Index

B

BpPosFlags (class in pyigd)

C

collect_next_site() (in module pyigd.extra)

D

description (pyigd.IGDReader property)

F

FLAG_IS_PHASED (pyigd.IGDConstants attribute) flags (pyigd.IGDHeader attribute) flags_is_missing() (in module pyigd)

fp_index (pyigd.IGDHeader attribute) fp_individualids (pyigd.IGDHeader attribute) fp_variantids (pyigd.IGDHeader attribute) fp_variants (pyigd.IGDHeader attribute)

G

get_alt_allele() (pyigd.IGDReader method) get_individual_ids() (pyigd.IGDReader method) get_inverse_sample_list() (in module pyigd.extra) get_position_and_flags() (pyigd.IGDReader method)

get_position_flags_copies() (pyigd.IGDReader method) get_ref_allele() (pyigd.IGDReader method) get_samples() (pyigd.IGDReader method) get_samples_bv() (pyigd.IGDReader method) get_variant_ids() (pyigd.IGDReader method)

H

HEADER_FORMAT (pyigd.IGDConstants attribute)

HEADER_MAGIC (pyigd.IGDConstants attribute)

I

IGDConstants (class in pyigd) IGDHeader (class in pyigd) IGDReader (class in pyigd) IGDTransformer (class in pyigd)

IGDWriter (class in pyigd) INDEX_ENTRY_BYTES (pyigd.IGDConstants attribute) IS_MISSING (pyigd.BpPosFlags attribute) is_phased (pyigd.IGDReader property)

L

lower_bound_position() (pyigd.IGDReader method)

M

magic (pyigd.IGDHeader attribute) MASK (pyigd.BpPosFlags attribute) modify_samples() (pyigd.IGDTransformer method)

module pyigd pyigd.extra

N

NUM_HEADER_BYTES (pyigd.IGDConstants attribute) num_individuals (pyigd.IGDHeader attribute) (pyigd.IGDReader property)

num_samples (pyigd.IGDReader property) num_variants (pyigd.IGDHeader attribute) (pyigd.IGDReader property)

P

pack() (pyigd.IGDHeader method) ploidy (pyigd.IGDHeader attribute) (pyigd.IGDReader property)

pyigd module pyigd.extra module

R

reserved (pyigd.IGDHeader attribute)

S

source (pyigd.IGDReader property) SPARSE (pyigd.BpPosFlags attribute)

sparse_threshold (pyigd.IGDHeader attribute) SUPPORTED_FILE_VERSION (pyigd.IGDConstants attribute)

T

transform() (pyigd.IGDTransformer method)

V

version (pyigd.IGDHeader attribute) (pyigd.IGDReader property)

W

write_header() (pyigd.IGDWriter method) write_index() (pyigd.IGDWriter method) write_individual_ids() (pyigd.IGDWriter method)

write_variant() (pyigd.IGDWriter method) write_variant_ids() (pyigd.IGDWriter method) write_variant_info() (pyigd.IGDWriter method)