Issues

• Read filtering should allow you to tell it to ignore gaps

  acorg/dark-matter#827 · Filter by author terrycojones opened on Sep 6, 2025
  

• Pylint alerts corrections as part of intervention experiment

  acorg/dark-matter#804 · Filter by author evidencebp opened on Oct 14, 2024

• window-split-alignment.py should have another option

  acorg/dark-matter#798 · Filter by author terrycojones opened on Sep 27, 2024
  

• Whitelist filtering

  acorg/dark-matter#784 · Filter by author bamueh opened on Mar 18, 2024
  6

• add flag to Taxonomy class to not create the db file if it doesn't exist

  acorg/dark-matter#775 · Filter by author imLew opened on Nov 6, 2023
  

• When writing to stdout, run-bowtie.py can throw an error

  acorg/dark-matter#771 · Filter by author terrycojones opened on Mar 23, 2023

• Try switching to pyfastx for fastq I/O

  acorg/dark-matter#765 · Filter by author terrycojones opened on May 8, 2022

• Tests fail due to DIAMOND bitscore change

  acorg/dark-matter#741 · Filter by author terrycojones opened on Jan 31, 2021
  

• Subsequence counting

  acorg/dark-matter#722 · Filter by author terrycojones opened on Mar 10, 2020
  1

  

• Reduce memory requirement of TitlesAlignments

  acorg/dark-matter#716 · Filter by author terrycojones opened on Mar 2, 2020
  

• gatk MarkDuplicates crashes if the BAM file has no reads

  acorg/dark-matter#715 · Filter by author terrycojones opened on Feb 25, 2020

• Add mapping quality filtering to SamFilter

  acorg/dark-matter#708 · Filter by author terrycojones opened on Jan 21, 2020

• AARead.ORFs doesn't return all ORFs.

  bug
  acorg/dark-matter#691 · Filter by author bamueh opened on Nov 7, 2019

• Add function to summarize protein/genome database

  acorg/dark-matter#688 · Filter by author terrycojones opened on Sep 2, 2019
  

• fasta-diff.sh issue

  acorg/dark-matter#674 · Filter by author TaliVeith opened on Apr 24, 2019

• filter-fasta.py runs out of memory

  acorg/dark-matter#669 · Filter by author terrycojones opened on Jan 25, 2019
  

• Fix DIAMOND hsp processing exception

  acorg/dark-matter#659 · Filter by author terrycojones opened on Dec 10, 2018
  1

  

• Add a sample-pathogens.index file to the out dir when making 04-panel in pipelines

  acorg/dark-matter#638 · Filter by author terrycojones opened on Nov 11, 2018

• Add pysam to requirements

  acorg/dark-matter#633 · Filter by author terrycojones opened on Oct 30, 2018

• Add --removeDuplicatesProb and --removeDuplicatesByShortId to filter-fasta.py

  enhancement
  acorg/dark-matter#626 · Filter by author terrycojones opened on Sep 19, 2018

• Add a method to write a MSA from a TitleAlignments

  enhancement
  acorg/dark-matter#539 · Filter by author terrycojones opened on Jul 21, 2017

• extract-orfs.py is out of date

  bug
  acorg/dark-matter#530 · Filter by author terrycojones opened on May 19, 2017
  

• Make it so that filter-reads-alignments.py can also save the corresponding JSON

  enhancement
  acorg/dark-matter#529 · Filter by author terrycojones opened on May 18, 2017
  

• rows can be 0 in virus panel grid calculation

  acorg/dark-matter#477 · Filter by author terrycojones opened on Dec 7, 2016

• proteins-to-viruses.py can generate a viral panel whose image is too large

  bug
  acorg/dark-matter#476 · Filter by author terrycojones opened on Dec 4, 2016