proper gzip file

#124 jganbat-fn closed 3 years ago
3
Bioconda atropos package tied to python 3.6

#123 gabeng opened 3 years ago
1
Atropos trim multi thread stuck in infinite loop on empty files.

#122 jganbat-fn closed 3 years ago
2
Cutadapt version

#121 Citteny closed 3 years ago
1
Add poweron architecture ppc64le to travis build

#120 asellappen closed 3 years ago
1
Implement non-internal adapters

#119 jdidion opened 3 years ago
0
multiqc support?

#118 plijnzaad closed 3 years ago
2
TypeError: 'CountingDict' object is not callable when using --metrics

#117 plijnzaad closed 3 years ago
2
Bundle adapters file with atropos wheel

#116 jdidion closed 3 years ago
1
Issue112

#115 plijnzaad closed 3 years ago
1
atropos --version exits with stack trace and error status

#114 plijnzaad closed 3 years ago
1
atropos --version prints errors and exits with error status

#113 plijnzaad closed 3 years ago
1
TypeError: can only concatenate tuple (not "list") to tuple

#112 plijnzaad closed 3 years ago
1
sequencing_adapters.fa : 404 not found

#111 plijnzaad closed 3 years ago
1
N-prefixes / wildcards before an adapter sequence leads to shortening *all* reads at the 3'-end ?

#110 plijnzaad closed 3 years ago
3
Retain SAM tags, add modifier to filter out specific/all SAM tags

#109 jdidion closed 4 years ago
0
Bug/102 json serialize

#108 jdidion closed 4 years ago
0
Fix #101

#107 jdidion closed 4 years ago
0
Trimmed fastq ordering is not deterministic

#106 annamerk closed 4 years ago
2
request: with --output-format sam , add @PG and @CO header lines to output

#105 plijnzaad closed 4 years ago
2
--output-sam sets all SAM flags to 0

#104 plijnzaad closed 4 years ago
1
--output-format sam discards all SAM tags !?

#103 plijnzaad closed 4 years ago
2
TypeError: Object of type 'ProgressBarType' is not JSON serializable

#102 plijnzaad closed 4 years ago
1
--output-format sam inserts extra header lines every batch-size output lines ?!

#101 plijnzaad closed 4 years ago
4
atropos qc multithreads not working ?

#100 aathbt closed 4 years ago
5
Add configuration option to choose which library to use for reading BAM

#99 jdidion opened 4 years ago
0
Bug/97 single end qc

#98 jdidion closed 4 years ago
0
atropos qc not handling single-end reads ?

#97 aathbt closed 4 years ago
3
bam (but not sam) reader crashes on '@CO' line in header

#96 plijnzaad closed 4 years ago
6
Add support for output to BAM

#95 plijnzaad opened 4 years ago
10
(partial) fix for issue #86

#94 plijnzaad closed 4 years ago
1
Push latest version to DockerHub

#93 jdidion opened 4 years ago
1
Update sequencing_adapters.fa

#92 amizeranschi opened 4 years ago
0
atropos crashes all the time

#91 antonkulaga closed 3 years ago
1
Dockerfile for atropos-paper fails to build due to required apt-get upgrade interactivity

#90 nkrumm closed 4 years ago
1
Dockerfile is missing pip `wheel` package

#89 nkrumm closed 4 years ago
1