Index

A

AlignbatchFileReader (class in xenomapper2.xenomapper2)

always_very_negative() (in module xenomapper2.xenomapper2) always_zero() (in module xenomapper2.xenomapper2)

C

calc_cigar_based_score() (in module xenomapper2.xenomapper2) close() (xenomapper2.xenomapper2.AlignbatchFileReader method) (xenomapper2.xenomapper2.DummyFile method) (xenomapper2.xenomapper2.XenomapperOutputWriter method)

conservative_state_map() (in module xenomapper2.xenomapper2)

D

DummyFile (class in xenomapper2.xenomapper2)

G

get_AS() (in module pylazybam.tags) get_bamprimary_AS_XS() (in module xenomapper2.xenomapper2) get_cigar_based_score() (in module xenomapper2.xenomapper2) get_full_raw_header() (xenomapper2.xenomapper2.AlignbatchFileReader method) get_int_tag() (in module pylazybam.tags) get_mapping_state() (in module xenomapper2.xenomapper2)

get_max_AS_XS() (in module xenomapper2.xenomapper2) get_MD() (in module pylazybam.tags) get_str_tag() (in module pylazybam.tags) get_updated_header() (xenomapper2.xenomapper2.AlignbatchFileReader method) (xenomapper2.xenomapper2.DummyFile method) get_XS() (in module pylazybam.tags) get_ZS() (in module pylazybam.tags)

H

header (xenomapper2.xenomapper2.AlignbatchFileReader attribute)

I

index_to_ref (xenomapper2.xenomapper2.AlignbatchFileReader attribute)

K

keys() (xenomapper2.xenomapper2.XenomapperOutputWriter method)

M

main() (in module xenomapper2.cli)

O

output_summary() (in module xenomapper2.xenomapper2)

P

pylazybam.tags (module)

R

raw_header (xenomapper2.xenomapper2.AlignbatchFileReader attribute) raw_refs (xenomapper2.xenomapper2.AlignbatchFileReader attribute)

ref_to_index (xenomapper2.xenomapper2.AlignbatchFileReader attribute) refs (xenomapper2.xenomapper2.AlignbatchFileReader attribute) reset_alignments() (xenomapper2.xenomapper2.AlignbatchFileReader method)

S

seekable() (xenomapper2.xenomapper2.DummyFile method)

split_forward_reverse() (in module xenomapper2.xenomapper2) state_map() (in module xenomapper2.xenomapper2)

U

update_header() (xenomapper2.xenomapper2.AlignbatchFileReader method) (xenomapper2.xenomapper2.DummyFile method)

update_header_length() (xenomapper2.xenomapper2.AlignbatchFileReader method) (xenomapper2.xenomapper2.DummyFile method)

W

writable() (xenomapper2.xenomapper2.DummyFile method)

write() (xenomapper2.xenomapper2.DummyFile method) write_header() (xenomapper2.xenomapper2.DummyFile method)

X

xenomap() (in module xenomapper2.xenomapper2) xenomap_states() (in module xenomapper2.xenomapper2)

xenomapper2.cli (module) xenomapper2.xenomapper2 (module) XenomapperOutputWriter (class in xenomapper2.xenomapper2)