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Read filtering should allow you to tell it to ignore gaps

Status: Open.

#827 In acorg/dark-matter;

· terrycojones opened on Sep 6, 2025

Pylint alerts corrections as part of intervention experiment

Status: Open.

#804 In acorg/dark-matter;

· evidencebp opened on Oct 14, 2024

window-split-alignment.py should have another option

Status: Open.

#798 In acorg/dark-matter;

· terrycojones opened on Sep 27, 2024

Whitelist filtering

Status: Open.

#784 In acorg/dark-matter;

· bamueh opened on Mar 18, 2024

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

Status: Open.

#775 In acorg/dark-matter;

· imLew opened on Nov 6, 2023

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

Status: Open.

#771 In acorg/dark-matter;

· terrycojones opened on Mar 23, 2023

Try switching to pyfastx for fastq I/O

Status: Open.

#765 In acorg/dark-matter;

· terrycojones opened on May 8, 2022

Tests fail due to DIAMOND bitscore change

Status: Open.

#741 In acorg/dark-matter;

· terrycojones opened on Jan 31, 2021

Subsequence counting

Status: Open.

#722 In acorg/dark-matter;

· terrycojones opened on Mar 10, 2020

Reduce memory requirement of TitlesAlignments

Status: Open.

#716 In acorg/dark-matter;

· terrycojones opened on Mar 2, 2020

gatk MarkDuplicates crashes if the BAM file has no reads

Status: Open.

#715 In acorg/dark-matter;

· terrycojones opened on Feb 25, 2020

Add mapping quality filtering to SamFilter

Status: Open.

#708 In acorg/dark-matter;

· terrycojones opened on Jan 21, 2020