From f8cb865ec5b174feb543274be22122eccd1c24dc Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 16 Sep 2017 22:52:26 -0400 Subject: [PATCH 1/2] fixed a few typos --- python/README.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/python/README.rst b/python/README.rst index 7eab1fe..5b6e5a2 100644 --- a/python/README.rst +++ b/python/README.rst @@ -9,7 +9,7 @@ minimap2 and provides a convenient interface to calling minimap2 in Python. Installation ------------ -The minimap2 model can be installed directly with: +The minimap2 module can be installed directly with: .. code:: shell @@ -31,13 +31,13 @@ The following Python program shows the key functionality of this module: .. code:: python import minimap2 as mm - a = mm.Aligner("test/MT-human.fa") + a = mm.Aligner("test/MT-human.fa") # load or build index if not a: raise Exception("ERROR: failed to load/build index") for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"): print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str)) It builds an index from the specified sequence file (or loads an index if a -pre-built index is supplied), aligns a sequence against it, traverses each hit +pre-built index is specified), aligns a sequence against it, traverses each hit and prints them out. APIs @@ -81,9 +81,9 @@ Arguments: .. code:: python - map(query_seq) + map(seq) -This methods maps :code:`query_seq` against the index. It *yields* a generator, +This method maps :code:`seq` against the index. It *yields* a generator, generating a series of :code:`Alignment` objects. Class minimap2.Alignment From 38aa9aa9a7588b8cf29017783eb8e5dde6a8cf34 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 16 Sep 2017 22:52:52 -0400 Subject: [PATCH 2/2] eh... a missing fix --- python/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/README.rst b/python/README.rst index 5b6e5a2..27a1cd3 100644 --- a/python/README.rst +++ b/python/README.rst @@ -118,7 +118,7 @@ This class has the following 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. -An Alignment object can be converted to a string in the following format: +An :code:`Alignment` object can be converted to a string in the following format: ::