Index

A

assert_mapping_results() (tentacle.mappers.blastn.Blastn method) (tentacle.mappers.gem.Gem method) (tentacle.mappers.mapper.Mapper method) (tentacle.mappers.pblat.Pblat method) (tentacle.mappers.razers3.Razers3 method) (tentacle.mappers.usearch.Usearch method)

B

Blastn (class in tentacle.mappers.blastn)

C

compute_and_write_coverage_statistics() (in module tentacle.coverage.compute_and_write_coverage_statistics) compute_region_statistics() (in module tentacle.coverage.statistics)

construct_mapper_call() (tentacle.mappers.blastn.Blastn method) (tentacle.mappers.gem.Gem method) (tentacle.mappers.mapper.Mapper method) (tentacle.mappers.pblat.Pblat method) (tentacle.mappers.razers3.Razers3 method) (tentacle.mappers.usearch.Usearch method) create_argparser() (tentacle.mappers.blastn.Blastn static method) (tentacle.mappers.gem.Gem static method) (tentacle.mappers.mapper.Mapper static method) (tentacle.mappers.pblat.Pblat static method) (tentacle.mappers.razers3.Razers3 static method) (tentacle.mappers.usearch.Usearch static method)

D

determine_if_read_is_inside_region() (in module tentacle.coverage.coverage)

E

Error, [1], [2], [3], [4], [5]

F

FileFormatError, [1], [2], [3], [4]

G

Gem (class in tentacle.mappers.gem)

I

initialize_annotation_counts() (in module tentacle.parsers.initialize_contig_data) initialize_contig_data() (in module tentacle.parsers.initialize_contig_data)

initialize_contig_keys() (in module tentacle.parsers.initialize_contig_data)

M

Mapper (class in tentacle.mappers.mapper)

mapper (module)

P

parse_blast8() (in module tentacle.parsers.blast8) parse_gem() (in module tentacle.parsers.gem) parse_razers3() (in module tentacle.parsers.razers3) parse_sam() (in module tentacle.parsers.sam)

ParseError, [1], [2], [3], [4], [5] Pblat (class in tentacle.mappers.pblat) prepare_reads() (tentacle.mappers.mapper.Mapper method) prepare_references() (tentacle.mappers.blastn.Blastn method) (tentacle.mappers.gem.Gem method) (tentacle.mappers.mapper.Mapper method) (tentacle.mappers.usearch.Usearch method)

R

Razers3 (class in tentacle.mappers.razers3)

run_mapper() (tentacle.mappers.mapper.Mapper method)

T

tentacle.coverage.compute_and_write_coverage_statistics (module) tentacle.coverage.coverage (module) tentacle.coverage.statistics (module) tentacle.mappers.blastn (module) tentacle.mappers.gem (module) tentacle.mappers.mapper (module) tentacle.mappers.pblat (module)

tentacle.mappers.razers3 (module) tentacle.mappers.usearch (module) tentacle.parsers.blast8 (module) tentacle.parsers.gem (module) tentacle.parsers.initialize_contig_data (module) tentacle.parsers.razers3 (module) tentacle.parsers.sam (module)

U

update_contig_data() (in module tentacle.coverage.coverage)

Usearch (class in tentacle.mappers.usearch)