acorg / dark-matter

Virus discovery

acorg/dark-matter Issues

Whitelist filtering
Updated 4 months ago6
bin/sam-reference-read-counts.py raises an IndexError when there are no reads
Closed 4 months ago
fasta-identity-table.py can raise a KeyError on a non-square table
Closed 4 months ago
add flag to Taxonomy class to not create the db file if it doesn't exist
Updated 9 months ago
When writing to stdout, run-bowtie.py can throw an error
Updated a year ago
Try switching to pyfastx for fastq I/O
Updated 2 years ago
There must be a bug in --removeDuplicatesUseMD5
Closed 3 years ago1
Remove pyfaidx usage
Closed 3 years ago
Tests fail due to DIAMOND bitscore change
Updated 3 years ago
ImportError: Bio.Alphabet has been removed from Biopython
Updated 3 years ago1
Make it possible to set perms on the tmp dir created by run-bowtie2.py
Closed 3 years ago
Add filtering options for maximum number of Ns in a sequence
Closed 4 years ago
Add collapsing of samples and pathogens, and maybe a next/prev button for both
Closed 4 years ago
Subsequence counting
Updated 4 years ago1
Add a parseRangeExpression to utils.py to expand range expressions
Closed 4 years ago
Add some way to make a protein/genome database that only has a single betacoronavirus
Closed 4 years ago
Add script to filter FASTA, only emitting variable sites
Closed 4 years ago
Reduce memory requirement of TitlesAlignments
Updated 4 years ago
gatk MarkDuplicates crashes if the BAM file has no reads
Updated 4 years ago
Add various options to some scripts
Closed 4 years ago
Add consensus-making script
Closed 4 years ago
Add run-bowtie2.py command
Closed 4 years ago
Add mapping quality filtering to SamFilter
Updated 5 years ago
Call to needle can result in error if sequences are too long
Closed 5 years ago
Add a script to print per-offset coverage and overall coverage stats from a SAM/BAM file
Closed 5 years ago
Add --minGenomeLength to make-protein-database.py
Closed 5 years ago
Add tool to summarize protein hits in a SAM/BAM file
Closed 5 years ago
Add filtering for percentage similarity on DIAMOND results
Closed 5 years ago
Add read filtering by percent identity match (in DIAMOND output)
Closed 5 years ago
Add --color and --defaultColor args to proteins-to-pathogens-civ.py
Closed 5 years ago
AARead.ORFs doesn't return all ORFs.
Updated 5 years ago
Add a pathogen taxonomy tree
Closed 5 years ago
Add function to summarize protein/genome database
Updated 5 years ago
Add options to proteins-to-pathogens.py to omit virus links and incorrect virus protein counts
Closed 5 years ago
Add file of all reads for a pathogen to HTML output
Closed 5 years ago
Add --blacklistFile and --whitelistFile options to noninteractive-alignment-panel.py
Closed 5 years ago
Add title regex (positive and negative) to protein grouper
Closed 5 years ago
Add a way to pass a title to proteins-to-pathogens.py for HTML output
Closed 5 years ago
Slightly refactor SAMFilter class so we can also filter alignments in a pileup
Closed 5 years ago
fasta-diff.sh issue
Updated 5 years ago
Add a script to make a protein database
Closed 5 years ago
ORFs yields incorrect AAReadORF
Closed 5 years ago
filter-fasta.py runs out of memory
Updated 5 years ago
Add the matchToString method (from midtools) to dna.py
Closed 6 years ago
Add --reverse and --reverseCompliment options to filter-fasta.py
Closed 6 years ago
Extract-ORFs.py mistranslates lowercase letters
Closed 6 years ago1
Allow a --sampleName option in proteins-to-pathogens
Closed 6 years ago
Fix DIAMOND hsp processing exception
Updated 6 years ago1
Add compareAAReads function (to match compareDNAReads)
Closed 6 years ago
Fix bug in extract-ORFs.py
Closed 6 years ago