Index

C

check() (sunbeam.project.SampleList method)

Config() (in module sunbeam.scripts)

E

Extend() (in module sunbeam.scripts)

F

fill_missing() (sunbeam.project.SunbeamConfig method) filter_ids() (in module sunbeam.bfx) format_string_to_regex() (sunbeam.project.SampleList static method)

from_file() (sunbeam.project.SunbeamConfig class method) from_template() (sunbeam.project.SunbeamConfig class method) (sunbeam.project.SunbeamProfile class method)

G

generate_subset() (sunbeam.project.SampleList method) get_extension_rules() (sunbeam.project.SunbeamConfig static method) get_extensions() (sunbeam.project.SunbeamConfig static method)

get_mapped_reads() (in module sunbeam.bfx) get_samples() (sunbeam.project.SampleList method) guess_format_string() (sunbeam.project.SampleList method)

I

Init() (in module sunbeam.scripts)

L

load_from_dir() (sunbeam.project.SampleList method)

load_from_file() (sunbeam.project.SampleList method)

M

modify() (sunbeam.project.SunbeamConfig method) module sunbeam sunbeam.bfx sunbeam.project sunbeam.scripts

O

output_subdir() (in module sunbeam.project)

P

parse_decontam_log() (in module sunbeam.bfx) parse_fasta() (in module sunbeam.bfx) parse_fastq() (in module sunbeam.bfx) parse_fastqc_quality() (in module sunbeam.bfx)

parse_komplexity_log() (in module sunbeam.bfx) parse_sam() (in module sunbeam.bfx) parse_trim_summary_paired() (in module sunbeam.bfx) parse_trim_summary_single() (in module sunbeam.bfx)

R

remove_pair_id() (in module sunbeam.bfx)

resolved_paths() (sunbeam.project.SunbeamConfig method) Run() (in module sunbeam.scripts)

S

SampleList (class in sunbeam.project) summarize_qual_decontam() (in module sunbeam.bfx) sunbeam module Sunbeam() (in module sunbeam.scripts) sunbeam.bfx module

sunbeam.project module sunbeam.scripts module SunbeamConfig (class in sunbeam.project) SunbeamProfile (class in sunbeam.project)

T

to_file() (sunbeam.project.SampleList method) (sunbeam.project.SunbeamConfig method) (sunbeam.project.SunbeamProfile method)

W

write_fasta() (in module sunbeam.bfx)

write_fastq() (in module sunbeam.bfx)