jdidion atropos issues - Githubissues

jdidion / atropos

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

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Atropos was stuck while waiting for a subprocess or worker thread to finish

#139 dgpinheiro opened 3 days ago
0
cython is required at build time but not install time

#138 tillea closed 11 months ago
1
Fix compatibility issues with Python 3.10-3.12

#137 jdidion closed 11 months ago
0
Replace SafeConfigParser with ConfigParser

#136 vpa1977 closed 11 months ago
0
Python 3.12 build errors due to SafeConfigParser removal

#135 vpa1977 closed 11 months ago
2
Move CI to github actions

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

#133 jdidion closed 11 months ago
0
Install Error

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

#131 jmarshall closed 2 years 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 3 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 4 years ago
1
Implement non-internal adapters

#119 jdidion opened 4 years ago
0
multiqc support?

#118 plijnzaad closed 4 years ago
2
TypeError: 'CountingDict' object is not callable when using --metrics

#117 plijnzaad closed 4 years ago
2
Bundle adapters file with atropos wheel

#116 jdidion closed 4 years ago
1
Issue112

#115 plijnzaad closed 4 years ago
1
atropos --version exits with stack trace and error status

#114 plijnzaad closed 4 years ago
1
atropos --version prints errors and exits with error status

#113 plijnzaad closed 4 years ago
1
TypeError: can only concatenate tuple (not "list") to tuple

#112 plijnzaad closed 4 years ago
1
sequencing_adapters.fa : 404 not found

#111 plijnzaad closed 4 years ago
1
N-prefixes / wildcards before an adapter sequence leads to shortening *all* reads at the 3'-end ?

#110 plijnzaad closed 4 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 4 years ago
1
Dockerfile for atropos-paper fails to build due to required apt-get upgrade interactivity

#90 nkrumm closed 4 years ago
1