bamnostic
0.8.4
Contents:
Installation
Getting Started
Module documentation
Citation and Support
bamnostic
Docs
»
Index
Index
_
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A
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B
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C
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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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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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W
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Y
_
_io (bamnostic.bai.Bai attribute)
(bamnostic.bgzf.BAMheader attribute)
_last_pos (bamnostic.bai.Bai attribute)
_LINEAR_INDEX_WINDOW (bamnostic.bai.Bai attribute)
_UNMAP_BIN (bamnostic.bai.Bai attribute)
A
AlignedSegment (class in bamnostic.core)
AlignmentFile (class in bamnostic.core)
B
Bai (class in bamnostic.bai)
BAMheader (class in bamnostic.bgzf)
bamnostic (module)
bamnostic.bai (module)
bamnostic.bgzf (module)
bamnostic.core (module)
bamnostic.utils (module)
BgzfReader (class in bamnostic.bgzf)
BgzfWriter (class in bamnostic.bgzf)
C
check_cigar_arg() (in module bamnostic.utils)
check_index() (bamnostic.bgzf.BgzfReader method)
Cigar (class in bamnostic.core)
cigar_alignment() (in module bamnostic.utils)
cigar_changes() (in module bamnostic.utils)
close() (bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
count() (bamnostic.bgzf.BgzfReader method)
count_coverage() (bamnostic.bgzf.BgzfReader method)
cull() (bamnostic.utils.LruDict method)
current_ref (bamnostic.bai.Bai attribute)
E
end_offset (bamnostic.bai.RefIdx attribute)
F
fetch() (bamnostic.bgzf.BgzfReader method)
fileno() (bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
flag_decode() (in module bamnostic.utils)
flush() (bamnostic.bgzf.BgzfWriter method)
format_warnings() (in module bamnostic.utils)
G
get_bins() (bamnostic.bai.Bai method)
get_block() (in module bamnostic.bgzf)
get_chunks() (bamnostic.bai.Bai method)
get_cigar_stats() (bamnostic.core.AlignedSegment method)
get_index_stats() (bamnostic.bgzf.BgzfReader method)
get_ints() (bamnostic.bai.Bai method)
get_ref() (bamnostic.bai.Bai method)
get_reference_name() (bamnostic.bgzf.BgzfReader method)
get_tag() (bamnostic.core.AlignedSegment method)
get_tags() (bamnostic.core.AlignedSegment method)
get_tid() (bamnostic.bgzf.BgzfReader method)
H
has_index() (bamnostic.bgzf.BgzfReader method)
head() (bamnostic.bgzf.BgzfReader method)
header (bamnostic.bgzf.BgzfReader attribute)
I
is_duplicate (bamnostic.core.AlignedSegment attribute)
is_paired (bamnostic.core.AlignedSegment attribute)
is_proper_pair (bamnostic.core.AlignedSegment attribute)
is_qcfail (bamnostic.core.AlignedSegment attribute)
is_read1 (bamnostic.core.AlignedSegment attribute)
is_read2 (bamnostic.core.AlignedSegment attribute)
is_reverse (bamnostic.core.AlignedSegment attribute)
is_secondary (bamnostic.core.AlignedSegment attribute)
is_supplementary (bamnostic.core.AlignedSegment attribute)
is_unmapped (bamnostic.core.AlignedSegment attribute)
is_valid_tid() (bamnostic.bgzf.BgzfReader method)
isatty() (bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
L
lengths (bamnostic.bgzf.BgzfReader attribute)
,
[1]
LruDict (class in bamnostic.utils)
M
magic (bamnostic.bai.Bai attribute)
make_virtual_offset() (in module bamnostic.utils)
mapped (bamnostic.bgzf.BgzfReader attribute)
mapping_quality (bamnostic.core.AlignedSegment attribute)
mate() (bamnostic.bgzf.BgzfReader method)
mate_is_reverse (bamnostic.core.AlignedSegment attribute)
mate_is_unmapped (bamnostic.core.AlignedSegment attribute)
md_changes() (in module bamnostic.utils)
N
n_bins (bamnostic.bai.RefIdx attribute)
n_no_coord (bamnostic.bai.Bai attribute)
n_op (bamnostic.core.Cigar attribute)
n_refs (bamnostic.bai.Bai attribute)
(bamnostic.bgzf.BAMheader attribute)
next() (bamnostic.bgzf.BgzfReader method)
next_reference_id (bamnostic.core.AlignedSegment attribute)
next_reference_name (bamnostic.core.AlignedSegment attribute)
next_reference_start (bamnostic.core.AlignedSegment attribute)
nocoordinate (bamnostic.bgzf.BgzfReader attribute)
,
[1]
nreferences (bamnostic.bgzf.BgzfReader attribute)
,
[1]
O
offset_qual() (in module bamnostic.core)
op_code (bamnostic.core.Cigar attribute)
op_id (bamnostic.core.Cigar attribute)
op_name (bamnostic.core.Cigar attribute)
P
parse_cigar() (in module bamnostic.utils)
parse_region() (in module bamnostic.utils)
Q
query() (bamnostic.bai.Bai method)
query_alignment_end (bamnostic.core.AlignedSegment attribute)
query_alignment_length (bamnostic.core.AlignedSegment attribute)
query_alignment_sequence (bamnostic.core.AlignedSegment attribute)
query_alignment_start (bamnostic.core.AlignedSegment attribute)
query_length (bamnostic.core.AlignedSegment attribute)
query_name (bamnostic.core.AlignedSegment attribute)
query_sequence (bamnostic.core.AlignedSegment attribute)
R
read() (bamnostic.bai.Bai method)
(bamnostic.bgzf.BgzfReader method)
readline() (bamnostic.bgzf.BgzfReader method)
ref2tid (bamnostic.bgzf.BgzfReader attribute)
ref_gen() (bamnostic.core.AlignedSegment method)
(in module bamnostic.utils)
ref_indices (bamnostic.bai.Bai attribute)
reference_end (bamnostic.core.AlignedSegment attribute)
reference_length (bamnostic.core.AlignedSegment attribute)
reference_start (bamnostic.core.AlignedSegment attribute)
references (bamnostic.bgzf.BgzfReader attribute)
,
[1]
RefIdx (class in bamnostic.bai)
refs (bamnostic.bgzf.BAMheader attribute)
reg2bin() (in module bamnostic.bai)
reg2bins() (in module bamnostic.bai)
Roi (class in bamnostic.utils)
S
SAMheader (bamnostic.bgzf.BAMheader attribute)
seek() (bamnostic.bai.Bai method)
(bamnostic.bgzf.BgzfReader method)
seekable() (bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
split_virtual_offset() (in module bamnostic.utils)
start_offset (bamnostic.bai.RefIdx attribute)
sys (bamnostic.utils.LruDict attribute)
T
tell() (bamnostic.bai.Bai method)
(bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
text (bamnostic.bgzf.BgzfReader attribute)
to_header() (bamnostic.bgzf.BAMheader method)
U
unmapped (bamnostic.bai.Bai attribute)
(bamnostic.bgzf.BgzfReader attribute)
,
[1]
unpack() (in module bamnostic.utils)
W
write() (bamnostic.bgzf.BgzfWriter method)
Y
yes_no() (in module bamnostic.utils)