Index

A

AGCFile (class in pgrtk.pgrtk)

append_from_fastx() (pgrtk.pgrtk.SeqIndexDB method)

C

compute_graph_diffusion_entropy() (in module pgrtk)

ctg_lens (pgrtk.pgrtk.AGCFile attribute)

G

generate_mapg_gfa() (pgrtk.pgrtk.SeqIndexDB method) generate_principal_mapg_gfa() (pgrtk.pgrtk.SeqIndexDB method) get_match_positions_with_fragment() (pgrtk.pgrtk.SeqIndexDB method) get_principal_bundle_decomposition() (pgrtk.pgrtk.SeqIndexDB method) get_principal_bundle_projection() (pgrtk.pgrtk.SeqIndexDB method) get_principal_bundles() (pgrtk.pgrtk.SeqIndexDB method) get_principle_bundle_bed_file_for_query() (in module pgrtk) get_seq() (pgrtk.pgrtk.AGCFile method) (pgrtk.pgrtk.SeqIndexDB method) get_seq_by_id() (pgrtk.pgrtk.SeqIndexDB method) get_shmmr_dots() (in module pgrtk.pgrtk) get_shmmr_map() (pgrtk.pgrtk.SeqIndexDB method)

get_shmmr_pair_count() (pgrtk.pgrtk.SeqIndexDB method) get_shmmr_pair_list() (pgrtk.pgrtk.SeqIndexDB method) get_shmmr_pair_source_count() (pgrtk.pgrtk.SeqIndexDB method) get_shmmr_pairs_from_seq() (in module pgrtk.pgrtk) get_shmmr_spec() (pgrtk.pgrtk.SeqIndexDB method) get_smp_adj_list() (pgrtk.pgrtk.SeqIndexDB method) get_sub_seq() (pgrtk.pgrtk.AGCFile method) (pgrtk.pgrtk.SeqIndexDB method) get_sub_seq_by_id() (pgrtk.pgrtk.SeqIndexDB method) get_variant_calls() (in module pgrtk) get_vertex_map_from_principal_bundles() (pgrtk.pgrtk.SeqIndexDB method) group_smps_by_principle_bundle_id() (in module pgrtk) guided_shmmr_dbg_consensus() (in module pgrtk.pgrtk)

L

load_from_agc_index() (pgrtk.pgrtk.SeqIndexDB method) load_from_fastx() (pgrtk.pgrtk.SeqIndexDB method)

load_from_frg_index() (pgrtk.pgrtk.SeqIndexDB method) load_from_seq_list() (pgrtk.pgrtk.SeqIndexDB method)

M

map_intervals_in_sdb() (in module pgrtk) map_positions_in_seq() (pgrtk.pgrtk.SeqIndexDB method) merge_regions() (in module pgrtk)

module pgrtk pgrtk.pgrtk

N

naive_dbg_consensus() (in module pgrtk.pgrtk)

O

output_variants_to_vcf_records() (in module pgrtk)

P

pgr_lib_version() (in module pgrtk.pgrtk) pgrtk module

pgrtk.pgrtk module

Q

query_fragment() (pgrtk.pgrtk.SeqIndexDB method)

query_fragment_to_hps() (pgrtk.pgrtk.SeqIndexDB method) query_sdb() (in module pgrtk)

R

rc() (in module pgrtk)

rc_byte_seq() (in module pgrtk) rc_u8_seq() (in module pgrtk)

S

seq_index (pgrtk.pgrtk.SeqIndexDB attribute) seq_info (pgrtk.pgrtk.SeqIndexDB attribute) SeqIndexDB (class in pgrtk.pgrtk) shmmr_dbg_consensus() (in module pgrtk.pgrtk)

shmmr_sparse_aln_consensus() (in module pgrtk.pgrtk) (pgrtk.pgrtk.SeqIndexDB method) sort_adj_list_by_weighted_dfs() (pgrtk.pgrtk.SeqIndexDB method) sparse_aln() (in module pgrtk.pgrtk) string_to_u8() (in module pgrtk)

U

u8_to_string() (in module pgrtk)

W

write_frag_and_index_files() (pgrtk.pgrtk.SeqIndexDB method)

write_mapg_idx() (pgrtk.pgrtk.SeqIndexDB method) write_midx_to_text_file() (pgrtk.pgrtk.SeqIndexDB method)