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ngless-toolkit
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ngless
NGLess: NGS with less work
https://ngless.embl.de
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Filtering a SAM/BAM file in a select() block inverts samline order
#105
unode
closed
5 years ago
0
can_gzip=False is not respected
#104
unode
closed
5 years ago
1
ZStandard compression breaks saving BAM files
#103
unode
closed
5 years ago
2
Add ability to strip sequences/qualities from SAM/BAM files
#102
unode
opened
5 years ago
7
bioconda recipe no longer works
#101
notestaff
closed
4 years ago
2
0.9 catalogs misnamed gene column
#100
unode
closed
5 years ago
1
Implement API to cleanup unnecessary files
#99
unode
opened
5 years ago
0
Version resources independently of releases
#98
unode
closed
5 years ago
0
orf_find(prots_out) usage?
#97
kubu4
closed
5 years ago
1
Ngless vs bionix comparison in faq?
#96
ghost
closed
5 years ago
4
Citations are printed multiple times
#95
unode
closed
5 years ago
1
Dependencies.Versions not found
#94
rekado
closed
5 years ago
5
MIN Fix errors/warnings with RefSeqInfoVector C code
#93
unode
closed
5 years ago
0
Broken pipe with samtools sort and multiple selects
#92
unode
closed
5 years ago
3
Strange error when QC some samples
#91
AlessioMilanese
closed
5 years ago
6
Rename --search-dir to --search-path
#90
unode
closed
5 years ago
3
Search-dir expansion with external modules
#89
unode
closed
5 years ago
0
Version files/indices created by bundled tools
#88
unode
closed
5 years ago
0
API for querying available versions of modules
#87
unode
opened
5 years ago
0
Pass arguments through to megahit
#86
luispedro
closed
5 years ago
0
--subsample option not working with writing out a FASTQ file.
#85
aniag
closed
5 years ago
0
Better error message when user uses MAJOR.MINOR.PATCH in the ngless version string
#84
luispedro
closed
5 years ago
0
Support `NO_COLOR` environmental variable
#83
luispedro
closed
5 years ago
0
samtools_sort API change
#82
unode
closed
5 years ago
0
It should be possible to have methods with same name on different types
#81
unode
closed
3 years ago
0
mapstats() should error with position sorted sam/bam files
#80
unode
opened
6 years ago
0
Garbage collect temporary files
#79
unode
closed
5 years ago
0
Ability to cast int/double <-> string
#78
unode
closed
3 years ago
1
tar expansion should not use so much memory
#77
luispedro
closed
5 years ago
1
Catalogs and Pig reference genome
#76
unode
closed
6 years ago
1
Improvements to qcstats (fastq, mapping) formats - explicit behavior?
#75
unode
opened
6 years ago
2
Decouple stats machinery from HTML reporting
#74
unode
opened
6 years ago
0
Include file grouping information in fqstats
#73
unode
opened
6 years ago
0
`as_reads` should not require that BAM file be sorted
#72
luispedro
opened
6 years ago
0
Implement a setup phase for external modules
#71
unode
opened
6 years ago
0
Search path API inconsistency
#70
unode
closed
5 years ago
0
select/filter reads matching/not-matching regions of interest
#69
unode
opened
6 years ago
2
lock1 fails if provided string contains folders
#68
unode
closed
6 years ago
8
TravisCI "make fast" error is non-fatal
#67
unode
closed
6 years ago
2
ENH+TST Expand subfeatures when counting with a GFF file
#66
unode
closed
6 years ago
3
Compute mapstats after select()
#65
luispedro
opened
6 years ago
0
GFF subfeature counting should be expanded
#64
unode
closed
6 years ago
1
Multiple `-1` with count() when multiple features/subfeatures are requested
#63
unode
closed
5 years ago
0
Early check for column headers in `count(.., functional_map="file.map")`
#62
luispedro
closed
4 years ago
1
Check whether file is sorted in countsfile()
#61
luispedro
closed
4 years ago
1
NGLess should restart when using `parallel` and tasks are not finished
#60
luispedro
opened
6 years ago
0
ngless copies files untouched if they are written after reading
#59
unode
closed
6 years ago
0
'when-true' unused in flags in external modules
#58
unode
closed
6 years ago
2
Decrease memory usage of count() with seqname
#57
luispedro
closed
6 years ago
1
--search-dir is not expanded prior to passing to external module
#56
unode
closed
5 years ago
4
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