Rust function index

Use functions in execution order to find the engine for a step. This index links 170 function declarations, sorted by file and name. It omits test directories and conventional in-file test modules. It is a source navigation aid, not a list of public or enabled APIs. Repeated names belong to different files or implementations.

Regenerate with python tools/render_function_index.py --write.

rust/aggregation_engine/build.rs

Function	Definition
main	Line 4

rust/aggregation_engine/src/main.rs

Function	Definition
apply_bh_correction	Line 920
build_functional_group_matrix	Line 1480
build_functional_peptide_matrix	Line 1548
build_peptide_matrix	Line 770
build_protein_group_matrix	Line 838
canonical_for_group	Line 1397
classify_group	Line 327
classify_group_with_hosts	Line 1143
find_sample_dirs	Line 442
group_value_votes	Line 1358
is_classifiable_accession	Line 318
is_host_member	Line 364
load_functional_lookup	Line 1253
load_host_accessions	Line 1108
load_search_q	Line 466
main	Line 1797
normalize_protein_group	Line 289
parse_intensity	Line 433
parse_lfq_sample	Line 535
parse_psm_sample	Line 677
parse_q	Line 421
parse_q_thresholds	Line 153
representative_protein	Line 402
resolve_functional_levels	Line 1783
resolve_level	Line 1444
sanitize_level	Line 1612
short	Line 225
split_functional_value	Line 1324
strip_source_tags	Line 259
validate_search_schema	Line 521
write_functional_group_matrix	Line 1625
write_functional_peptide_matrix	Line 1682
write_group_metadata	Line 1166
write_group_to_level_map	Line 1742
write_peptide_matrix	Line 995
write_protein_group_matrix	Line 1050

rust/common/dianovo.rs

Function	Definition
parse_prediction	Line 11

rust/fasta_export/build.rs

Function	Definition
main	Line 4

rust/fasta_export/src/main.rs

Function	Definition
compute_fdp_combined	Line 447
compute_fdp_lower	Line 465
count_entrapment_hits	Line 475
export_fasta	Line 380
extract_entry_gene	Line 219
extract_gmgc_gene	Line 244
extract_gn	Line 191
extract_gnomad_gene	Line 231
extract_os	Line 206
generate_decoys	Line 318
heal_fasta	Line 410
heal_for_diann	Line 270
heal_for_msfragger	Line 297
heal_for_sage	Line 260
heal_header	Line 303
main	Line 535
parse_header	Line 89

rust/fasta_extractor_v2/build.rs

Function	Definition
main	Line 4

rust/fasta_extractor_v2/src/bin/fasta_sort_by_id.rs

Function	Definition
main	Line 58

rust/fasta_extractor_v2/src/bin/hash_fasta.rs

Function	Definition
emit	Line 55
hash_hex	Line 50
main	Line 62
normalize	Line 38

rust/fasta_extractor_v2/src/bin/lake_builder.rs

Function	Definition
extract_clean_sequence	Line 329
fmt_num	Line 193
main	Line 363
parse_fasta_regions	Line 297
parse_source_spec	Line 239
progress_bar	Line 341
sha256_hex	Line 205
sort_joint_headers	Line 219
sort_joint_headers_source_blind	Line 234

rust/fasta_extractor_v2/src/bin/mass_corasick.rs

Function	Definition
aa_mass	Line 34
build	Line 84
load_predictions	Line 197
main	Line 378
mass_to_bin	Line 65
sweep_protein	Line 128

rust/fasta_extractor_v2/src/bin/mass_corasick_v2.rs

Function	Definition
aa_mass	Line 23
build	Line 102
get_bin	Line 203
load_predictions	Line 266
main	Line 426
mass_to_bin	Line 71
sweep_protein	Line 213

rust/fasta_extractor_v2/src/bin/mass_corasick_v3.rs

Function	Definition
aa_mass	Line 28
build	Line 106
compute_kmer_bins	Line 71
find_csv_files	Line 272
get_bin	Line 165
is_valid_peptide	Line 53
load_csv_peptides	Line 222
load_proteins	Line 295
main	Line 892
mass_to_bin	Line 48
run_merge	Line 690
run_prep	Line 342
run_rescue	Line 505
sweep_protein	Line 174

rust/fasta_extractor_v2/src/bin/mass_kmer_anchor.rs

Function	Definition
aa_mass	Line 32
build	Line 152
exact_match	Line 486
kmer_mass	Line 91
load_fasta	Line 292
load_predictions	Line 338
load_predictions_from_file	Line 392
main	Line 571
mass_to_bin	Line 64
new	Line 76
new	Line 117
peptide_mass	Line 95
query	Line 192
theoretical_mass	Line 101

rust/fasta_extractor_v2/src/bin/parsimony.rs

Function	Definition
collect_csvs	Line 694
load_fasta	Line 656
main	Line 105
normalize	Line 649
parse_prediction_csv	Line 713
run_bayesian_em	Line 454
run_info_score	Line 565
run_razor	Line 601
walk	Line 696

rust/fasta_extractor_v2/src/main.rs

Function	Definition
add	Line 373
collect_csvs	Line 387
extract_sequence	Line 293
is_low_complexity	Line 310
load_peptides	Line 493
load_peptides_single_csv	Line 540
load_peptides_top_percent	Line 412
load_peptides_top_percent_single_csv	Line 572
load_peptides_txt	Line 629
main	Line 672
new	Line 363
normalize_il_seq	Line 304
parse_fasta_regions	Line 258
parse_prediction_csv	Line 140
walk	Line 389

rust/lake_stats/build.rs

Function	Definition
main	Line 4

rust/lake_stats/src/main.rs

Function	Definition
is_clean	Line 42
main	Line 152
new	Line 95
next	Line 105
trypsin_into	Line 55

rust/parsimony_engine/build.rs

Function	Definition
main	Line 4

rust/parsimony_engine/src/main.rs

Function	Definition
classify_by_prefix	Line 388
credit_order	Line 960
extract_mgyg_species	Line 439
fnv1a64	Line 924
fnv1a_pep_acc	Line 913
get_db_type	Line 372
is_low_complexity	Line 448
load_fasta	Line 635
load_peptides	Line 484
load_source_map	Line 418
load_weights	Line 279
main	Line 1475
map_peptides_parallel	Line 692
normalize_il	Line 273
run_bayesian	Line 1289
run_info_score	Line 1242
run_razor	Line 791
run_species_budget	Line 985
run_uniform	Line 1122
run_uniform_2pep	Line 1215
strip_source_tags	Line 333
write_fasta	Line 1444

rust/shared_peptide_classifier/build.rs

Function	Definition
main	Line 4

rust/shared_peptide_classifier/src/main.rs

Function	Definition
load_cluster_subset	Line 115
load_lake_subset	Line 155
load_rescued	Line 76
main	Line 203