From fb48b7a62920a316b8f75740386c514d2a2d1961 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Thu, 9 Jan 2025 12:02:47 -0700 Subject: [PATCH] updates --- docs/api.rst | 4 ++-- docs/conf.py | 5 ++++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/api.rst b/docs/api.rst index 1d98080..35fcbe8 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -27,7 +27,7 @@ or from pybwa import BwaMem mem = BwaMem(prefix="/path/to/genome.fasta") -The :meth:`pybwa.BwaAln.align` method accepts a list of reads (as either strings or :class:`pysam.FastxRecord`s) to +The :meth:`pybwa.BwaAln.align` method accepts a list of reads (as either strings or :class:`pysam.FastxRecord` s) to align and return a *single* :class:`~pysam.AlignedSegment` per input read: .. code-block:: python @@ -41,7 +41,7 @@ gives: read.1 0 chr1 1 37 7M * 0 0 GATTACA * XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:7 -The :meth:`pybwa.BwaMem.align` method accepts a list of reads (as either strings or :class:`pysam.FastxRecord`s) to +The :meth:`pybwa.BwaMem.align` method accepts a list of reads (as either strings or :class:`pysam.FastxRecord` s) to align and return a *list* of :class:`pysam.AlignedSegment` per input read: .. code-block:: python diff --git a/docs/conf.py b/docs/conf.py index 55e28c4..7b40bec 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -32,7 +32,10 @@ 'sphinx.ext.intersphinx', 'sphinx.ext.napoleon'] -intersphinx_mapping = {'python': ('http://docs.python.org/3.8', None)} +intersphinx_mapping = { + 'python': ('http://docs.python.org/3.8', None), + 'pysam': ('https://pysam.readthedocs.io/en/latest', None) +} # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates']