Index

A

add_contig() (nasp.nasp_objects.GenomeStatus method) add_failed_genome() (nasp.nasp_objects.GenomeCollection method) add_generators() (nasp.nasp_objects.GenomeMeta method)

add_genome() (nasp.nasp_objects.GenomeCollection method) aligner (nasp.matrix_DTO.NaspFile attribute) append_contig() (nasp.nasp_objects.GenomeStatus method)

B

begin() (in module nasp.dispatcher)

C

CollectionStatistics (class in nasp.nasp_objects)

complete() (in module nasp.nasp)

D

determine_file_type() (in module nasp.vcf_to_matrix)

E

extend_contig() (nasp.nasp_objects.GenomeStatus method)

F

FastaGenome (class in nasp.nasp_objects) fetch_next_record() (nasp.nasp_objects.VCFRecord method) file_path() (nasp.nasp_objects.GenomeMeta method)

file_type() (nasp.nasp_objects.GenomeMeta method) flush_cumulative_stat_cache() (nasp.nasp_objects.CollectionStatistics method) format_fasta() (in module nasp.format_fasta)

G

generate_delta_file() (in module nasp.convert_external_genome) generate_nickname_from_filename() (nasp.nasp_objects.GenomeMeta static method) Genome (class in nasp.nasp_objects) GenomeCollection (class in nasp.nasp_objects) GenomeMeta (class in nasp.nasp_objects) GenomeStatus (class in nasp.nasp_objects) get_call() (nasp.nasp_objects.Genome method) get_contig() (nasp.nasp_objects.VCFRecord method) get_contig_length() (nasp.nasp_objects.GenomeStatus method) get_contig_stat() (nasp.nasp_objects.CollectionStatistics method) get_contigs() (nasp.nasp_objects.GenomeCollection method) (nasp.nasp_objects.GenomeStatus method) get_coverage() (nasp.nasp_objects.VCFRecord method) get_coverage_pass() (nasp.nasp_objects.FastaGenome method) (nasp.nasp_objects.VCFGenome method) get_cumulative_stat() (nasp.nasp_objects.CollectionStatistics method)

get_dups_call() (nasp.nasp_objects.GenomeCollection method) (nasp.nasp_objects.ReferenceGenome method) get_file_path() (in module nasp.vcf_to_matrix) get_position() (nasp.nasp_objects.VCFRecord method) get_proportion() (nasp.nasp_objects.VCFRecord method) get_proportion_pass() (nasp.nasp_objects.FastaGenome method) (nasp.nasp_objects.VCFGenome method) get_reference_call() (nasp.nasp_objects.VCFRecord method) get_sample_call() (nasp.nasp_objects.VCFRecord method) get_sample_info() (nasp.nasp_objects.VCFRecord method) get_sample_stat() (nasp.nasp_objects.CollectionStatistics method) get_samples() (nasp.nasp_objects.VCFRecord method) get_value() (nasp.nasp_objects.GenomeStatus method) get_was_called() (nasp.nasp_objects.FastaGenome method) (nasp.nasp_objects.VCFGenome method) gonasp_path() (in module nasp.nasp)

I

identifier() (nasp.nasp_objects.GenomeMeta method) import_dups_file() (nasp.nasp_objects.ReferenceGenome method) import_external_fasta() (in module nasp.vcf_to_matrix) import_fasta_file() (nasp.nasp_objects.Genome method)

import_reference() (in module nasp.vcf_to_matrix) increment_contig_stat() (nasp.nasp_objects.CollectionStatistics method) IndelList (class in nasp.nasp_objects) InvalidContigName

M

main() (in module nasp.configuration_parser) (in module nasp.convert_external_genome) (in module nasp.dispatcher) (in module nasp.find_duplicates) (in module nasp.format_fasta) (in module nasp.matrix_DTO) (in module nasp.nasp) (in module nasp.nasp_objects) (in module nasp.vcf_to_matrix) MalformedInputFile

manage_input_thread() (in module nasp.vcf_to_matrix)

N

name (nasp.matrix_DTO.NaspFile attribute) nasp (module) nasp.configuration_parser (module) nasp.convert_external_genome (module) nasp.dispatcher (module) nasp.find_duplicates (module) nasp.format_fasta (module)

nasp.matrix_DTO (module) nasp.nasp (module) nasp.nasp_objects (module) nasp.vcf_to_matrix (module) NaspFile (class in nasp.matrix_DTO) nickname() (nasp.nasp_objects.GenomeMeta method)

P

parse_config() (in module nasp.configuration_parser) parse_delta_file() (in module nasp.convert_external_genome) (in module nasp.find_duplicates) parse_dto() (in module nasp.matrix_DTO)

parse_input_files() (in module nasp.vcf_to_matrix) path (nasp.matrix_DTO.NaspFile attribute)

R

read_vcf_file() (in module nasp.vcf_to_matrix) record_sample_stat() (nasp.nasp_objects.CollectionStatistics method) reference() (nasp.nasp_objects.GenomeCollection method) ReferenceCallMismatch

ReferenceGenome (class in nasp.nasp_objects) reverse_complement() (nasp.nasp_objects.Genome static method) (nasp.nasp_objects.GenomeMeta static method) run_nucmer_on_reference() (in module nasp.find_duplicates)

S

send_to_fasta_handle() (nasp.nasp_objects.GenomeStatus method) send_to_matrix_handles() (nasp.nasp_objects.GenomeCollection method) set_call() (nasp.nasp_objects.Genome method) set_coverage_pass() (nasp.nasp_objects.VCFGenome method) set_current_contig() (nasp.nasp_objects.GenomeCollection method) (nasp.nasp_objects.GenomeStatus method) set_file_path() (nasp.nasp_objects.GenomeMeta method) set_file_type() (nasp.nasp_objects.GenomeMeta method) set_genome_metadata() (in module nasp.vcf_to_matrix)

set_nickname() (nasp.nasp_objects.GenomeMeta method) set_proportion_pass() (nasp.nasp_objects.VCFGenome method) set_reference() (nasp.nasp_objects.GenomeCollection method) set_value() (nasp.nasp_objects.GenomeStatus method) set_was_called() (nasp.nasp_objects.VCFGenome method) simple_call() (nasp.nasp_objects.Genome static method) snpcaller (nasp.matrix_DTO.NaspFile attribute)

V

VCFGenome (class in nasp.nasp_objects)

VCFRecord (class in nasp.nasp_objects)

W

write_config() (in module nasp.configuration_parser) write_dto() (in module nasp.matrix_DTO) write_output_matrices() (in module nasp.vcf_to_matrix) write_stats_data() (in module nasp.vcf_to_matrix)

write_to_fasta_file() (nasp.nasp_objects.GenomeStatus method) write_to_matrices() (nasp.nasp_objects.GenomeCollection method) write_to_stats_files() (nasp.nasp_objects.GenomeCollection method)