Index

Symbols

--exp_cutoff learn_beta command line option --fdr_cutoff learn_beta command line option

--outfile learn_beta command line option

B

bamfile (class in footprint_tools.cutcounts) BEDGRAPH_FILE learn_beta command line option

bias_model (class in footprint_tools.modeling.bias)

C

close() (footprint_tools.cutcounts.bamfile method)

E

ERROR_5PROXIMITY (footprint_tools.cutcounts.ReadError attribute) ERROR_ALIGNMENT (footprint_tools.cutcounts.ReadError attribute)

ERROR_BASEQ (footprint_tools.cutcounts.ReadError attribute) ERROR_GENOTYPE (footprint_tools.cutcounts.ReadError attribute) ERROR_MISMATCH (footprint_tools.cutcounts.ReadError attribute)

F

footprint_tools.cutcounts module

footprint_tools.modeling.bias module

G

GenotypeError

K

kmer_model (class in footprint_tools.modeling.bias)

L

learn_beta command line option --exp_cutoff --fdr_cutoff --outfile BEDGRAPH_FILE

lookup() (footprint_tools.cutcounts.bamfile method) lookup_allelic() (footprint_tools.cutcounts.bamfile method)

M

module footprint_tools.cutcounts footprint_tools.modeling.bias

O

offset() (footprint_tools.modeling.bias.bias_model method)

P

predict() (footprint_tools.modeling.bias.bias_model method)

probs() (footprint_tools.modeling.bias.kmer_model method) (footprint_tools.modeling.bias.uniform_model method)

R

read_model() (footprint_tools.modeling.bias.kmer_model method)

read_pair_generator() (footprint_tools.cutcounts.bamfile method) ReadError

S

shuffle() (footprint_tools.modeling.bias.bias_model method)

U

uniform_model (class in footprint_tools.modeling.bias)

V

validate_read() (footprint_tools.cutcounts.bamfile method)