fgpyo
latest
FGPYO
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fgpyo
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
A
add() (fgpyo.fasta.builder.ContigBuilder method)
(fgpyo.fasta.builder.FastaBuilder method)
(fgpyo.vcf.builder.VariantBuilder method)
add_filter_header() (fgpyo.vcf.builder.VariantBuilder method)
add_format_header() (fgpyo.vcf.builder.VariantBuilder method)
add_header_line() (fgpyo.vcf.builder.VariantBuilder method)
add_info_header() (fgpyo.vcf.builder.VariantBuilder method)
add_pair() (fgpyo.sam.builder.SamBuilder method)
add_single() (fgpyo.sam.builder.SamBuilder method)
all_recs() (fgpyo.sam.Template method)
ANY_LENGTH_CHAR (in module fgpyo.read_structure)
assembly (fgpyo.fasta.builder.ContigBuilder attribute)
(fgpyo.fasta.builder.FastaBuilder attribute)
assert_directory_exists() (in module fgpyo.io)
assert_path_is_readable() (in module fgpyo.io)
assert_path_is_writeable() (in module fgpyo.io)
attr_from() (in module fgpyo.util.inspect)
AttrsInstance (class in fgpyo.util.inspect)
B
bases (fgpyo.fasta.builder.ContigBuilder attribute)
(fgpyo.read_structure.SubReadWithoutQuals attribute)
(fgpyo.read_structure.SubReadWithQuals attribute)
build() (fgpyo.sam.Template static method)
C
calculate_edit_info() (in module fgpyo.sam)
can_peek() (fgpyo.collections.PeekableIterator method)
character (fgpyo.sam.CigarOp attribute)
Cigar (class in fgpyo.sam)
cigar (fgpyo.sam.SupplementaryAlignment attribute)
CigarElement (class in fgpyo.sam)
CigarOp (class in fgpyo.sam)
CigarParsingException
ClippingInfo (class in fgpyo.sam.clipping)
close() (fgpyo.fastx.FastxZipped method)
code (fgpyo.sam.CigarOp attribute)
column_it() (in module fgpyo.util.string)
complement() (in module fgpyo.sequence)
consumes_query (fgpyo.sam.CigarOp attribute)
consumes_target (fgpyo.sam.CigarOp attribute)
contig_builders (fgpyo.fasta.builder.FastaBuilder attribute)
ContigBuilder (class in fgpyo.fasta.builder)
Coordinate (fgpyo.sam.SamOrder attribute)
count (fgpyo.util.logging.ProgressLogger attribute)
D
D (fgpyo.sam.CigarOp attribute)
DataclassesProtocol (class in fgpyo.util.inspect)
default_rg() (fgpyo.sam.builder.SamBuilder static method)
default_sd() (fgpyo.sam.builder.SamBuilder static method)
(fgpyo.vcf.builder.VariantBuilder class method)
deleted_bases (fgpyo.sam.ReadEditInfo attribute)
deletions (fgpyo.sam.ReadEditInfo attribute)
dict_parser() (in module fgpyo.util.inspect)
dropwhile() (fgpyo.collections.PeekableIterator method)
E
end (fgpyo.sam.SupplementaryAlignment property)
EQ (fgpyo.sam.CigarOp attribute)
ext (fgpyo.sam.SamFileType attribute)
extract() (fgpyo.read_structure.ReadSegment method)
(fgpyo.read_structure.ReadStructure method)
extract_with_quals() (fgpyo.read_structure.ReadSegment method)
(fgpyo.read_structure.ReadStructure method)
F
FastaBuilder (class in fgpyo.fasta.builder)
FastxZipped (class in fgpyo.fastx)
fgpyo.collections
module
fgpyo.fasta.builder
module
fgpyo.fastx
module
fgpyo.io
module
fgpyo.read_structure
module
fgpyo.sam
module
fgpyo.sam.builder
module
fgpyo.sam.clipping
module
fgpyo.sequence
module
fgpyo.util.inspect
module
fgpyo.util.logging
module
fgpyo.util.metric
module
fgpyo.util.string
module
fgpyo.util.types
module
fgpyo.vcf
module
fgpyo.vcf.builder
module
FieldType (in module fgpyo.util.inspect)
fixed_length (fgpyo.read_structure.ReadSegment property)
(fgpyo.read_structure.ReadStructure property)
format_value() (fgpyo.util.metric.Metric class method)
formatted_values() (fgpyo.util.metric.Metric method)
from_character() (fgpyo.sam.CigarOp static method)
from_cigarstring() (fgpyo.sam.Cigar class method)
from_cigartuples() (fgpyo.sam.Cigar class method)
from_code() (fgpyo.sam.CigarOp static method)
from_path() (fgpyo.sam.SamFileType class method)
