Index

A

abssum() (aldy.lpinterface.Gurobi method) activity (aldy.gene.MinorAllele property) addConstr() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method) addVar() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method) aldy.cn module aldy.common module aldy.coverage module aldy.diplotype module aldy.gene module aldy.genotype module

aldy.lpinterface module aldy.major module aldy.minor module aldy.profile module aldy.sam module AldyException allele_name() (in module aldy.common) alleles (aldy.gene.CNConfig attribute) (aldy.gene.Gene attribute) alt_name (aldy.gene.MinorAllele attribute) aminoacid (aldy.gene.Gene attribute) average_coverage() (aldy.coverage.Coverage method)

B

basic_filter() (aldy.coverage.Coverage method)

C

CBC (class in aldy.lpinterface) chr (aldy.gene.Gene attribute) chr_prefix() (in module aldy.common) chr_to_ref (aldy.gene.Gene attribute) cn (aldy.gene.CNConfig attribute) cn_config (aldy.gene.MajorAllele attribute) cn_configs (aldy.gene.Gene attribute) cn_diff (aldy.profile.Profile attribute) cn_fit (aldy.profile.Profile attribute) cn_fusion_left (aldy.profile.Profile attribute) cn_fusion_right (aldy.profile.Profile attribute)

cn_max (aldy.profile.Profile attribute) cn_parsimony (aldy.profile.Profile attribute) cn_pce_penalty (aldy.profile.Profile attribute) cn_region (aldy.profile.Profile attribute) cn_solution (aldy.profile.Profile attribute) CNConfig (class in aldy.gene) CNConfigType (class in aldy.gene) colorize() (in module aldy.common) common_tandems (aldy.gene.Gene attribute) Coverage (class in aldy.coverage) coverage() (aldy.coverage.Coverage method) CUSTOM (aldy.gene.CNConfigType attribute)

D

data (aldy.profile.Profile attribute) debug_novel (aldy.profile.Profile attribute) debug_probe (aldy.profile.Profile attribute) DEFAULT (aldy.gene.CNConfigType attribute) DELETION (aldy.gene.CNConfigType attribute) deletion_allele() (aldy.gene.Gene method) description (aldy.gene.CNConfig attribute)

detect_genome() (in module aldy.sam) diploid_avg_coverage() (aldy.coverage.Coverage method) display_format (aldy.profile.Profile attribute) do_copy_number (aldy.gene.Gene attribute) dump() (aldy.coverage.Coverage method) (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method)

E

ensembl (aldy.gene.Gene attribute) escape_name() (in module aldy.lpinterface) estimate_cn() (in module aldy.cn) estimate_cpic() (in module aldy.diplotype)

estimate_diplotype() (in module aldy.diplotype) estimate_major() (in module aldy.major) estimate_minor() (in module aldy.minor) evidence (aldy.gene.MinorAllele attribute) exons (aldy.gene.Gene attribute)

F

filtered() (aldy.coverage.Coverage method)

freezekey() (in module aldy.common) func_muts (aldy.gene.MajorAllele attribute)

G

gap (aldy.profile.Profile attribute) gene (aldy.sam.Sample attribute) Gene (class in aldy.gene) genome (aldy.gene.Gene attribute) genotype() (in module aldy.genotype) get_allele() (aldy.gene.Gene method) get_functional() (aldy.gene.Gene method) get_minor_mutations() (aldy.gene.MajorAllele method)

get_refseq() (aldy.gene.Gene method) get_rsid() (aldy.gene.Gene method) get_sam_profile_data() (aldy.profile.Profile static method) get_wide_region() (aldy.gene.Gene method) getValue() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method) GRange (class in aldy.common) Gurobi (class in aldy.lpinterface)

H

has_coverage() (aldy.gene.Gene method)

I

indelpost (aldy.profile.Profile attribute) is_binary() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method)

is_functional() (aldy.gene.Gene method) is_long_read (aldy.sam.Sample attribute)

J

JsonDict (class in aldy.common)

K

kind (aldy.gene.CNConfig attribute)

L

LEFT_FUSION (aldy.gene.CNConfigType attribute)

load() (aldy.profile.Profile static method) log (in module aldy.common)

