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Add support for databases

Status: Open.

#268 In karel-brinda/Phylign;

· karel-brinda opened on May 23, 2024

Failed to run with custom data

Status: Open.

#265 In karel-brinda/Phylign;

· shenwei356 opened on Mar 17, 2024

LFS cluster mode: only snakemake 7.32.4 worked, 6.x or 8.x failed.

bugSomething isn't workingSomething isn't working

Status: Open.

#264 In karel-brinda/Phylign;

· shenwei356 opened on Mar 17, 2024

Add support for gzipped input files

enhancementNew feature or requestNew feature or request

Status: Open.

#259 In karel-brinda/Phylign;

· karel-brinda opened on Feb 20, 2024

Add a possibility to plug another mapper

enhancementNew feature or requestNew feature or request

Status: Open.

#231 In karel-brinda/Phylign;

· karel-brinda opened on Nov 2, 2023

batch_align.py loads up the whole query fasta into RAM

Status: Open.

#225 In karel-brinda/Phylign;

· leoisl opened on Apr 3, 2023

Add a param for no filtration appended to COBS

enhancementNew feature or requestNew feature or request

Status: Open.

#187 In karel-brinda/Phylign;

· karel-brinda opened on Sep 28, 2022

When too many query/ref pairs are reported, final_stats uses too much of memory due to its naive Python implementation

bugSomething isn't workingSomething isn't working

paper

Status: Open.

#185 In karel-brinda/Phylign;

· karel-brinda opened on Sep 23, 2022

Separate benchmarks for individual steps of <code>make match</code> and <code>make map</code> (computation, then collection of results + filtering)

enhancementNew feature or requestNew feature or request

paper

Status: Open.

#182 In karel-brinda/Phylign;

· karel-brinda opened on Sep 21, 2022

COBS postprocessing slower than COBS

fix_later

Status: Open.

#178 In karel-brinda/Phylign;

· karel-brinda opened on Sep 21, 2022

Add 3 different types of match filtration

enhancementNew feature or requestNew feature or request

low-priority

Status: Open.

#20 In karel-brinda/Phylign;

· karel-brinda opened on Apr 2, 2022

[Batch map] Consider decompressing by the tar tool instead of Python (should be much faster)

enhancementNew feature or requestNew feature or request

low-priority

Status: Open.

#7 In karel-brinda/Phylign;

· karel-brinda opened on Mar 28, 2022