pore_c.analyses.alignments module
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pore_c.analyses.alignments.apply_per_read_filters(read_df)[source]
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pore_c.analyses.alignments.assign_fragment(pore_c_table, fragment_df, min_overlap_length: int, containment_cutoff: float)[source]
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pore_c.analyses.alignments.assign_fragments(align_table: AlignmentRecordDf, fragment_df: FragmentRecordDf, mapping_quality_cutoff: int = 1, min_overlap_length: int = 10, containment_cutoff: float = 99.0) → PoreCRecordDf[source]
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pore_c.analyses.alignments.bwa_gapscore(length, O=5, E=2)[source]
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pore_c.analyses.alignments.create_align_graph(aligns, gap_fn)[source]
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pore_c.analyses.alignments.filter_exact_overlap_on_query(read_df)[source]
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pore_c.analyses.alignments.filter_shortest_path(read_df, aligner='minimap2')[source]
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pore_c.analyses.alignments.filter_singleton(read_df)[source]
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pore_c.analyses.alignments.minimap_gapscore(length, o1=4, o2=24, e1=2, e2=1)[source]
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pore_c.analyses.alignments.to_contacts(df: PoreCRecordDf) → PoreCContactRecordDf[source]
