Counting Module API
===================

The counting module provides functions for allele-specific read counting from BAM files.

count_alleles
-------------

.. automodule:: counting.count_alleles
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count_alleles_sc
----------------

.. automodule:: counting.count_alleles_sc
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filter_variant_data
-------------------

.. automodule:: counting.filter_variant_data
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parse_gene_data
---------------

.. automodule:: counting.parse_gene_data
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run_counting
------------

.. automodule:: counting.run_counting
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   :exclude-members: bam_file, variant_file, region_file, samples, out_file, temp_loc, variant_prefix, vcf_bed, skip_vcf_to_bed, region_type, is_gene_file, use_region_names, intersect_file, skip_intersect, gtf_bed

run_counting_sc
---------------

.. automodule:: counting.run_counting_sc
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CLI Entry Point
---------------

.. automodule:: counting.__main__
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