.. _references_io:

References (IO / file formats)
##############################

.. contents::
   :local:

FASTA
=====

.. automodule:: sequana.fasta
    :members:
    :undoc-members:

.. automodule:: sequana.protein
    :members:
    :undoc-members:

FASTQ
=====

.. automodule:: sequana.fastq
    :members:
    :undoc-members:

.. automodule:: sequana.fastq_splitter
    :members:
    :undoc-members:

.. automodule:: sequana.fastqc
    :members:
    :undoc-members:

BED / wig / mpileup
===================

.. automodule:: sequana.bed
    :members:
    :undoc-members:

.. automodule:: sequana.wigtools
    :members:
    :undoc-members:

.. automodule:: sequana.mpileup
    :members:
    :undoc-members:

GFF / GTF / GenBank / GFA
=========================

.. automodule:: sequana.gff3
    :members:
    :undoc-members:

.. automodule:: sequana.genbank
    :members:
    :undoc-members:

.. automodule:: sequana.gtf_fixer
    :members:
    :undoc-members:

.. automodule:: sequana.gfa
    :members:
    :undoc-members:

.. automodule:: sequana.fasta_gff_correction
    :members:
    :undoc-members:

.. automodule:: sequana.annotation
    :members:
    :undoc-members:

VCF
===

.. automodule:: sequana.freebayes_vcf_filter
    :members:
    :undoc-members:

.. automodule:: sequana.vcftools
    :members:
    :undoc-members:

.. automodule:: sequana.variants
    :members:
    :undoc-members:

Other formats
=============

.. automodule:: sequana.hmmtools
    :members:
    :undoc-members:

.. automodule:: sequana.mgi
    :members:
    :undoc-members:

.. automodule:: sequana.iem
    :members:
    :undoc-members:

.. automodule:: sequana.cigar
    :members:
    :undoc-members:

.. automodule:: sequana.sniffer
    :members:
    :undoc-members: