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#+ ViralSeq::SeqHash
#a3g_hypermut ViralSeq::SeqHash
#aa_array ViralSeq::Sequence
#aa_hash ViralSeq::SeqHash
#aa_length ViralSeq::Sequence
#aa_string ViralSeq::Sequence
align ViralSeq::Muscle
#align ViralSeq::SeqHash
#calculate ViralSeq::Rubystats::FishersExactTest
calculate_cut_off ViralSeq::TcsCore
calculate_pid_cut_off ViralSeq::Math
check_R ViralSeq::R
check_R_packages ViralSeq::R
#check_drm ViralSeq::Sequence
check_muscle? ViralSeq::Muscle
#check_nt_size ViralSeq::SeqHash
#collapse ViralSeq::SeqHash
#compare_with String
#complete_with_ref ViralSeq::SeqHash
config_version ViralSeq::DrmVersion
#consensus ViralSeq::SeqHash
construct ViralSeq::DrmVersion
#count_freq Enumerable
#count_freq2 Enumerable
define ViralSeq::Recency
detection_limit ViralSeq::TcsCore
#difference Hash
#dna ViralSeq::Sequence
#dna_hash ViralSeq::SeqHashPair
#dna_hash ViralSeq::SeqHash
#dna_length ViralSeq::Sequence
dpi ViralSeq::Recency
#drm ViralSeq::SeqHash
#drm_class ViralSeq::DrmRegionConfig
#drm_json ViralSeq::DrmRegionConfig
#drm_list ViralSeq::DrmRegionConfig
#drm_range ViralSeq::DrmVersion
#drm_range ViralSeq::DrmRegionConfig
#drm_version ViralSeq::DrmRegionConfig
#drm_version ViralSeq::DrmVersion
#error_table ViralSeq::SeqHash
#exact ViralSeq::Rubystats::FishersExactTest
#factorial Integer
#fdr ViralSeq::SeqHash
#file ViralSeq::SeqHashPair
#file ViralSeq::SeqHash
#filter_for_drm ViralSeq::SeqHash
filter_r1 ViralSeq::TcsCore
filter_r2 ViralSeq::TcsCore
#filter_similar_pid ViralSeq::SeqHash
#gap_strip ViralSeq::SeqHash
#gap_strip_ends ViralSeq::SeqHash
generate ViralSeq::TcsJson
generate ViralSeq::RecencyReport
generate_pool ViralSeq::PID
get ViralSeq::RefSeq
#get_reading_frame_number ViralSeq::DrmRegionConfig
get_sdrm_rscript ViralSeq::R
#hiv_seq_qc ViralSeq::SeqHash
#hyper ViralSeq::Rubystats::FishersExactTest
#hyper0 ViralSeq::Rubystats::FishersExactTest
#hyper_323 ViralSeq::Rubystats::FishersExactTest
#initialize ViralSeq::Math::BinomCI
#initialize ViralSeq::Rubystats::FishersExactTest
#initialize ViralSeq::Sequence
#initialize ViralSeq::SeqHash
#initialize ViralSeq::DrmVersion
#initialize ViralSeq::Math::RandomGaussian
#initialize ViralSeq::Math::PoissonDist
#initialize ViralSeq::SeqHashPair
#initialize ViralSeq::DrmRegionConfig
#join1 ViralSeq::SeqHashPair
#join2 ViralSeq::SeqHashPair
#k ViralSeq::Math::PoissonDist
#lnbico ViralSeq::Rubystats::FishersExactTest
#lnfact ViralSeq::Rubystats::FishersExactTest
#lngamm ViralSeq::Rubystats::FishersExactTest
#locator ViralSeq::Sequence
log_and_abort ViralSeq::TcsCore
#lower ViralSeq::Math::BinomCI
#lower_quartile Enumerable
#mean ViralSeq::Math::BinomCI
#mean Enumerable
#median Enumerable
#mutation ViralSeq::SeqHash
#mutation String
#n1 ViralSeq::Math::BinomCI
#n2 ViralSeq::Math::BinomCI
#name ViralSeq::Sequence
new_from_aa_fasta ViralSeq::SeqHash
new_from_array ViralSeq::SeqHash
new_from_fasta ViralSeq::SeqHash
new_from_fasta ViralSeq::SeqHashPair
new_from_fastq ViralSeq::SeqHash
#nt_diff String
#nt_parser String
#nt_range ViralSeq::SeqHash
#nt_to_array String
#nt_variants ViralSeq::SeqHash
#nucleotide_pi ViralSeq::SeqHash
#poisson_hash ViralSeq::Math::PoissonDist
#poisson_minority_cutoff ViralSeq::SeqHash
possible_dual_infection ViralSeq::Recency
#pull_drm_json ViralSeq::DrmVersion
#qc_hash ViralSeq::SeqHash
#qc_indel ViralSeq::SeqHash
#query_region ViralSeq::DrmVersion
#r1_r2_length ViralSeq::DrmRegionConfig
r1r2 ViralSeq::TcsCore
#rand ViralSeq::Math::RandomGaussian
#random_select ViralSeq::SeqHash
#rate ViralSeq::Math::PoissonDist
#rc String
#ref_info ViralSeq::DrmRegionConfig
#ref_info ViralSeq::DrmVersion
#region ViralSeq::DrmRegionConfig
#rev_complement ViralSeq::Sequence
#rev_complement! ViralSeq::Sequence
root ViralSeq
#sample ViralSeq::SeqHash
#sample_variance Enumerable
#sdrm ViralSeq::Sequence
sdrm_hash ViralSeq::DRMs
#sdrm_hiv_in ViralSeq::SeqHash
#sdrm_hiv_pr ViralSeq::SeqHash
#sdrm_hiv_rt ViralSeq::SeqHash
sdrm_json ViralSeq::DRMs
#seq_coord ViralSeq::DrmRegionConfig
#seq_coord ViralSeq::DrmVersion
#seq_drm_correlation ViralSeq::DrmVersion
#sequence_clip ViralSeq::Sequence
#sequence_locator ViralSeq::SeqHash
#shannons_entropy ViralSeq::SeqHash
#size ViralSeq::SeqHash
#size ViralSeq::SeqHashPair
sort_by_lib ViralSeq::TcsCore
#stdev Enumerable
#stop_codon ViralSeq::SeqHash
#sub ViralSeq::SeqHash
#title ViralSeq::SeqHashPair
#title ViralSeq::SeqHash
#tn93 ViralSeq::SeqHash
#to_list String
#to_rsphylip ViralSeq::SeqHash
#translate ViralSeq::Sequence
#translate ViralSeq::SeqHash
#trim ViralSeq::SeqHash
#uniq_dna_hash ViralSeq::SeqHash
#uniq_hash Hash
#upper ViralSeq::Math::BinomCI
#upper_quartile Enumerable
validate_file_name ViralSeq::TcsCore
#write_nt_fa ViralSeq::SeqHash