Add bw_long option to mappy's Aligner class #1124
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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 lh3#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 lh3#1111
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Mar 13, 2024
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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 500,500was observed to be partially non-applicable since the Python Wrapper,mappy, only allowed manipulation of parameterbw.In response to issue #1111, where this was originally reported, this commit introduces a modification in the Python wrapper,
mappy. Until now,mappyonly allowed manipulation of thebwparameter, preventing the suggested fix of setting-r 500,500.This commit introduces a modification in the Python wrapper to include the
bw_longoption in theAlignerclass. Consequently, both parametersbwandbw_longcan 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