from_read() (fgpyo.sam.SupplementaryAlignment class method)
from_segments() (fgpyo.read_structure.ReadStructure class method)
G
get_fields() (in module fgpyo.util.inspect)
get_fields_dict() (in module fgpyo.util.inspect)
H
H (fgpyo.sam.CigarOp attribute)
has_fixed_length (fgpyo.read_structure.ReadSegment property)
(fgpyo.read_structure.ReadStructure property)
header (fgpyo.sam.builder.SamBuilder property)
(fgpyo.vcf.builder.VariantBuilder attribute)
header() (fgpyo.util.metric.Metric class method)
I
I (fgpyo.sam.CigarOp attribute)
inserted_bases (fgpyo.sam.ReadEditInfo attribute)
insertions (fgpyo.sam.ReadEditInfo attribute)
InspectException
is_attr_class() (in module fgpyo.util.inspect)
is_clipping (fgpyo.sam.CigarOp property)
is_constructible_from_str() (in module fgpyo.util.types)
is_forward (fgpyo.sam.SupplementaryAlignment attribute)
is_indel (fgpyo.sam.CigarOp property)
is_list_like() (in module fgpyo.util.types)
isize() (in module fgpyo.sam)
iterator() (fgpyo.sam.Template static method)
K
kind (fgpyo.read_structure.ReadSegment attribute)
(fgpyo.read_structure.SubReadWithoutQuals property)
(fgpyo.read_structure.SubReadWithQuals property)
L
length (fgpyo.read_structure.ReadSegment attribute)
(fgpyo.read_structure.ReadStructure property)
length_on_query (fgpyo.sam.CigarElement property)
length_on_query() (fgpyo.sam.Cigar method)
length_on_target (fgpyo.sam.CigarElement property)
length_on_target() (fgpyo.sam.Cigar method)
line_length (fgpyo.fasta.builder.FastaBuilder attribute)
list_parser() (in module fgpyo.util.inspect)
log_last() (fgpyo.util.logging.ProgressLogger method)
M
M (fgpyo.sam.CigarOp attribute)
make_enum_parser() (in module fgpyo.util.types)
make_literal_parser() (in module fgpyo.util.types)
make_union_parser() (in module fgpyo.util.types)
mapq (fgpyo.sam.SupplementaryAlignment attribute)
matches (fgpyo.sam.ReadEditInfo attribute)
Metric (class in fgpyo.util.metric)
mismatches (fgpyo.sam.ReadEditInfo attribute)
mode (fgpyo.sam.SamFileType attribute)
module
fgpyo.collections
fgpyo.fasta.builder
fgpyo.fastx
fgpyo.io
fgpyo.read_structure
fgpyo.sam
fgpyo.sam.builder
fgpyo.sam.clipping
fgpyo.sequence
fgpyo.util.inspect
fgpyo.util.logging
fgpyo.util.metric
fgpyo.util.string
fgpyo.util.types
fgpyo.vcf
fgpyo.vcf.builder
MolecularBarcode (fgpyo.read_structure.SegmentType attribute)
N
N (fgpyo.sam.CigarOp attribute)
name (fgpyo.fasta.builder.ContigBuilder attribute)
(fgpyo.sam.Template attribute)
nm (fgpyo.sam.ReadEditInfo attribute)
(fgpyo.sam.SupplementaryAlignment attribute)
NO_REF_INDEX (in module fgpyo.sam)
NO_REF_NAME (in module fgpyo.sam)
NO_REF_POS (in module fgpyo.sam)
none_parser() (in module fgpyo.util.types)
noun (fgpyo.util.logging.ProgressLogger attribute)
O
offset (fgpyo.read_structure.ReadSegment attribute)
P
P (fgpyo.sam.CigarOp attribute)
parse() (fgpyo.sam.SupplementaryAlignment static method)
(fgpyo.util.metric.Metric class method)
parse_bool() (in module fgpyo.util.types)
parse_sa_tag() (fgpyo.sam.SupplementaryAlignment static method)
ParserNotFoundException
peek() (fgpyo.collections.PeekableIterator method)
PeekableIterator (class in fgpyo.collections)
primary_recs() (fgpyo.sam.Template method)
printer (fgpyo.util.logging.ProgressLogger attribute)
ProgressLogger (class in fgpyo.util.logging)
pysam_dict() (in module fgpyo.fasta.builder)
pysam_faidx() (in module fgpyo.fasta.builder)
Q
quals (fgpyo.read_structure.SubReadWithQuals attribute)
query_bases_clipped (fgpyo.sam.clipping.ClippingInfo attribute)
QueryName (fgpyo.sam.SamOrder attribute)
R
r1 (fgpyo.sam.Template attribute)
r1_secondaries (fgpyo.sam.Template attribute)
r1_supplementals (fgpyo.sam.Template attribute)
r2 (fgpyo.sam.Template attribute)
r2_secondaries (fgpyo.sam.Template attribute)
