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allow mappy to change scoring

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Heng Li
2018-08-06 09:52:13 -04:00
parent 8e606bcc06
commit 9a567e4b37
2 changed files with 15 additions and 1 deletions
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python/README.rst
+6
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@@ -88,6 +88,12 @@ This constructor accepts the following arguments:
* **fn_idx_out**: name of file to which the index is written. This parameter
has no effect if **seq** is set.
* **scoring**: scoring system. It is a tuple/list consisting of 4, 6 or 7
positive integers. The first 4 elements specify match scoring, mismatch
penalty, gap open and gap extension penalty. The 5th and 6th elements, if
present, set long-gap open and long-gap extension penalty. The 7th sets a
mismatch penalty involving ambiguous bases.
.. code:: python
mappy.Aligner.map(seq, seq2=None, cs=False, MD=False)