api.rst

FGPYO

API

SAM/BAM/CRAM files

.. automodule:: fgpyo.sam
   :members:

.. automodule:: fgpyo.sam.builder
   :members:

.. automodule:: fgpyo.sam.clipping
   :members:

VCF/BCF files

.. automodule:: fgpyo.vcf
   :members:

.. automodule:: fgpyo.vcf.builder
   :members:

FASTA files

.. automodule:: fgpyo.fasta.builder
   :members:

FASTX files

.. automodule:: fgpyo.fastx
   :members:

Metric files

.. automodule:: fgpyo.util.metric
   :members:

.. autofunction:: fgpyo.util.inspect.attr_from
   :noindex:

.. seealso::

   https://docs.python.org/3/library/dataclasses.html
       Documentation for the dataclasses standard module

   https://www.attrs.org/en/stable/examples.html

       The attrs website for bringing back the joy to writing classes.

Read Structures

.. automodule:: fgpyo.read_structure
   :members:

.. seealso::

   https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures

       The fgbio wiki for an explanation of Read Structures.

Manipulating DNA and RNA Sequences

.. automodule:: fgpyo.sequence
   :members:

Collections

.. automodule:: fgpyo.collections
   :members:

Logging

.. automodule:: fgpyo.util.logging
   :members:

IO

.. automodule:: fgpyo.io
   :members:

Utility Functions

.. automodule:: fgpyo.util.inspect
   :members:

.. automodule:: fgpyo.util.string
   :members:

.. automodule:: fgpyo.util.types
   :members: