Make "API" a top-level heading
This makes it available as an entry in the navigation menu
pysam - An interface for reading and writing SAM files
======================================================
-Introduction
-============
-
Pysam is a python module that makes it easy to read and manipulate
mapped short read sequence data stored in SAM/BAM files. It is a
lightweight wrapper of the htslib_ C-API.
@@ -130,11 +127,12 @@ More detailed usage instructions is at :ref:`usage`.
The pysam website containing documentation
+===
API
===
SAM/BAM/CRAM files
--------------------
+==================
Objects of type :class:`~pysam.AlignmentFile` allow working with
BAM/SAM formatted files.
@@ -162,7 +160,7 @@ a SAM/BAM file.
Tabix files
------------
+===========
:class:`~pysam.TabixFile` opens tabular files that have been
indexed with tabix_.
@@ -192,13 +190,13 @@ To iterate over tabix files, use :func:`~pysam.tabix_iterator`:
Fasta files
------------
+===========
.. autoclass:: pysam.FastaFile
:members:
Fastq files
------------
+===========
.. autoclass:: pysam.FastxFile
:members:
@@ -209,7 +207,7 @@ Fastq files
VCF files
----------
+=========
.. autoclass:: pysam.VariantFile
:members:
@@ -224,7 +222,7 @@ VCF files
:members:
HTSFile
--------
+=======
HTSFile is the base class for :class:`pysam.AlignmentFile` and
:class:`pysam.VariantFile`.
