Donaim ae05f8485f Add bw_long option to mappy's Aligner class (#1124) ...

The Minimap2 behavior was found to handle sequences with large
deletions differently when upgraded from v2.17 to v2.26, causing
potential issues in projects mapping extensive deletions of ~1200 base
pairs. The originally suggested solution of setting `-r 500,500` was
observed to be partially non-applicable since the Python Wrapper,
`mappy`, only allowed manipulation of parameter `bw`.

In response to issue #1111, where this was originally reported,
this commit introduces a modification in the Python wrapper,
`mappy`. Until now, `mappy` only allowed manipulation of the `bw`
parameter, preventing the suggested fix of setting `-r 500,500`.

This commit introduces a modification in the Python wrapper to include
the `bw_long` option in the `Aligner` class. Consequently, both
parameters `bw` and `bw_long` can be manipulated, thereby allowing the
desired Minimap2 behavior encountered in version 2.17. As a result,
this patch ensures consistent handling of sequences containing large
deletions irrespective of the version upgrade."

Closes #1111

2023-10-24 09:23:06 -04:00

6.4 KiB

Raw Blame History

View Raw