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explain added parameters

This commit is contained in:
Heng Li 2018-08-05 21:32:05 -04:00
parent b0f39a1a61
commit a1b7219b5d
1 changed files with 10 additions and 3 deletions
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python/README.rst
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@ -50,13 +50,17 @@ Class mappy.Aligner
.. code:: python .. code:: python
mappy.Aligner(fn_idx_in, preset=None, ...) mappy.Aligner(fn_idx_in=None, preset=None, ...)
This constructor accepts the following arguments: This constructor accepts the following arguments:
* **fn_idx_in**: index or sequence file name. Minimap2 automatically tests the * **fn_idx_in**: index or sequence file name. Minimap2 automatically tests the
file type. If a sequence file is provided, minimap2 builds an index. The file type. If a sequence file is provided, minimap2 builds an index. The
sequence file can be optionally gzip'd. sequence file can be optionally gzip'd. This option has no effect if **seq**
is set.
* **seq**: a single sequence to index. The sequence name will be set to
:code:`N/A`.
* **preset**: minimap2 preset. Currently, minimap2 supports the following * **preset**: minimap2 preset. Currently, minimap2 supports the following
presets: **sr** for single-end short reads; **map-pb** for PacBio presets: **sr** for single-end short reads; **map-pb** for PacBio
@ -79,7 +83,10 @@ This constructor accepts the following arguments:
* **n_threads**: number of indexing threads; 3 by default * **n_threads**: number of indexing threads; 3 by default
* **fn_idx_out**: name of file to which the index is written * **extra_flags**: additional flags defined in minimap.h
* **fn_idx_out**: name of file to which the index is written. This parameter
has no effect if **seq** is set.
.. code:: python .. code:: python