Index

A

add_expression() (hylite.Organism.Organism method) add_organism_list() (hylite.Hylite.Hylite method) add_snp() (hylite.Fingerprint.Fingerprint method) (hylite.Lane.Lane method) (hylite.Organism.Organism method) (hylite.Read.Read method)

B

bowtie2_wrapper (class in hylite.bowtie2_wrapper)

build_command_line() (hylite.Generic_wrapper.Generic_wrapper method) build_index() (hylite.bowtie2_wrapper.bowtie2_wrapper method)

C

categorize() (hylite.Read.Read method) clear() (hylite.Hylite.Hylite method) (hylite.Organism.Organism method) close() (hylite.Pileup_Reader.Pileup_Reader method) (hylite.Protocol_Reader.Protocol_Reader method)

close_pileup() (hylite.Snp_Generator.Snp_Generator method) create_index() (hylite.Hylite.Hylite method) create_snp() (hylite.Snp_Generator.Snp_Generator method) cross() (hylite.Read.Read method)

D

decompose_pileup_line() (hylite.Snp_Generator.Snp_Generator method)

detect_snp() (hylite.Snp_Generator.Snp_Generator method)

F

faidx() (hylite.samtools_wrapper.samtools_wrapper method)

Fingerprint (class in hylite.Fingerprint) finish_reads() (hylite.Lane.Lane method)

G

Generic_Pileup_Reader (class in hylite.Generic_Pileup_Reader) Generic_wrapper (class in hylite.Generic_wrapper) get_all_fingerprint() (hylite.Organism.Organism method) get_all_genes() (hylite.Output_manager.Output_manager method) get_count() (hylite.Lane.Lane method) get_fingerprint() (hylite.Fingerprint.Fingerprint method) (hylite.Organism.Organism method)

get_nb_reads() (hylite.Lane.Lane method) (hylite.Snp_Generator.Snp_Generator method) give_line() (hylite.Generic_Pileup_Reader.Generic_Pileup_Reader method) (hylite.Pileup_Reader.Pileup_Reader method) (hylite.Snp_Generator.Snp_Generator method)

H

has_SNP() (hylite.SNP.SNP method) Hylite (class in hylite.Hylite) hylite.bowtie2_wrapper module hylite.Fingerprint module hylite.Generic_Pileup_Reader module hylite.Generic_wrapper module hylite.Hylite module hylite.Lane module hylite.Organism module hylite.Output_manager module

hylite.Parameters module hylite.Picklablefile module hylite.Pileup_Reader module hylite.Protocol_Reader module hylite.Read module hylite.samtools_wrapper module hylite.SNP module hylite.Snp_Generator module

I

index() (hylite.samtools_wrapper.samtools_wrapper method)

L

Lane (class in hylite.Lane)

listed_org() (hylite.SNP.SNP method)

M

mappe_versus() (hylite.bowtie2_wrapper.bowtie2_wrapper method) mapping() (hylite.Hylite.Hylite method) module hylite.bowtie2_wrapper hylite.Fingerprint hylite.Generic_Pileup_Reader hylite.Generic_wrapper hylite.Hylite hylite.Lane hylite.Organism hylite.Output_manager hylite.Parameters hylite.Picklablefile hylite.Pileup_Reader hylite.Protocol_Reader hylite.Read hylite.samtools_wrapper hylite.SNP hylite.Snp_Generator

mpileup() (hylite.samtools_wrapper.samtools_wrapper method)

N

no_coverage() (hylite.SNP.SNP method)

no_SNP() (hylite.SNP.SNP method)

O

Organism (class in hylite.Organism) output() (hylite.Hylite.Hylite method)

Output_manager (class in hylite.Output_manager) output_summary() (hylite.Hylite.Hylite method)

P

Parameters (in module hylite.Parameters) Picklablefile (class in hylite.Picklablefile) pickle() (hylite.Hylite.Hylite method) pileup_init() (hylite.Hylite.Hylite method) pileup_read() (hylite.Hylite.Hylite method) Pileup_Reader (class in hylite.Pileup_Reader)

pipeline() (hylite.samtools_wrapper.samtools_wrapper method) pipeline_sequential() (hylite.samtools_wrapper.samtools_wrapper method) precompute_expression_data_towrite() (hylite.Output_manager.Output_manager method) prep_sam_file() (hylite.samtools_wrapper.samtools_wrapper method) print_command_line() (hylite.Generic_wrapper.Generic_wrapper method) Protocol_Reader (class in hylite.Protocol_Reader)

R

Read (class in hylite.Read) read() (hylite.Protocol_Reader.Protocol_Reader method)

restaure() (hylite.Hylite.Hylite method) (hylite.Snp_Generator.Snp_Generator method) run() (hylite.Generic_wrapper.Generic_wrapper method)

S

samtobam() (hylite.samtools_wrapper.samtools_wrapper method) samtools_pipeline() (hylite.Hylite.Hylite method) samtools_wrapper (class in hylite.samtools_wrapper) set_referencefile() (hylite.Hylite.Hylite method)

simplify_category() (hylite.Output_manager.Output_manager method) SNP (class in hylite.SNP) Snp_Generator (class in hylite.Snp_Generator) sort() (hylite.samtools_wrapper.samtools_wrapper method)

T

treat_pileup_line() (hylite.Snp_Generator.Snp_Generator method)

truncate_gene() (hylite.Hylite.Hylite method)

U

update() (hylite.Lane.Lane method)

update_tags() (hylite.Lane.Lane method) (hylite.Snp_Generator.Snp_Generator method)

W

write_complete_expression_file() (hylite.Output_manager.Output_manager method) write_read() (hylite.Output_manager.Output_manager method) write_read_summary() (hylite.Output_manager.Output_manager method)

write_run_summary() (hylite.Output_manager.Output_manager method) write_snp() (hylite.Output_manager.Output_manager method) write_snp_summary() (hylite.Output_manager.Output_manager method)