Index

Symbols

--bam <path> cli-detect command line option --cutoff <int> cli-detect command line option --gffdb <path> cli-detect command line option --out <path> cli-detect command line option --out-directory <path> cli-build command line option --parallel cli-detect command line option --quality <int> cli-detect command line option --reference <path> cli-detect command line option

--verbose cli command line option --version cli command line option -b cli-detect command line option -c cli-detect command line option -db cli-detect command line option -o cli-build command line option cli-detect command line option -q cli-detect command line option -r cli-detect command line option

A

add_read() (ce_detector.detector.JunctionMap method) annotate_junction() (ce_detector.annotator.Annotator method)

Annotator (class in ce_detector.annotator) assign_value() (in module ce_detector.scanner)

C

ce_detector.annotator module ce_detector.detector module ce_detector.scanner module check() (in module ce_detector.scanner) check_strand() (ce_detector.detector.JunctionDetector static method) cli command line option --verbose --version cli-build command line option --out-directory <path> -o GFF

cli-detect command line option --bam <path> --cutoff <int> --gffdb <path> --out <path> --parallel --quality <int> --reference <path> -b -c -db -o -q -r

D

detect_property() (ce_detector.annotator.Annotator static method)

F

find_ce() (in module ce_detector.scanner)

G

GFF cli-build command line option

J

JunctionDetector (class in ce_detector.detector)

JunctionMap (class in ce_detector.detector)

M

module ce_detector.annotator ce_detector.detector ce_detector.scanner

R

Read (class in ce_detector.detector) run() (ce_detector.annotator.Annotator method) (ce_detector.detector.JunctionDetector method) (ce_detector.scanner.Scanner method)

S

Scanner (class in ce_detector.scanner)

split_ce() (in module ce_detector.scanner)

W

worker() (ce_detector.detector.JunctionDetector method)

write2file() (ce_detector.detector.JunctionMap method) (ce_detector.scanner.Scanner method)