Index

Symbols

--bin-size finaletoolkit-frag-length-bins command line option --blacklist finaletoolkit-delfi command line option finaletoolkit-filter-file command line option --chrom-sizes finaletoolkit-wps command line option --contig finaletoolkit-frag-length-bins command line option --edge-size finaletoolkit-adjust-wps command line option --gap-file finaletoolkit-delfi command line option --header finaletoolkit-mds command line option finaletoolkit-regional-mds command line option --histogram finaletoolkit-frag-length-bins command line option --intersect-policy finaletoolkit-coverage command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option --interval-size finaletoolkit-adjust-wps command line option finaletoolkit-wps command line option --kmer-length finaletoolkit-breakpoint-motifs command line option finaletoolkit-end-motifs command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option --max-length finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option --mean finaletoolkit-adjust-wps command line option finaletoolkit-agg-bw command line option --median-window-size finaletoolkit-adjust-wps command line option finaletoolkit-agg-bw command line option --merge-bins finaletoolkit-delfi command line option --merge-size finaletoolkit-delfi command line option --min-length finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option --min-mapq finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option --no-gc-correct finaletoolkit-delfi command line option --no-merge-bins finaletoolkit-delfi command line option --no-remove-nocov finaletoolkit-delfi command line option --no-savgol finaletoolkit-adjust-wps command line option --normalize finaletoolkit-coverage command line option --output finaletoolkit-adjust-wps command line option finaletoolkit-agg-bw command line option finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option --pad-left finaletoolkit-cleavage-profile command line option --pad-right finaletoolkit-cleavage-profile command line option --reference finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-wps command line option --remove-nocov finaletoolkit-delfi command line option --savgol finaletoolkit-adjust-wps command line option --savgol-poly-deg finaletoolkit-adjust-wps command line option --savgol-window-size finaletoolkit-adjust-wps command line option --scale-factor finaletoolkit-coverage command line option --sep finaletoolkit-mds command line option finaletoolkit-regional-mds command line option --short-threshold finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option --start finaletoolkit-frag-length-bins command line option --stop finaletoolkit-frag-length-bins command line option --strand finaletoolkit-breakpoint-motifs command line option finaletoolkit-end-motifs command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option

--subtract-edges finaletoolkit-adjust-wps command line option --summary-stats finaletoolkit-frag-length-bins command line option --threads finaletoolkit-adjust-wps command line option finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option --verbose finaletoolkit-adjust-wps command line option finaletoolkit-agg-bw command line option finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option --version finaletoolkit command line option --whitelist finaletoolkit-filter-file command line option --window-size finaletoolkit-wps command line option -b finaletoolkit-delfi command line option finaletoolkit-filter-file command line option -c finaletoolkit-frag-length-bins command line option -E finaletoolkit-frag-length-bins command line option -g finaletoolkit-delfi command line option -i finaletoolkit-adjust-wps command line option finaletoolkit-wps command line option -k finaletoolkit-breakpoint-motifs command line option finaletoolkit-end-motifs command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option -m finaletoolkit-adjust-wps command line option finaletoolkit-agg-bw command line option -n finaletoolkit-coverage command line option -o finaletoolkit-adjust-wps command line option finaletoolkit-agg-bw command line option finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option -p finaletoolkit-coverage command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option -q finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option -r finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-wps command line option -S finaletoolkit-frag-length-bins command line option -s finaletoolkit-mds command line option finaletoolkit-regional-mds command line option -t finaletoolkit-adjust-wps command line option finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option -v finaletoolkit command line option finaletoolkit-adjust-wps command line option finaletoolkit-agg-bw command line option finaletoolkit-breakpoint-motifs command line option finaletoolkit-cleavage-profile command line option finaletoolkit-coverage command line option finaletoolkit-delfi command line option finaletoolkit-end-motifs command line option finaletoolkit-filter-file command line option finaletoolkit-frag-length-bins command line option finaletoolkit-frag-length-intervals command line option finaletoolkit-interval-breakpoint-motifs command line option finaletoolkit-interval-end-motifs command line option finaletoolkit-wps command line option -W finaletoolkit-wps command line option -w finaletoolkit-filter-file command line option

