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Issues: czbiohub-sf/orpheum

32 Open 14 Closed
32 Open 14 Closed
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Issues list

Accept 10x bam as input and output tagged bam
#106 opened Jul 12, 2022 by olgabot
3
[Question] Use of Orpheum for non mammalian species ?
#105 opened Oct 27, 2021 by RxLoutre
Output only noncoding reads in --noncoding-nucleotide-fasta
#104 opened Aug 17, 2021 by taylorreiter
orpheum translate assigns all reads to non-coding with a jaccard index of 0
#103 opened Aug 5, 2021 by taylorreiter
1
rename jaccard to containment
#95 opened Oct 11, 2020 by pranathivemuri
rename sencha to leaftea
#94 opened Oct 11, 2020 by pranathivemuri
Output gzipped fasta files
#87 opened Aug 6, 2020 by olgabot
1
Consider using "sourmash search --containment" for "translate"
#86 opened Aug 3, 2020 by olgabot
1
Consider using MyST for Sphinx-compatible Markdown documentation
#79 opened Jun 13, 2020 by olgabot
1
What to do about B and Z amino acid letters?
#78 opened Jun 5, 2020 by olgabot
Update to sourmash Nodegraph instead of khmer to allow for computation of minimum read length
#77 opened Jun 1, 2020 by olgabot v1.1.0
1
Actually have documentation, either on readthedocs or github.io
#76 opened May 29, 2020 by olgabot
Warn users if the bloom filter table size is too small
#73 opened May 28, 2020 by olgabot
Ignore k-mers with stop codons, Selenocysteine and other nontraditional amino acids
#72 opened May 28, 2020 by olgabot
Add option to ignore short sequences when building an index
#71 opened May 28, 2020 by olgabot
add github action for auto linting with black
#70 opened May 15, 2020 by pranathivemuri
1
How big of a bloom filter should one use?
#62 opened Apr 29, 2020 by olgabot
1
Add sonarcloud code quality/smell analysis
#55 opened Apr 6, 2020 by olgabot
Revamp indexing and translating to use multiple bloom filters of different encodings and ksizes enhancement New feature or request
#52 opened Mar 24, 2020 by olgabot
Add --sensitive and --specific flags to "translate"
#51 opened Mar 23, 2020 by olgabot 1.0.0 release
Valid translation frames shouldn't be from opposite strands
#48 opened Mar 18, 2020 by olgabot
More strict filtering of low-complexity sequences enhancement New feature or request
#46 opened Mar 13, 2020 by olgabot 1.0.0 release
1
Use XOR filter instead of bloom filter for storing reference proteome
#45 opened Mar 10, 2020 by olgabot
Provide pre-computed bloom filters for extracting protein coding
#40 opened Mar 5, 2020 by olgabot 1.0.0 release
Support all-by-all comparison for noncoding / nucleotides enhancement New feature or request
#39 opened Mar 5, 2020 by olgabot
ProTip! Adding no:label will show everything without a label.