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Functions
3,192 in github.com/chhylp123/hifiasm
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Functions
3,192
◇
Types & classes
18
↓ 2 callers
Function
yak_ch_restore_core
Trio.cpp:66
↓ 2 callers
Function
yak_cputime
sys.cpp:9
↓ 1 callers
Function
CommandLine_process
CommandLines.cpp:865
↓ 1 callers
Function
GetCeilIndex
Binary search
Purge_Dups.cpp:1619
↓ 1 callers
Function
InitHaplotypeEvdience_buf
Correct.h:940
↓ 1 callers
Function
InsertSNPVector
Correct.h:655
↓ 1 callers
Function
LeastSquare_advance
hic.cpp:6820
↓ 1 callers
Function
Merge_DAGCon
Correct.cpp:5031
↓ 1 callers
Function
Merge_In_Nodes
Correct.cpp:4806
↓ 1 callers
Function
Merge_Out_Nodes
Correct.cpp:4700
↓ 1 callers
Function
Pop_Node
POA.h:216
↓ 1 callers
Function
Preorder_Merge_Advance_Repeat
Correct.cpp:7787
↓ 1 callers
Function
_count_seq_buf
buf is the read block, k is the k-mer length, p = 12, len is the read length, seq is the read**/
htab.cpp:608
↓ 1 callers
Function
_count_seq_buf_HPC
htab.cpp:627
↓ 1 callers
Function
_ha_pt_insert_list
htab.cpp:646
↓ 1 callers
Function
_pt_insert_buf
htab.cpp:697
↓ 1 callers
Function
_qfw
sketch.cpp:226
↓ 1 callers
Function
_refine_sketch
sketch.cpp:376
↓ 1 callers
Function
_select_mz_h
sketch.cpp:247
↓ 1 callers
Function
add_cigar_to_cigar
Correct.cpp:5681
↓ 1 callers
Function
add_cns_arc_bp
ecovlp.cpp:602
↓ 1 callers
Function
add_deletionEdge_weight
POA.h:559
↓ 1 callers
Function
add_existing_cell_to_cigar_record
Correct.cpp:11352
↓ 1 callers
Function
add_insertionEdge_weight
POA.h:731
↓ 1 callers
Function
add_mismatchEdge_weight
just for mimatch edges
POA.h:494
↓ 1 callers
Function
add_mul_convex
hic.cpp:5676
↓ 1 callers
Function
add_new_cell_to_cigar_record
Correct.cpp:11333
↓ 1 callers
Function
add_overlaps
Overlaps.cpp:790
↓ 1 callers
Function
add_single_deletionEdge_weight
POA.h:536
↓ 1 callers
Function
add_to_result_snp_vector
Correct.cpp:7527
↓ 1 callers
Function
adjust_base_coordinates
Correct.cpp:16547
↓ 1 callers
Function
adjust_contig_partition
hic.cpp:11041
↓ 1 callers
Function
adjust_exact_match
ecovlp.cpp:3454
↓ 1 callers
Function
adjust_gap
Correct.cpp:25167
↓ 1 callers
Function
adjust_specific_ext_offset
Correct.cpp:14424
↓ 1 callers
Function
adjust_weight_kv_u_trans_advance
hic.cpp:15893
↓ 1 callers
Function
align_hc_ed_post_non_retrieve_extz
Correct.cpp:13014
↓ 1 callers
Function
alignment_ul_pipeline
inter.cpp:12868
↓ 1 callers
Function
all_to_all_deduplicate
note: to use this function, don't renew unitig graph!!!!!!!!!
