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r819: mappy to support cs/MD

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Heng Li
2018-07-24 23:29:55 -04:00
parent 8c064a5f29
commit ff9917a1c4
11 changed files with 115 additions and 28 deletions
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13
python/README.rst
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@@ -43,7 +43,7 @@ The following Python script demonstrates the key functionality of mappy:
APIs
----
Mappy implements two classes and one global function.
Mappy implements two classes and two global function.
Class mappy.Aligner
~~~~~~~~~~~~~~~~~~~
@@ -83,13 +83,15 @@ This constructor accepts the following arguments:
.. code:: python
mappy.Aligner.map(seq, seq2=None)
mappy.Aligner.map(seq, seq2=None, cs=False, MD=False)
This method aligns :code:`seq` against the index. It is a generator, *yielding*
a series of :code:`mappy.Alignment` objects. If :code:`seq2` is present, mappy
performs paired-end alignment, assuming the two ends are in the FR orientation.
Alignments of the two ends can be distinguished by the :code:`read_num` field
(see Class mappy.Alignment below).
(see Class mappy.Alignment below). Argument :code:`cs` asks mappy to generate
the :code:`cs` tag; :code:`MD` is similar. These two arguments might slightly
degrade performance and are not enabled by default.
.. code:: python
@@ -139,6 +141,11 @@ properties:
* **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two
numbers give the length and the operator of each CIGAR operation.
* **MD**: the :code:`MD` tag as in the SAM format. It is an empty string unless
the :code:`MD` argument is applied when calling :code:`mappy.Aligner.map()`.
* **cs**: the :code:`cs` tag.
An :code:`Alignment` object can be converted to a string with :code:`str()` in
the following format: