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38 Open 354 Closed
38 Open 354 Closed
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Issues list

Pylint alerts corrections as part of intervention experiment
#804 opened Oct 14, 2024 by evidencebp
window-split-alignment.py should have another option
#798 opened Sep 27, 2024 by terrycojones
@terrycojones
Whitelist filtering
#784 opened Mar 18, 2024 by bamueh
6
add flag to Taxonomy class to not create the db file if it doesn't exist
#775 opened Nov 6, 2023 by imLew
@imLew
When writing to stdout, run-bowtie.py can throw an error
#771 opened Mar 23, 2023 by terrycojones
Try switching to pyfastx for fastq I/O
#765 opened May 8, 2022 by terrycojones
Tests fail due to DIAMOND bitscore change
#741 opened Jan 31, 2021 by terrycojones
@terrycojones
ImportError: Bio.Alphabet has been removed from Biopython
#739 opened Jan 28, 2021 by UdoGi
1
Subsequence counting
#722 opened Mar 10, 2020 by terrycojones
@TaliVeith
1
Reduce memory requirement of TitlesAlignments
#716 opened Mar 2, 2020 by terrycojones
@terrycojones
gatk MarkDuplicates crashes if the BAM file has no reads
#715 opened Feb 25, 2020 by terrycojones
Add mapping quality filtering to SamFilter
#708 opened Jan 21, 2020 by terrycojones
AARead.ORFs doesn't return all ORFs. bug
#691 opened Nov 7, 2019 by bamueh
Add function to summarize protein/genome database
#688 opened Sep 2, 2019 by terrycojones
@terrycojones
fasta-diff.sh issue
#674 opened Apr 24, 2019 by TaliVeith
filter-fasta.py runs out of memory
#669 opened Jan 25, 2019 by terrycojones
@terrycojones
Fix DIAMOND hsp processing exception
#659 opened Dec 10, 2018 by terrycojones
@terrycojones
1
Add a sample-pathogens.index file to the out dir when making 04-panel in pipelines
#638 opened Nov 11, 2018 by terrycojones
Add pysam to requirements
#633 opened Oct 30, 2018 by terrycojones
Add --removeDuplicatesProb and --removeDuplicatesByShortId to filter-fasta.py enhancement
#626 opened Sep 19, 2018 by terrycojones
Add a method to write a MSA from a TitleAlignments enhancement
#539 opened Jul 21, 2017 by terrycojones
extract-orfs.py is out of date bug
#530 opened May 19, 2017 by terrycojones
@terrycojones
Make it so that filter-reads-alignments.py can also save the corresponding JSON enhancement
#529 opened May 18, 2017 by terrycojones
@terrycojones
rows can be 0 in virus panel grid calculation
#477 opened Dec 7, 2016 by terrycojones
proteins-to-viruses.py can generate a viral panel whose image is too large bug
#476 opened Dec 4, 2016 by terrycojones
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