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fixed a few typos
eh... a missing fix
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@@ -9,7 +9,7 @@ minimap2 and provides a convenient interface to calling minimap2 in Python.
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Installation
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------------
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The minimap2 model can be installed directly with:
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The minimap2 module can be installed directly with:
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.. code:: shell
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@@ -31,13 +31,13 @@ The following Python program shows the key functionality of this module:
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.. code:: python
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import minimap2 as mm
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a = mm.Aligner("test/MT-human.fa")
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a = mm.Aligner("test/MT-human.fa") # load or build index
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if not a: raise Exception("ERROR: failed to load/build index")
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for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
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print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
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It builds an index from the specified sequence file (or loads an index if a
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pre-built index is supplied), aligns a sequence against it, traverses each hit
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pre-built index is specified), aligns a sequence against it, traverses each hit
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and prints them out.
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APIs
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@@ -81,9 +81,9 @@ Arguments:
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.. code:: python
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map(query_seq)
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map(seq)
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This methods maps :code:`query_seq` against the index. It *yields* a generator,
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This method maps :code:`seq` against the index. It *yields* a generator,
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generating a series of :code:`Alignment` objects.
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Class minimap2.Alignment
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@@ -118,7 +118,7 @@ This class has the following properties:
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* **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two
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numbers give the length and the operator of each CIGAR operation.
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An Alignment object can be converted to a string in the following format:
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An :code:`Alignment` object can be converted to a string in the following format:
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::
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