M

major_novel (aldy.profile.Profile attribute) MajorAllele (class in aldy.gene) male (aldy.profile.Profile attribute) max_minor_solutions (aldy.profile.Profile attribute) min_avg_coverage (aldy.profile.Profile attribute) min_coverage (aldy.profile.Profile attribute) min_mapq (aldy.profile.Profile attribute) min_quality (aldy.profile.Profile attribute) minor_add (aldy.profile.Profile attribute) minor_miss (aldy.profile.Profile attribute) minor_phase (aldy.profile.Profile attribute) minor_phase_vars (aldy.profile.Profile attribute) MinorAllele (class in aldy.gene) minors (aldy.gene.MajorAllele attribute)

model() (in module aldy.lpinterface) module aldy.cn aldy.common aldy.coverage aldy.diplotype aldy.gene aldy.genotype aldy.lpinterface aldy.major aldy.minor aldy.profile aldy.sam Mutation (class in aldy.gene) mutations (aldy.gene.Gene attribute)

N

name (aldy.gene.Gene attribute) (aldy.gene.MajorAllele attribute) (aldy.gene.MinorAllele attribute) (aldy.profile.Profile attribute) (aldy.sam.Sample attribute)

neutral_muts (aldy.gene.MinorAllele attribute) neutral_value (aldy.profile.Profile attribute) NoSolutionsError

O

op (aldy.gene.Mutation attribute)

OUTPUT_COLS (in module aldy.diplotype)

P

parse_cn_region() (in module aldy.common) path (aldy.sam.Sample attribute) percentage() (aldy.coverage.Coverage method) pharmvar (aldy.gene.Gene attribute) (aldy.gene.MinorAllele attribute) phase (aldy.profile.Profile attribute) phaseable (aldy.sam.Sample attribute)

phases (aldy.sam.Sample attribute) pos (aldy.gene.Mutation attribute) pp() (in module aldy.common) prod() (aldy.lpinterface.Gurobi method) profile (aldy.sam.Sample attribute) Profile (class in aldy.profile) PROTEINS (in module aldy.common) pseudogenes (aldy.gene.Gene attribute)

Q

quality_filter() (aldy.coverage.Coverage method)

quicksum() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method)

R

random_mutations (aldy.gene.Gene attribute) ref_to_chr (aldy.gene.Gene attribute) refseq (aldy.gene.Gene attribute) region_at() (aldy.gene.Gene method)

region_coverage() (aldy.coverage.Coverage method) regions (aldy.gene.Gene attribute) rev_comp() (in module aldy.common) REV_COMPLEMENT (in module aldy.common) RIGHT_FUSION (aldy.gene.CNConfigType attribute)

S

sam_long_reads (aldy.profile.Profile attribute) sam_mappy_preset (aldy.profile.Profile attribute) Sample (class in aldy.sam) samtools() (aldy.common.GRange method) script_path() (in module aldy.common) seq (aldy.gene.Gene attribute) seq_to_amino() (in module aldy.common) setObjective() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method) single_copy() (aldy.coverage.Coverage method)

SOLUTION_PRECISION (in module aldy.common) solutions() (aldy.lpinterface.Gurobi method) solve() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method) solve_cn_model() (in module aldy.cn) solve_major_model() (in module aldy.major) solve_minor_model() (in module aldy.minor) SOLVER_PRECISON (in module aldy.lpinterface) sorted_tuple() (in module aldy.common) strand (aldy.gene.Gene attribute)

T

td() (in module aldy.common) threshold (aldy.profile.Profile attribute)

Timing (class in aldy.common) total() (aldy.coverage.Coverage method)

U

unique_regions (aldy.gene.Gene attribute) update() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method) (aldy.profile.Profile method)

V

variables() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method) varName() (aldy.lpinterface.CBC method) (aldy.lpinterface.Gurobi method)

vcf_sample_idx (aldy.profile.Profile attribute) vector (aldy.gene.CNConfig property) version (aldy.gene.Gene attribute)

W

write_decomposition() (in module aldy.diplotype)

write_vcf() (in module aldy.diplotype)