From a1b7219b5dac16c2df4432407b5359f156e850c4 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 5 Aug 2018 21:32:05 -0400 Subject: [PATCH] explain added parameters --- python/README.rst | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/python/README.rst b/python/README.rst index a1e346f..7adfdd6 100644 --- a/python/README.rst +++ b/python/README.rst @@ -50,13 +50,17 @@ Class mappy.Aligner .. code:: python - mappy.Aligner(fn_idx_in, preset=None, ...) + mappy.Aligner(fn_idx_in=None, preset=None, ...) This constructor accepts the following arguments: * **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 - 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 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 -* **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