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

python/README.rst

@@ -77,7 +77,9 @@ This constructor accepts the following arguments:
 
 * **min_chain_score**: minimum chaing score
 
-* **bw**: chaining and alignment band width
+* **bw**: chaining and alignment band width (initial chaining and extension)
+
+* **bw_long**: chaining and alignment band width (RMQ-based rechaining and closing gaps)
 
 * **best_n**: max number of alignments to return