Index

A

all_ratio (lorals.annotate.AnnotatedStat property) allelic_stats() (in module lorals.ase) AllelicStat (class in lorals.ase) alt (lorals.features.Bpileup property) alt_count (lorals.ase.AllelicStat property)

alt_indel (lorals.ase.AllelicStat property) alts (lorals.features.Bpileup property) annotate_bed() (in module lorals.annotate) annotate_genes() (in module lorals.annotate) annotate_genotypes() (in module lorals.annotate) AnnotatedStat (class in lorals.annotate)

B

bam_to_bed() (in module lorals.asts) bed() (lorals.features.Bpileup method) bed_intersect() (in module lorals.asts)

bias_stats() (in module lorals.annotate) blacklisted (lorals.annotate.AnnotatedStat property) Bpileup (class in lorals.features)

C

chrom (lorals.features.Bpileup property)

Cigar (class in lorals.cigar) ColoredFormatter (class in lorals.fancy_logging)

D

deduplicate_bpileup() (in module lorals.asts) default (lorals.features.Bpileup property) default_id() (lorals.features.Bpileup static method)

depth (lorals.ase.AllelicStat property) dictsearch() (in module lorals.utils) dummy (lorals.features.Bpileup property)

F

filter_stats() (in module lorals.ase) find_open() (in module lorals.utils) fmttime() (in module lorals.fancy_logging) format() (lorals.fancy_logging.ColoredFormatter method) (lorals.fancy_logging.StrippedFormatter method)

frombpileup() (lorals.ase.AllelicStat class method) frominterval() (lorals.features.Bpileup class method) fromstring() (lorals.ase.AllelicStat class method) fullpath() (in module lorals.utils)

G

gene (lorals.annotate.AnnotatedStat property)

H

HEADER (lorals.annotate.AnnotatedStat attribute) (lorals.ase.AllelicStat attribute)

I

indel_ratio (lorals.annotate.AnnotatedStat property) indel_threshold (lorals.annotate.AnnotatedStat attribute)

indel_warning (lorals.annotate.AnnotatedStat property) iter_var() (in module lorals.features)

L

lorals module lorals.annotate module lorals.ase module lorals.asts module lorals.cigar module

lorals.fancy_logging module lorals.features module lorals.maths module lorals.scripts module lorals.utils module

M

median() (in module lorals.maths) module lorals lorals.annotate lorals.ase lorals.asts lorals.cigar lorals.fancy_logging lorals.features lorals.maths lorals.scripts lorals.utils

multi_mapping (lorals.annotate.AnnotatedStat property)

N

name (lorals.features.Bpileup property)

null_ratio (lorals.annotate.AnnotatedStat property)

O

oper_map (lorals.cigar.Cigar attribute) other_count (lorals.ase.AllelicStat property)

other_threshold (lorals.annotate.AnnotatedStat attribute) other_warning (lorals.annotate.AnnotatedStat property)

P

percentile() (in module lorals.maths) position (lorals.features.Bpileup property)

print_bpileup() (lorals.ase.AllelicStat method) pvalue (lorals.annotate.AnnotatedStat property) pvalue_adjust() (in module lorals.maths)

Q

qvalue (lorals.annotate.AnnotatedStat property)

R

ref (lorals.features.Bpileup property) ref_count (lorals.ase.AllelicStat property)

ref_indel (lorals.ase.AllelicStat property) ref_ratio (lorals.annotate.AnnotatedStat property)

S

StrippedFormatter (class in lorals.fancy_logging)

T

total_count (lorals.ase.AllelicStat property)

U

unpack() (in module lorals.utils)

V

vcf_bpileup() (in module lorals.asts)

W

warning (lorals.annotate.AnnotatedStat property) where() (in module lorals.utils)

window() (in module lorals.utils) write_bed() (in module lorals.features)