zhemingfan

Multithreading support?

2

Hi @cjain7, I was wondering if there was any multithreading support for Winnowmap.

Feature Request: Flag in ampliconclip to clip out everything except target sequence

2

#### Is your feature request related to a problem? Please specify. Though `ampliconclip` was meant to clip out primer locations, I'm working on a problem involved currently interested in only...

Unused variables in validation module

2

Certain parts of the validate module contains redundant code: For example - count: https://github.com/bcgsc/mavis/blob/develop_v3/src/mavis/validate/align.py#L417 Align_options for BWA-MEM, which doesn't use any additional align parameter. https://github.com/bcgsc/mavis/blob/develop_v3/src/mavis/validate/align.py#L464 These should be removed or...

Change support for MAVIS input

1

Addresses issues in https://github.com/bcgsc/mavis/issues/307

Add local assembly support for breakpoint validation in Nanopore inputs

1

## **Overview** From internal testing, [wtdbg2](https://github.com/ruanjue/wtdbg2) (long read SV assembler) performs well for assembly of breakpoints, something that MAVIS must implement. The following changes must be made to integrate [wtdbg2](https://github.com/ruanjue/wtdbg2):...

Hg38 will remain the workhorse genome for annotation work, but in case users are interested in working with CHM13-T2T in the future - there should be a feature that converts...

Sometimes gene fusion products are far away from the spliced sites. In the future, it would be ideal if MAVIS could integrate transcriptomic data with the fusion calls with genomics...

Currently, a call with: `chr1: chr2 bp1_start: 79836749 IMPRECISE SVTYPE=DEL SVLEN=-28364; ND=79865113 CIPOS=-29,29 CILEN=-53635,53635 ` is being improperly converted to a BPP(Breakpoint(2:79836720-79836778R), Breakpoint(2:79851791-79852493L)

## **Overview** Currently, the Summary module takes in a tab delimited file (similar to a `.bed` file) as the input. For future iterations, we want to change it to a...

**Describe the bug** The sections on the [annotation page of the documentation](https://mavis.readthedocs.io/en/latest/package/mavis/annotate/ ) are not rendering the images. **To Reproduce** Visible on the [annotation page](https://mavis.readthedocs.io/en/latest/package/mavis/annotate/). **Expected behavior** Image for the...