A

adjust_wps() (in module finaletoolkit.frag)

agg_bw() (in module finaletoolkit.utils) AlignmentWrapper (class in finaletoolkit.io)

B

b37() (finaletoolkit.genome.GenomeGaps class method) b37_gap_bed() (in module finaletoolkit.genome)

breakpoint_motifs() (in module finaletoolkit.frag) BreakpointMotifFreqs (class in finaletoolkit.frag) BreakpointMotifsIntervals (class in finaletoolkit.frag)

C

chrom_sizes_to_dict() (in module finaletoolkit.utils) chrom_sizes_to_list() (in module finaletoolkit.utils) chroms (finaletoolkit.io.AlignmentWrapper property) (finaletoolkit.io.ReferenceWrapper property) cleavage_profile() (in module finaletoolkit.frag) close() (finaletoolkit.io.AlignmentWrapper method) (finaletoolkit.io.ReferenceWrapper method) contig (finaletoolkit.frag.CoverageResult attribute) (finaletoolkit.frag.FragLengthStats attribute) (finaletoolkit.io.Fragment attribute)

ContigGaps (class in finaletoolkit.genome) ContigMismatchError ContigNotFoundError count (finaletoolkit.frag.FragLengthStats attribute) coverage (finaletoolkit.frag.CoverageResult attribute) coverage() (in module finaletoolkit.frag) CoverageResult (class in finaletoolkit.frag)

D

delfi() (in module finaletoolkit.frag)

delfi_gc_correct() (in module finaletoolkit.frag) delfi_merge_bins() (in module finaletoolkit.frag)

E

end_motifs() (in module finaletoolkit.frag)

EndMotifFreqs (class in finaletoolkit.frag) EndMotifsIntervals (class in finaletoolkit.frag)

F

fetch() (finaletoolkit.io.AlignmentWrapper method) filter_file() (in module finaletoolkit.utils) finaletoolkit command line option --version -v finaletoolkit-adjust-wps command line option --edge-size --interval-size --mean --median-window-size --no-savgol --output --savgol --savgol-poly-deg --savgol-window-size --subtract-edges --threads --verbose -i -m -o -t -v finaletoolkit-agg-bw command line option --mean --median-window-size --output --verbose -m -o -v finaletoolkit-breakpoint-motifs command line option --kmer-length --max-length --min-length --min-mapq --output --strand --threads --verbose -k -o -q -t -v finaletoolkit-cleavage-profile command line option --max-length --min-length --min-mapq --output --pad-left --pad-right --reference --threads --verbose -o -q -r -t -v finaletoolkit-coverage command line option --intersect-policy --max-length --min-length --min-mapq --normalize --output --reference --scale-factor --threads --verbose -n -o -p -q -r -t -v finaletoolkit-delfi command line option --blacklist --gap-file --merge-bins --merge-size --min-mapq --no-gc-correct --no-merge-bins --no-remove-nocov --output --remove-nocov --threads --verbose -b -g -o -q -t -v finaletoolkit-end-motifs command line option --kmer-length --max-length --min-length --min-mapq --output --strand --threads --verbose -k -o -q -t -v finaletoolkit-filter-file command line option --blacklist --intersect-policy --max-length --min-length --min-mapq --output --threads --verbose --whitelist -b -o -p -q -t -v -w