Overlaps.cpp:20458
↓ 1 callers
Function
append_aligned_integer_seq_by_aln_pair
gfa_ut.cpp:5644
↓ 1 callers
Function
append_boundary_chain
hic.cpp:9516
↓ 1 callers
Function
append_connective
gfa_ut.cpp:4670
↓ 1 callers
Function
append_inexact_edges
inter.cpp:20962
↓ 1 callers
Function
append_inexact_overlap_region_alloc
Hash_Table.cpp:340
↓ 1 callers
Function
append_ma_utg_t
Overlaps.cpp:27910
↓ 1 callers
Function
append_miss_nid
Overlaps.cpp:21514
↓ 1 callers
Function
append_notrans_e
gfa_ut.cpp:2019
↓ 1 callers
Function
append_path_connec
inter.cpp:19229
↓ 1 callers
Function
append_tig_link
hic.cpp:4711
↓ 1 callers
Function
append_trans_check
gfa_ut.cpp:2060
↓ 1 callers
Function
append_trans_hits
hic.cpp:15797
↓ 1 callers
Function
append_unmatch_integer_seq
gfa_ut.cpp:5421
↓ 1 callers
Function
append_utg
Overlaps.cpp:32221
↓ 1 callers
Function
append_utg_es
gfa_ut.cpp:7913
↓ 1 callers
Function
append_utg_inexact_overlap_region_alloc
Hash_Table.cpp:507
↓ 1 callers
Function
append_wcigar
Correct.cpp:15955
↓ 1 callers
Function
asg_F_seq_set
Overlaps.cpp:913
↓ 1 callers
Function
asg_arc_cut_bub_links
gfa_ut.cpp:2355
↓ 1 callers
Function
asg_arc_cut_complex_bub_links
gfa_ut.cpp:2453
↓ 1 callers
Function
asg_arc_decompress_mul
tovlp.cpp:1132
↓ 1 callers
Function
asg_arc_del_asymm
remove asymmetric arcs: u->v is present, but v'->u' not
Overlaps.cpp:1008
↓ 1 callers
Function
asg_arc_del_single_node_directly
Overlaps.cpp:5104
↓ 1 callers
Function
asg_arc_index
Overlaps.cpp:892
↓ 1 callers
Function
asg_arc_index_core
Overlaps.cpp:872
↓ 1 callers
Function
asg_arc_push_contain_trans
inter.cpp:21742
↓ 1 callers
Function
asg_arc_rest
Overlaps.cpp:26496
↓ 1 callers
Function
asg_arc_rm
hard remove arcs marked as "del"
Overlaps.cpp:932
↓ 1 callers
Function
asg_arc_sort
Overlaps.cpp:784
↓ 1 callers
Function
asg_bub_backtrack_check_switch
in a resolved bubble, mark unused vertices and arcs as "reduced"
Overlaps.cpp:24185
↓ 1 callers
Function
asg_bub_backtrack_primary_cov
in a resolved bubble, mark unused vertices and arcs as "reduced"
Overlaps.cpp:23909
↓ 1 callers
Function
asg_bub_collect_ovlp
tovlp.cpp:707
↓ 1 callers
Function
asg_bub_pop1_purge_graph
Purge_Dups.cpp:3624
↓ 1 callers
Function
asg_clean_idx_tig
inter.cpp:19299
↓ 1 callers
Function
asg_cut_chimeric_bub
gfa_ut.cpp:2578
↓ 1 callers
Function
asg_cut_large_indel
gfa_ut.cpp:2636
↓ 1 callers
Function
asg_pop_bubble_primary_trio
tovlp.cpp:1040
↓ 1 callers
Function
asg_pop_bubble_purge_graph
pop bubbles
Purge_Dups.cpp:3742
↓ 1 callers
Function
assgin_mb_node
rcut.cpp:419
↓ 1 callers
Function
assign_per_unitig_G_partition
hic.cpp:12424
↓ 1 callers
Function
ava_pass_unique_bridge_cov
gfa_ut.cpp:13238
↓ 1 callers
Function
ava_pass_unique_bridge_tips
gfa_ut.cpp:12249
↓ 1 callers
Function
benchmark_hic_graph
Overlaps.cpp:17793
↓ 1 callers
Function
best_bp
rcut.cpp:1973
↓ 1 callers
Function
boundary_verify
Overlaps.cpp:2043
↓ 1 callers
Function
bp_solve
hic.cpp:17164
↓ 1 callers
Function
break_all_contigs
Overlaps.cpp:12340
↓ 1 callers
Function
break_phasing_utg
horder.cpp:1787
↓ 1 callers
Function
bub_complex
Overlaps.cpp:36549
↓ 1 callers
Function
bub_complex_hamming
Overlaps.cpp:24456
↓ 1 callers
Function
bub_pop_merge
Overlaps.cpp:26561
↓ 1 callers
Function
build_DAGCon
Correct.cpp:5374
↓ 1 callers
Function
cal_ave_ovlp
hic.cpp:17536
↓ 1 callers
Function
cal_bub_best_by_len
gfa_ut.cpp:17891
↓ 1 callers
Function
cal_clus_sc0
rcut.cpp:2540
↓ 1 callers
Function
cal_ec_multiple
ecovlp.cpp:6063
↓ 1 callers
Function
cal_ec_r
ecovlp.cpp:6268
↓ 1 callers
Function
cal_ec_r_dbg
ecovlp.cpp:6364
↓ 1 callers
Function
cal_estimate_err
Correct.cpp:15369
↓ 1 callers
Function
cal_exact_non_retrieve_exz
Correct.cpp:15769
↓ 1 callers
Function
cal_exact_simi_exz
Correct.cpp:15918
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