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pore_c.analyses.contacts module

pore_c.analyses.contacts.export_to_cooler(contact_table, output_prefix, cooler_resolution, fragment_table, chromsizes, query, query_columns=None, by_haplotype=False)

pore_c.analyses.contacts.export_to_merged_no_dups(contact_table, output_prefix, reference_fasta, query, query_columns=None, read_length=50)

pore_c.analyses.contacts.export_to_paired_end_fastq(contact_table, output_prefix, reference_fasta, query, query_columns=None, read_length=50)

pore_c.analyses.contacts.export_to_pairs(contact_table, output_prefix, chromsizes, query, query_columns)

pore_c.analyses.contacts.export_to_salsa_bed(contact_table, output_prefix, query, query_columns)

pore_c.analyses.contacts.gather_concatemer_stats(contact_df: PoreCContactRecordDf) → PoreCConcatemerRecordDf

pore_c.analyses.contacts.summarize_concatemer_table(concatemer_df: PoreCConcatemerRecordDf, read_summary_table: str, user_metadata: Optional[Dict] = None) → pandas.core.frame.DataFrame

pore_c.analyses.alignments module pore_c.analyses.reads module