samwell
stable
Samwell: a python package for using genomic files… well.
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samwell
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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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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() (samwell.overlap_detector.OverlapDetector method)
add_all() (samwell.overlap_detector.OverlapDetector method)
add_fasta_header_to_xr (samwell.sam.bwa_mem.InputOutputOptions attribute)
add_pair() (samwell.sam.sambuilder.SamBuilder method)
AlgorithmOptions (class in samwell.sam.bwa_mem)
align() (in module samwell.sam.bwa_mem)
all_alignments (samwell.sam.bwa_mem.InputOutputOptions attribute)
alts_as_primary (samwell.sam.bwa_mem.InputOutputOptions attribute)
append_fastq_comment (samwell.sam.bwa_mem.InputOutputOptions attribute)
B
band_width (samwell.sam.bwa_mem.AlgorithmOptions attribute)
bases (samwell.sam.bwa_mem.FastqRecord attribute)
bases_per_batch (samwell.sam.bwa_mem.InputOutputOptions attribute)
build() (samwell.sam.bwa_mem.FastqRecord class method)
C
can_peek() (samwell.itertools.PeekableIterator method)
character (samwell.sam.CigarOp attribute)
Cigar (class in samwell.sam)
CigarElement (class in samwell.sam)
CigarOp (class in samwell.sam)
CigarParsingException
clipping_penalty (samwell.sam.bwa_mem.ScoringOptions attribute)
ClippingInfo (class in samwell.sam.clipping)
coalesce() (samwell.sam.Cigar method)
code (samwell.sam.CigarOp attribute)
consumes_query (samwell.sam.CigarOp attribute)
consumes_target (samwell.sam.CigarOp attribute)
Coordinate (samwell.sam.SamOrder attribute)
D
D (samwell.sam.CigarOp attribute)
default_rg() (samwell.sam.sambuilder.SamBuilder static method)
default_sd() (samwell.sam.sambuilder.SamBuilder static method)
drop_ratio (samwell.sam.bwa_mem.AlgorithmOptions attribute)
dropwhile() (samwell.itertools.PeekableIterator method)
E
end (samwell.overlap_detector.Interval attribute)
EQ (samwell.sam.CigarOp attribute)
ext (samwell.sam.SamFileType attribute)
F
FastqRecord (class in samwell.sam.bwa_mem)
from_bed() (samwell.overlap_detector.OverlapDetector class method)
from_character() (samwell.sam.CigarOp static method)
from_cigarstring() (samwell.sam.Cigar class method)
from_cigartuples() (samwell.sam.Cigar class method)
from_code() (samwell.sam.CigarOp static method)
from_path() (samwell.sam.SamFileType class method)
G
gap_extend (samwell.sam.bwa_mem.ScoringOptions attribute)
gap_open (samwell.sam.bwa_mem.ScoringOptions attribute)
get_enclosed() (samwell.overlap_detector.OverlapDetector method)
get_enclosing_intervals() (samwell.overlap_detector.OverlapDetector method)
get_overlaps() (samwell.overlap_detector.OverlapDetector method)
get_qc_fail() (in module samwell.sam)
get_qc_fail_by_tool() (in module samwell.sam)
H
H (samwell.sam.CigarOp attribute)
has_long_homopolymer() (in module samwell.dnautils)
header_insert (samwell.sam.bwa_mem.InputOutputOptions attribute)
I
I (samwell.sam.CigarOp attribute)
InputOutputOptions (class in samwell.sam.bwa_mem)
insert_size_params (samwell.sam.bwa_mem.InputOutputOptions attribute)
interleaved_pairs (samwell.sam.bwa_mem.InputOutputOptions attribute)
internal_seeds_length_factor (samwell.sam.bwa_mem.AlgorithmOptions attribute)
Interval (class in samwell.overlap_detector)
is_indel (samwell.sam.CigarOp property)
isize() (in module samwell.sam)
L
length() (samwell.overlap_detector.Interval method)
length_on_query (samwell.sam.CigarElement property)
length_on_query() (samwell.sam.Cigar method)
length_on_target (samwell.sam.CigarElement property)
length_on_target() (samwell.sam.Cigar method)
M
M (samwell.sam.CigarOp attribute)
mask_long_homopolymers() (in module samwell.dnautils)
match_score (samwell.sam.bwa_mem.ScoringOptions attribute)