r2_supplementals (fgpyo.sam.Template attribute)
read() (fgpyo.util.metric.Metric class method)
read_lines() (in module fgpyo.io)
ReadEditInfo (class in fgpyo.sam)
reader() (in module fgpyo.sam)
(in module fgpyo.vcf)
ReadSegment (class in fgpyo.read_structure)
ReadStructure (class in fgpyo.read_structure)
record() (fgpyo.util.logging.ProgressLogger method)
record_alignment() (fgpyo.util.logging.ProgressLogger method)
records (fgpyo.vcf.builder.VariantBuilder attribute)
redirect_to_dev_null() (in module fgpyo.io)
ref_bases_clipped (fgpyo.sam.clipping.ClippingInfo attribute)
reference_name (fgpyo.sam.SupplementaryAlignment attribute)
reverse_complement() (in module fgpyo.sequence)
reversed() (fgpyo.sam.Cigar method)
rg() (fgpyo.sam.builder.SamBuilder method)
rg_id() (fgpyo.sam.builder.SamBuilder method)
S
S (fgpyo.sam.CigarOp attribute)
SamBuilder (class in fgpyo.sam.builder)
SamFileType (class in fgpyo.sam)
SamOrder (class in fgpyo.sam)
SamPath (in module fgpyo.sam)
sample_ids (fgpyo.vcf.builder.VariantBuilder attribute)
SampleBarcode (fgpyo.read_structure.SegmentType attribute)
sd (fgpyo.vcf.builder.VariantBuilder attribute)
segment (fgpyo.read_structure.SubReadWithoutQuals attribute)
(fgpyo.read_structure.SubReadWithQuals attribute)
segments (fgpyo.read_structure.ReadStructure attribute)
segments_by_kind() (fgpyo.read_structure.ReadStructure method)
SegmentType (class in fgpyo.read_structure)
seq_idx_lookup (fgpyo.vcf.builder.VariantBuilder attribute)
set_pair_info() (in module fgpyo.sam)
set_parser() (in module fgpyo.util.inspect)
set_tag() (fgpyo.sam.Template method)
setup_logging() (in module fgpyo.util.logging)
Skip (fgpyo.read_structure.SegmentType attribute)
softclip_end_of_alignment_by_query() (in module fgpyo.sam.clipping)
softclip_end_of_alignment_by_ref() (in module fgpyo.sam.clipping)
softclip_start_of_alignment_by_query() (in module fgpyo.sam.clipping)
softclip_start_of_alignment_by_ref() (in module fgpyo.sam.clipping)
species (fgpyo.fasta.builder.ContigBuilder attribute)
(fgpyo.fasta.builder.FastaBuilder attribute)
split_at_given_level() (in module fgpyo.util.inspect)
start (fgpyo.sam.SupplementaryAlignment attribute)
SubReadWithoutQuals (class in fgpyo.read_structure)
SubReadWithQuals (class in fgpyo.read_structure)
SupplementaryAlignment (class in fgpyo.sam)
suppress_stderr() (in module fgpyo.io)
T
takewhile() (fgpyo.collections.PeekableIterator method)
Template (class in fgpyo.sam)
(fgpyo.read_structure.SegmentType attribute)
TemplateIterator (class in fgpyo.sam)
to_file() (fgpyo.fasta.builder.FastaBuilder method)
to_list() (fgpyo.util.metric.Metric class method)
to_path() (fgpyo.sam.builder.SamBuilder method)
(fgpyo.vcf.builder.VariantBuilder method)
to_reader() (in module fgpyo.io)
to_sorted_list() (fgpyo.sam.builder.SamBuilder method)
(fgpyo.vcf.builder.VariantBuilder method)
to_unsorted_list() (fgpyo.sam.builder.SamBuilder method)
(fgpyo.vcf.builder.VariantBuilder method)
to_writer() (in module fgpyo.io)
tuple_parser() (in module fgpyo.util.inspect)
U
unit (fgpyo.util.logging.ProgressLogger attribute)
Unsorted (fgpyo.sam.SamOrder attribute)
V
validate() (fgpyo.sam.Template method)
values() (fgpyo.util.metric.Metric method)
VariantBuilder (class in fgpyo.vcf.builder)
VcfFieldNumber (class in fgpyo.vcf.builder)
VcfFieldType (class in fgpyo.vcf.builder)
verb (fgpyo.util.logging.ProgressLogger attribute)
W
with_variable_last_segment() (fgpyo.read_structure.ReadStructure method)
write() (fgpyo.util.metric.Metric class method)
write_lines() (in module fgpyo.io)
write_to() (fgpyo.sam.Template method)
writer() (in module fgpyo.sam)
(in module fgpyo.vcf)
X
X (fgpyo.sam.CigarOp attribute)
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