From internal testing, 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:
[x] Ensure that local assemblies can validate known breakpoints
[ ] @zhemingfan will add a test for collecting informative reads from a bam file (add a function to the gather.py file and accompanying unit tests
[ ] @creisle will add a function to the bam.read module to process/simplify long read assembly alignments by removing indels below a certain size threshold as they are likely to be artifacts. This will ensure we can still use the CIGAR string of the alignment to call events downstream
[ ] TODO: add option to config to support bam types (long read vs paired end short read etc)
Overview
From internal testing, 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: