modos.genomics.cram

Utilities to interact with genomic intervals in CRAM files.

Functions

extract_metadata(instance, base_path)	Extract metadata from the CRAM file header and
validate_cram_files(cram_path)	Validate CRAM files using pysam.
create_sequence_id(name, sequence_md5)	Helper function to create a unique id from a sequence name and md5 hash

Module Contents

modos.genomics.cram.extract_metadata(instance, base_path)

Extract metadata from the CRAM file header and convert specific attributes according to the modo schema.

Parameters:

• instance (modos_schema.datamodel.AlignmentSet)

• base_path (pathlib.Path)

Return type:

list[modos_schema.datamodel.ReferenceSequence]

modos.genomics.cram.validate_cram_files(cram_path)

Validate CRAM files using pysam. Checks if the file is sorted and has an index.

Parameters:

cram_path (str)

modos.genomics.cram.create_sequence_id(name, sequence_md5)

Helper function to create a unique id from a sequence name and md5 hash

Parameters:

• name (str)

• sequence_md5 (str)

Return type:

str