bamnostic
latest
Contents:
Installation
Getting Started
Module documentation
Citation and Support
bamnostic
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
W
|
Y
_
_io (bamnostic.bai.Bai attribute)
(bamnostic.bam.BAMheader attribute)
(bamnostic.csi.Csi attribute)
_last_pos (bamnostic.bai.Bai attribute)
(bamnostic.csi.Csi attribute)
_LINEAR_INDEX_WINDOW (bamnostic.bai.Bai attribute)
_UNMAP_BIN (bamnostic.bai.Bai attribute)
(bamnostic.csi.Csi attribute)
A
AlignedSegment (class in bamnostic.core)
AlignmentFile (class in bamnostic.core)
B
Bai (class in bamnostic.bai)
BAMheader (class in bamnostic.bam)
bamnostic (module)
bamnostic.bai (module)
bamnostic.bam (module)
bamnostic.bgzf (module)
bamnostic.core (module)
bamnostic.csi (module)
bamnostic.utils (module)
BamReader (class in bamnostic.bam)
BamWriter (class in bamnostic.bam)
BgzfReader (class in bamnostic.bgzf)
BgzfWriter (class in bamnostic.bgzf)
C
check_cigar_arg() (in module bamnostic.utils)
check_index() (bamnostic.bam.BamReader 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.bam.BamReader method)
count_coverage() (bamnostic.bam.BamReader method)
Csi (class in bamnostic.csi)
cull() (bamnostic.utils.LruDict method)
current_ref (bamnostic.bai.Bai attribute)
(bamnostic.csi.Csi attribute)
E
end_offset (bamnostic.bai.RefIdx attribute)
F
fetch() (bamnostic.bam.BamReader 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() (bamnostic.utils.LruDict method)
get_bins() (bamnostic.bai.Bai method)
(bamnostic.csi.Csi method)
get_block() (in module bamnostic.bgzf)
get_chunks() (bamnostic.bai.Bai method)
(bamnostic.csi.Csi method)
get_cigar_stats() (bamnostic.core.AlignedSegment method)
get_index_stats() (bamnostic.bam.BamReader method)
get_ints() (bamnostic.bai.Bai method)
get_ref (bamnostic.bai.Bai attribute)
(bamnostic.csi.Csi attribute)
get_reference_name() (bamnostic.bam.BamReader method)
get_tag() (bamnostic.core.AlignedSegment method)
get_tags() (bamnostic.core.AlignedSegment method)
get_tid() (bamnostic.bam.BamReader method)
H
has_index() (bamnostic.bam.BamReader method)
head() (bamnostic.bam.BamReader method)
header (bamnostic.bam.BamReader 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.bam.BamReader method)
isatty() (bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
L
lengths (bamnostic.bam.BamReader attribute)
,
[1]
LruDict (class in bamnostic.utils)
M
magic (bamnostic.bai.Bai attribute)
(bamnostic.csi.Csi attribute)
make_virtual_offset() (in module bamnostic.utils)
mapped (bamnostic.bam.BamReader attribute)
mapping_quality (bamnostic.core.AlignedSegment attribute)
mate() (bamnostic.bam.BamReader 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)
(bamnostic.csi.Csi attribute)
n_op (bamnostic.core.Cigar attribute)
n_refs (bamnostic.bai.Bai attribute)
(bamnostic.bam.BAMheader attribute)
(bamnostic.csi.Csi attribute)
next() (bamnostic.bam.BamReader method)
next_reference_id (bamnostic.core.AlignedSegment attribute)
next_reference_name (bamnostic.core.AlignedSegment attribute)
next_reference_start (bamnostic.core.AlignedSegment attribute)
nocoordinate (bamnostic.bam.BamReader attribute)
,
[1]
nreferences (bamnostic.bam.BamReader 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)
(bamnostic.csi.Csi 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.bam.BamReader attribute)
ref_gen() (bamnostic.core.AlignedSegment method)
(in module bamnostic.utils)
ref_indices (bamnostic.bai.Bai attribute)
(bamnostic.csi.Csi attribute)
reference_end (bamnostic.core.AlignedSegment attribute)
reference_length (bamnostic.core.AlignedSegment attribute)
reference_start (bamnostic.core.AlignedSegment attribute)
references (bamnostic.bam.BamReader attribute)
,
[1]
RefIdx (class in bamnostic.bai)
refs (bamnostic.bam.BAMheader attribute)
reg2bin() (in module bamnostic.bai)
reg2bin_csi() (in module bamnostic.csi)
reg2bins() (in module bamnostic.bai)
reg2bins_csi() (in module bamnostic.csi)
Roi (class in bamnostic.utils)
S
SAMheader (bamnostic.bam.BAMheader attribute)
seek() (bamnostic.bai.Bai method)
(bamnostic.bgzf.BgzfReader method)
seekable() (bamnostic.bam.BamReader method)
(bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
split_virtual_offset() (in module bamnostic.utils)
start_offset (bamnostic.bai.RefIdx attribute)
T
tell() (bamnostic.bai.Bai method)
(bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
text (bamnostic.bam.BamReader attribute)
to_bam() (bamnostic.core.AlignedSegment method)
to_header() (bamnostic.bam.BAMheader method)
U
unmapped (bamnostic.bai.Bai attribute)
(bamnostic.bam.BamReader attribute)
,
[1]
(bamnostic.csi.Csi attribute)
unpack() (in module bamnostic.utils)
unpack_bgzf_metaheader() (in module bamnostic.bgzf)
unpack_bid_loffset_nchunk() (in module bamnostic.csi)
unpack_bid_nchunk() (in module bamnostic.bai)
unpack_chunk() (in module bamnostic.bai)
(in module bamnostic.csi)
unpack_gzip_header() (in module bamnostic.bgzf)
unpack_gzip_integrity() (in module bamnostic.bgzf)
unpack_int32() (in module bamnostic.bai)
(in module bamnostic.bam)
(in module bamnostic.bgzf)
(in module bamnostic.core)
(in module bamnostic.csi)
(in module bamnostic.utils)
unpack_int32L() (in module bamnostic.bai)
(in module bamnostic.bam)
(in module bamnostic.bgzf)
(in module bamnostic.core)
(in module bamnostic.csi)
(in module bamnostic.utils)
unpack_intervals() (in module bamnostic.bai)
unpack_subfields() (in module bamnostic.bgzf)
unpack_unmapped() (in module bamnostic.bai)
(in module bamnostic.csi)
update() (bamnostic.utils.LruDict method)
W
write() (bamnostic.bam.BamWriter method)
(bamnostic.bgzf.BgzfWriter method)
write_header() (bamnostic.bam.BamWriter method)
Y
yes_no() (in module bamnostic.utils)
Read the Docs
v: latest
Versions
latest
stable
Downloads
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.