Index

C

contig (vamp.utils.ContigComposition attribute) contig_end (vamp.utils.ContigComposition attribute) contig_size (vamp.utils.ContigComposition attribute) contig_start (vamp.utils.ContigComposition attribute)

ContigComposition (class in vamp.utils) convert_interval_gapped_to_nongapped() (in module seq_utils.utils) convert_interval_nongapped_to_gapped() (in module seq_utils.utils)

E

end (vamp.utils.ContigComposition attribute)

F

find_aligned_position() (in module seq_utils.convert_coordinates)

find_deletions() (in module vamp.utils)

G

get_block_by_label() (in module vamp.utils) get_sequence_length_from_maf() (in module vamp.utils)

get_sequence_net_alignment() (in module vamp.utils) get_vamp_home() (in module vamp.utils)

M

main() (in module seq_utils.summarize_alignments)

mismatch_string() (in module seq_utils.summarize_alignments)

P

parse_event() (in module seq_utils.summarize_alignments)

R

read_contig_composition_summary() (in module vamp.utils)

replace_alignment_with_block() (in module vamp.utils)

S

seq (vamp.utils.ContigComposition attribute) seq_utils.convert_coordinates (module) seq_utils.fasta_from_gff (module) seq_utils.summarize_alignments (module) seq_utils.utils (module)

start (vamp.utils.ContigComposition attribute) strand (vamp.utils.ContigComposition attribute) subtract_intervals() (in module vamp.utils) summarize_contig_composition() (in module vamp.utils) summary_of_alignment() (in module seq_utils.summarize_alignments)

T

tab_headings() (vamp.utils.ContigComposition static method)

to_tab() (vamp.utils.ContigComposition method)

U

update_contig_composition_summary() (in module vamp.utils)

update_sequence_with_replacements() (in module vamp.utils)

V

vamp.utils (module)

verify_maf_fasta() (in module vamp.utils)