Index

A

add() (pysinger.data.arg.ARG method), [1] (pysinger.data.recombination.Recombination method), [1] (pysinger.data.tree.Tree method), [1] add_mutation() (pysinger.data.node.Node method), [1] add_node() (pysinger.data.arg.ARG method) add_sample() (pysinger.data.arg.ARG method), [1]

affect() (pysinger.data.recombination.Recombination method), [1] approx_sample_recombinations() (pysinger.data.arg.ARG method), [1] ARG (class in pysinger.data.arg), [1] arg_to_tskit() (in module pysinger.io.tskit_writer), [1] assign_time() (pysinger.data.interval.Interval method) assign_weight() (pysinger.data.interval.Interval method) avg_num_states() (pysinger.hmm.bsp.BSP method), [1]

B

backward_update() (pysinger.data.tree.Tree method), [1] BinaryEmission (class in pysinger.hmm.emission), [1] Branch (class in pysinger.data.branch), [1]

branch (pysinger.data.interval.Interval attribute), [1], [2] (pysinger.data.interval.IntervalInfo attribute) BSP (class in pysinger.hmm.bsp), [1] build_singleton_arg() (pysinger.data.arg.ARG method), [1]

C

children (pysinger.data.tree.Tree attribute), [1] clear_remove_info() (pysinger.data.arg.ARG method), [1] CoalescentCalculator (class in pysinger.hmm.coalescent), [1] compute() (pysinger.hmm.coalescent.CoalescentCalculator method), [1] compute_rhos_thetas() (pysinger.data.arg.ARG method), [1] coordinates (pysinger.data.arg.ARG attribute), [1]

copy() (pysinger.data.tree.Tree method), [1] count_flipping() (pysinger.data.arg.ARG method) count_incompatibility() (pysinger.data.arg.ARG method) create() (pysinger.data.recombination.Recombination method), [1] cumulative_distance() (pysinger.rates.rate_map.RateMap method) cut_tree (pysinger.data.arg.ARG attribute), [1]

D

delete_branch() (pysinger.data.tree.Tree method), [1] deleted_branches (pysinger.data.recombination.Recombination attribute), [1]

deleted_node (pysinger.data.recombination.Recombination attribute), [1] discretize() (pysinger.data.arg.ARG method), [1]

E

Emission (class in pysinger.hmm.emission) emit() (pysinger.hmm.emission.BinaryEmission method), [1] (pysinger.hmm.emission.Emission method) (pysinger.hmm.emission.PolarEmission method), [1]

F

fill_time() (pysinger.data.interval.Interval method), [1] find_joining_branch() (pysinger.data.tree.Tree method), [1] find_sibling() (pysinger.data.tree.Tree method), [1] FitchReconstruction (class in pysinger.reconstruction.fitch), [1]

forward() (pysinger.hmm.bsp.BSP method), [1] (pysinger.hmm.tsp.TSP method), [1] forward_update() (pysinger.data.tree.Tree method), [1] full() (pysinger.data.interval.Interval method), [1]

G

get_arg_length() (pysinger.data.arg.ARG method), [1] get_branches() (pysinger.data.tree.Tree method), [1] get_check_points() (pysinger.data.arg.ARG method), [1]

get_index() (pysinger.data.arg.ARG method), [1] get_query_node_at() (pysinger.data.arg.ARG method), [1] get_state() (pysinger.data.node.Node method), [1] get_tree_at() (pysinger.data.arg.ARG method), [1]

I

index (pysinger.data.node.Node attribute) insert_branch() (pysinger.data.tree.Tree method), [1] inserted_branches (pysinger.data.recombination.Recombination attribute), [1] inserted_node (pysinger.data.recombination.Recombination attribute), [1] internal_backward_update() (pysinger.data.tree.Tree method), [1] internal_forward_update() (pysinger.data.tree.Tree method), [1]

internal_rethread() (pysinger.mcmc.threader.Threader method), [1] internal_sample() (pysinger.sampler.Sampler method), [1] Interval (class in pysinger.data.interval), [1] IntervalInfo (class in pysinger.data.interval), [1] is_null() (pysinger.data.branch.Branch method), [1] iterative_start() (pysinger.sampler.Sampler method), [1]

J

joining_branches (pysinger.data.arg.ARG attribute), [1]

L

lb (pysinger.data.interval.Interval attribute), [1], [2] (pysinger.data.interval.IntervalInfo attribute) length (pysinger.data.branch.Branch property), [1]

length() (pysinger.data.tree.Tree method), [1] load_map() (pysinger.rates.rate_map.RateMap method), [1] load_vcf() (pysinger.sampler.Sampler method), [1] lower_node (pysinger.data.branch.Branch attribute)

M

mean_rate() (pysinger.rates.rate_map.RateMap method) merging_branch (pysinger.data.recombination.Recombination attribute), [1] module pysinger.data.arg pysinger.data.branch pysinger.data.interval pysinger.data.node pysinger.data.recombination pysinger.data.tree pysinger.hmm.bsp pysinger.hmm.coalescent pysinger.hmm.emission pysinger.hmm.tsp pysinger.io.tskit_writer, [1] pysinger.io.vcf_reader, [1] pysinger.mcmc.threader pysinger.rates.rate_map pysinger.reconstruction.fitch pysinger.sampler

mut_emit() (pysinger.hmm.bsp.BSP method), [1] (pysinger.hmm.emission.BinaryEmission method), [1] (pysinger.hmm.emission.Emission method) (pysinger.hmm.emission.PolarEmission method), [1] (pysinger.hmm.tsp.TSP method), [1] mutation_branches (pysinger.data.arg.ARG attribute), [1] mutation_sites (pysinger.data.arg.ARG attribute), [1] (pysinger.data.node.Node attribute)

