bamnostic
1.1.8
Contents:
Installation
Getting Started
Module documentation
Citation and Support
bamnostic
»
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.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 property)
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 method)
(bamnostic.csi.Csi method)
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 property)
is_paired (bamnostic.core.AlignedSegment property)
is_proper_pair (bamnostic.core.AlignedSegment property)
is_qcfail (bamnostic.core.AlignedSegment property)
is_read1 (bamnostic.core.AlignedSegment property)
is_read2 (bamnostic.core.AlignedSegment property)
is_reverse (bamnostic.core.AlignedSegment property)
is_secondary (bamnostic.core.AlignedSegment property)
is_supplementary (bamnostic.core.AlignedSegment property)
is_unmapped (bamnostic.core.AlignedSegment property)
is_valid_tid() (bamnostic.bam.BamReader method)
isatty() (bamnostic.bgzf.BgzfReader method)
(bamnostic.bgzf.BgzfWriter method)
L
lengths (bamnostic.bam.BamReader attribute)
(bamnostic.bam.BamReader property)
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 property)
mapping_quality (bamnostic.core.AlignedSegment property)
mate() (bamnostic.bam.BamReader method)
mate_is_reverse (bamnostic.core.AlignedSegment property)
mate_is_unmapped (bamnostic.core.AlignedSegment property)
md_changes() (in module bamnostic.utils)
module
bamnostic
bamnostic.bai
bamnostic.bam
bamnostic.bgzf
bamnostic.core
bamnostic.csi
bamnostic.utils
N
n_bins (bamnostic.bai.RefIdx property)
n_no_coord (bamnostic.bai.Bai attribute)
(bamnostic.csi.Csi attribute)
n_op (bamnostic.core.Cigar property)
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 property)
next_reference_name (bamnostic.core.AlignedSegment property)
next_reference_start (bamnostic.core.AlignedSegment property)
nocoordinate (bamnostic.bam.BamReader attribute)
(bamnostic.bam.BamReader property)
nreferences (bamnostic.bam.BamReader attribute)
(bamnostic.bam.BamReader property)
O
offset_qual() (in module bamnostic.core)
op_code (bamnostic.core.Cigar property)
op_id (bamnostic.core.Cigar property)
op_name (bamnostic.core.Cigar property)
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 property)
query_alignment_length (bamnostic.core.AlignedSegment property)
query_alignment_sequence (bamnostic.core.AlignedSegment property)
query_alignment_start (bamnostic.core.AlignedSegment property)
query_length (bamnostic.core.AlignedSegment property)
query_name (bamnostic.core.AlignedSegment property)
query_sequence (bamnostic.core.AlignedSegment property)
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 property)
reference_length (bamnostic.core.AlignedSegment property)
reference_start (bamnostic.core.AlignedSegment property)
references (bamnostic.bam.BamReader attribute)
(bamnostic.bam.BamReader property)
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 property)
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)
(bamnostic.bam.BamReader property)
(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)