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nh13 committed Jan 9, 2025
1 parent 8430d73 commit fb48b7a
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4 changes: 2 additions & 2 deletions docs/api.rst
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Expand Up @@ -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
Expand All @@ -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
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5 changes: 4 additions & 1 deletion docs/conf.py
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Expand Up @@ -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']
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