N

Ne (pysinger.data.arg.ARG attribute), [1] Node (class in pysinger.data.node), [1] node (pysinger.data.interval.Interval attribute), [1], [2] node_set (pysinger.data.arg.ARG attribute), [1] null_emit() (pysinger.hmm.bsp.BSP method), [1] (pysinger.hmm.emission.BinaryEmission method), [1] (pysinger.hmm.emission.Emission method) (pysinger.hmm.emission.PolarEmission method), [1] (pysinger.hmm.tsp.TSP method), [1]

num_unmapped() (pysinger.data.arg.ARG method)

P

parents (pysinger.data.tree.Tree attribute), [1] PolarEmission (class in pysinger.hmm.emission), [1] pos (pysinger.data.recombination.Recombination attribute), [1] prob() (pysinger.hmm.coalescent.CoalescentCalculator method), [1] pysinger.data.arg module pysinger.data.branch module pysinger.data.interval module pysinger.data.node module pysinger.data.recombination module pysinger.data.tree module pysinger.hmm.bsp module

pysinger.hmm.coalescent module pysinger.hmm.emission module pysinger.hmm.tsp module pysinger.io.tskit_writer module, [1] pysinger.io.vcf_reader module, [1] pysinger.mcmc.threader module pysinger.rates.rate_map module pysinger.reconstruction.fitch module pysinger.sampler module

Q

quantile() (pysinger.hmm.coalescent.CoalescentCalculator method), [1]

R

RateMap (class in pysinger.rates.rate_map), [1] read_vcf_haploid() (in module pysinger.io.vcf_reader), [1] read_vcf_phased() (in module pysinger.io.vcf_reader), [1] Recombination (class in pysinger.data.recombination), [1] recombinations (pysinger.data.arg.ARG attribute), [1] recombine() (pysinger.hmm.tsp.TSP method), [1] recombined_branch (pysinger.data.recombination.Recombination attribute), [1] reconstruct() (pysinger.reconstruction.fitch.FitchReconstruction method), [1]

remove() (pysinger.data.arg.ARG method), [1] (pysinger.data.recombination.Recombination method), [1] (pysinger.data.tree.Tree method), [1] removed_branches (pysinger.data.arg.ARG attribute), [1] reserve_memory() (pysinger.hmm.bsp.BSP method) (pysinger.hmm.tsp.TSP method) rhos (pysinger.data.arg.ARG attribute), [1] root (pysinger.data.arg.ARG attribute), [1]

S

sample_internal_cut() (pysinger.data.arg.ARG method), [1] sample_joining_branches() (pysinger.hmm.bsp.BSP method), [1] sample_joining_nodes() (pysinger.hmm.tsp.TSP method), [1] sample_nodes (pysinger.data.arg.ARG attribute), [1] Sampler (class in pysinger.sampler), [1] sanity_check() (pysinger.hmm.bsp.BSP method), [1] seed_pos (pysinger.data.interval.IntervalInfo attribute) segment_distance() (pysinger.rates.rate_map.RateMap method) sequence_length (pysinger.data.arg.ARG attribute), [1] set_check_points() (pysinger.hmm.bsp.BSP method) (pysinger.hmm.tsp.TSP method) set_cutoff() (pysinger.hmm.bsp.BSP method) set_emission() (pysinger.hmm.bsp.BSP method) (pysinger.hmm.tsp.TSP method)

set_gap() (pysinger.hmm.tsp.TSP method) set_pos() (pysinger.data.recombination.Recombination method) set_precision() (pysinger.sampler.Sampler method) set_rng() (pysinger.hmm.bsp.BSP method) (pysinger.hmm.tsp.TSP method) (pysinger.mcmc.threader.Threader method) set_seed() (pysinger.sampler.Sampler method) source_branch (pysinger.data.recombination.Recombination attribute), [1] source_intervals (pysinger.data.interval.Interval attribute), [1], [2] source_weights (pysinger.data.interval.Interval attribute), [1], [2] start() (pysinger.hmm.bsp.BSP method), [1] (pysinger.hmm.tsp.TSP method), [1] start_pos (pysinger.data.interval.Interval attribute), [1], [2] start_time (pysinger.data.recombination.Recombination attribute), [1]

T

target_branch (pysinger.data.recombination.Recombination attribute), [1] thetas (pysinger.data.arg.ARG attribute), [1] thread() (pysinger.mcmc.threader.Threader method), [1] Threader (class in pysinger.mcmc.threader), [1] time (pysinger.data.interval.Interval attribute), [1], [2] (pysinger.data.node.Node attribute)

time() (pysinger.hmm.coalescent.CoalescentCalculator method), [1] trace_backward() (pysinger.data.recombination.Recombination method), [1] trace_forward() (pysinger.data.recombination.Recombination method), [1] transfer() (pysinger.hmm.bsp.BSP method), [1] (pysinger.hmm.tsp.TSP method), [1] Tree (class in pysinger.data.tree), [1] TSP (class in pysinger.hmm.tsp), [1]

U

ub (pysinger.data.interval.Interval attribute), [1], [2] (pysinger.data.interval.IntervalInfo attribute)

update() (pysinger.reconstruction.fitch.FitchReconstruction method), [1] upper_node (pysinger.data.branch.Branch attribute)

W

weight (pysinger.data.interval.Interval attribute), [1], [2]

weight() (pysinger.hmm.coalescent.CoalescentCalculator method), [1] write_state() (pysinger.data.node.Node method), [1]