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Feature: Improve paired-end file handling to avoid comma-separated format

enhancementNew feature or requestNew feature or request

Status: Open.

#89 In scholl-lab/plasmicheck;

· berntpopp opened on Jul 7, 2025

Refactor: Centralize common CLI arguments to reduce code duplication

enhancementNew feature or requestNew feature or request

Status: Open.

#88 In scholl-lab/plasmicheck;

· berntpopp opened on Jul 7, 2025

Refactor: Implement singleton pattern for configuration management

enhancementNew feature or requestNew feature or request

Status: Open.

#87 In scholl-lab/plasmicheck;

· berntpopp opened on Jul 7, 2025

Bug: Race condition in create_indexes.py when multiple processes create indices simultaneously

bugSomething isn't workingSomething isn't working

Status: Open.

#86 In scholl-lab/plasmicheck;

· berntpopp opened on Jul 7, 2025

Performance: Optimize memory usage in compare_alignments.py for large BAM files

enhancementNew feature or requestNew feature or request

Status: Open.

#85 In scholl-lab/plasmicheck;

· berntpopp opened on Jul 7, 2025

Feat: extract splice positions (exon boundaries) from alignment

enhancementNew feature or requestNew feature or request

Status: Open.

#84 In scholl-lab/plasmicheck;

· berntpopp opened on Jan 20, 2025

feature request: other plasmid formats

enhancementNew feature or requestNew feature or request

Status: Open.

#83 In scholl-lab/plasmicheck;

· berntpopp opened on Jan 20, 2025

Feat: filter out ambigious reads or reads mapping only to the plamid on calculation somehow

enhancementNew feature or requestNew feature or request

Status: Open.

#82 In scholl-lab/plasmicheck;

· berntpopp opened on Jan 20, 2025

Bug:template files not integrated in package or not found correctly

bugSomething isn't workingSomething isn't working

Status: Open.

#81 In scholl-lab/plasmicheck;

· berntpopp opened on Jan 20, 2025

Chore: structure the output folders more with subfodlers

enhancementNew feature or requestNew feature or request

Status: Open.

#80 In scholl-lab/plasmicheck;

· berntpopp opened on Jan 20, 2025

bug: alt has "wahr" in excel

bugSomething isn't workingSomething isn't working

Status: Open.

#79 In scholl-lab/plasmicheck;

· berntpopp opened on Jan 20, 2025

bug: jobs not finished in snakemake script (randomly, restart and they finish)

bugSomething isn't workingSomething isn't working

Status: Open.

#78 In scholl-lab/plasmicheck;

· berntpopp opened on Jan 20, 2025