finaletoolkit-frag-length-bins command line option --bin-size --contig --histogram --intersect-policy --max-length --min-length --min-mapq --output --reference --short-threshold --start --stop --summary-stats --verbose -c -E -o -p -q -r -S -v finaletoolkit-frag-length-intervals command line option --intersect-policy --max-length --min-length --min-mapq --output --reference --short-threshold --threads --verbose -o -p -q -r -t -v finaletoolkit-interval-breakpoint-motifs command line option --kmer-length --max-length --min-length --min-mapq --output --strand --threads --verbose -k -o -q -t -v finaletoolkit-interval-end-motifs command line option --kmer-length --max-length --min-length --min-mapq --output --strand --threads --verbose -k -o -q -t -v finaletoolkit-mds command line option --header --sep -s finaletoolkit-regional-mds command line option --header --sep -s finaletoolkit-wps command line option --chrom-sizes --interval-size --max-length --min-length --min-mapq --output --reference --threads --verbose --window-size -i -o -q -r -t -v -W finaletoolkit.exceptions module FinaleToolkitError frac_short_reads (finaletoolkit.frag.FragLengthStats attribute) frag_array() (in module finaletoolkit.utils) frag_generator() (in module finaletoolkit.utils) frag_length() (in module finaletoolkit.frag) frag_length_bins() (in module finaletoolkit.frag) frag_length_intervals() (in module finaletoolkit.frag) FragLengthStats (class in finaletoolkit.frag) Fragment (class in finaletoolkit.io)

G

GenomeGaps (class in finaletoolkit.genome) get_arm() (finaletoolkit.genome.ContigGaps method) (finaletoolkit.genome.GenomeGaps method)

get_contig_gaps() (finaletoolkit.genome.GenomeGaps method)

H

hg38() (finaletoolkit.genome.GenomeGaps class method)

I

in_gap() (finaletoolkit.genome.ContigGaps method) in_tcmere() (finaletoolkit.genome.ContigGaps method) (finaletoolkit.genome.GenomeGaps method) interval_breakpoint_motifs() (in module finaletoolkit.frag)

interval_end_motifs() (in module finaletoolkit.frag) InvalidInputError is_forward (finaletoolkit.io.Fragment attribute) is_sam (finaletoolkit.io.AlignmentWrapper property)

L

low_quality_read_pairs() (in module finaletoolkit.utils)

M

mapq (finaletoolkit.io.Fragment attribute) maximum (finaletoolkit.frag.FragLengthStats attribute) mean (finaletoolkit.frag.FragLengthStats attribute) median (finaletoolkit.frag.FragLengthStats attribute) minimum (finaletoolkit.frag.FragLengthStats attribute)

MissingIndexError MissingReferenceError module finaletoolkit.exceptions multi_cleavage_profile() (in module finaletoolkit.frag) multi_wps() (in module finaletoolkit.frag)

N

name (finaletoolkit.frag.CoverageResult attribute) (finaletoolkit.frag.FragLengthStats attribute)

O

OutOfBoundsError

overlaps() (in module finaletoolkit.utils) overlaps_gap() (finaletoolkit.genome.GenomeGaps method)

R

ReferenceWrapper (class in finaletoolkit.io)

region_breakpoint_motifs() (in module finaletoolkit.frag) region_end_motifs() (in module finaletoolkit.frag)

S

sequence() (finaletoolkit.io.ReferenceWrapper method) single_coverage() (in module finaletoolkit.frag) start (finaletoolkit.frag.CoverageResult attribute) (finaletoolkit.frag.FragLengthStats attribute) (finaletoolkit.io.Fragment attribute)

stdev (finaletoolkit.frag.FragLengthStats attribute) stop (finaletoolkit.frag.CoverageResult attribute) (finaletoolkit.frag.FragLengthStats attribute) (finaletoolkit.io.Fragment attribute)

T

to_bed() (finaletoolkit.genome.GenomeGaps method)

U

ucsc_hg19() (finaletoolkit.genome.GenomeGaps class method) ucsc_hg19_gap_bed() (in module finaletoolkit.genome)

ucsc_hg38_gap_bed() (in module finaletoolkit.genome) UnsupportedFormatError

W

wps() (in module finaletoolkit.frag)