Index

A | B | C | D | F | G | H | I | L | M | N | O | P | R | S | T | U | W

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)
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)