max_hits_within_max_score (samwell.sam.bwa_mem.InputOutputOptions attribute)
max_mate_rescue_rounds (samwell.sam.bwa_mem.AlgorithmOptions attribute)
max_seed_occurrence (samwell.sam.bwa_mem.AlgorithmOptions attribute)
max_third_seed_occurrence (samwell.sam.bwa_mem.AlgorithmOptions attribute)
maybe_peek() (samwell.itertools.PeekableIterator method)
MergingIterator (class in samwell.itertools)
min_alignment_score (samwell.sam.bwa_mem.InputOutputOptions attribute)
min_chain_weight (samwell.sam.bwa_mem.AlgorithmOptions attribute)
min_seed_len (samwell.sam.bwa_mem.AlgorithmOptions attribute)
mismatch_score (samwell.sam.bwa_mem.ScoringOptions attribute)
mode (samwell.sam.SamFileType attribute)
module
samwell.dnautils
samwell.itertools
samwell.overlap_detector
samwell.sam
samwell.sam.bwa_mem
samwell.sam.clipping
samwell.sam.sambuilder
N
N (samwell.sam.CigarOp attribute)
name (samwell.overlap_detector.Interval attribute)
(samwell.sam.bwa_mem.FastqRecord attribute)
needs_alignment (samwell.sam.bwa_mem.FastqRecord attribute)
negative (samwell.overlap_detector.Interval attribute)
NO_REF_INDEX (in module samwell.sam)
NO_REF_NAME (in module samwell.sam)
O
off_diagonal_dropoff (samwell.sam.bwa_mem.AlgorithmOptions attribute)
overlap() (samwell.overlap_detector.Interval method)
OverlapDetector (class in samwell.overlap_detector)
overlaps_any() (samwell.overlap_detector.OverlapDetector method)
P
P (samwell.sam.CigarOp attribute)
peek() (samwell.itertools.PeekableIterator method)
peekable() (in module samwell.itertools)
PeekableIterator (class in samwell.itertools)
Q
quals (samwell.sam.bwa_mem.FastqRecord attribute)
query_bases_clipped (samwell.sam.clipping.ClippingInfo attribute)
(samwell.sam.clipping.ClippingInfo property)
QueryName (samwell.sam.SamOrder attribute)
R
read_group (samwell.sam.bwa_mem.InputOutputOptions attribute)
read_number (samwell.sam.bwa_mem.FastqRecord attribute)
read_type (samwell.sam.bwa_mem.ScoringOptions attribute)
reader() (in module samwell.sam)
ReadType (class in samwell.sam.bwa_mem)
ref_bases_clipped (samwell.sam.clipping.ClippingInfo attribute)
(samwell.sam.clipping.ClippingInfo property)
refname (samwell.overlap_detector.Interval attribute)
reverse_complement() (in module samwell.dnautils)
reversed() (samwell.sam.Cigar method)
rg() (samwell.sam.sambuilder.SamBuilder method)
rg_id() (samwell.sam.sambuilder.SamBuilder method)
S
S (samwell.sam.CigarOp attribute)
SamBuilder (class in samwell.sam.sambuilder)
SamFileType (class in samwell.sam)
SamOrder (class in samwell.sam)
SamPath (in module samwell.sam)
samwell.dnautils
module
samwell.itertools
module
samwell.overlap_detector
module
samwell.sam
module
samwell.sam.bwa_mem
module
samwell.sam.clipping
module
samwell.sam.sambuilder
module
ScoringOptions (class in samwell.sam.bwa_mem)
set_pair_info() (in module samwell.sam)
set_qc_fail() (in module samwell.sam)
skip_mate_rescue (samwell.sam.bwa_mem.AlgorithmOptions attribute)
skip_pairing (samwell.sam.bwa_mem.AlgorithmOptions attribute)
softclip_end_of_alignment_by_query() (in module samwell.sam.clipping)
softclip_end_of_alignment_by_ref() (in module samwell.sam.clipping)
softclip_start_of_alignment_by_query() (in module samwell.sam.clipping)
softclip_start_of_alignment_by_ref() (in module samwell.sam.clipping)
softclip_supplementary (samwell.sam.bwa_mem.InputOutputOptions attribute)
source (samwell.sam.bwa_mem.FastqRecord attribute)
split_hits_are_secondary (samwell.sam.bwa_mem.InputOutputOptions attribute)
start (samwell.overlap_detector.Interval attribute)
str_with_read_number() (samwell.sam.bwa_mem.FastqRecord method)
T
takewhile() (samwell.itertools.PeekableIterator method)
threads (samwell.sam.bwa_mem.AlgorithmOptions attribute)
to_path() (samwell.sam.sambuilder.SamBuilder method)
to_sorted_list() (samwell.sam.sambuilder.SamBuilder method)
to_unsorted_list() (samwell.sam.sambuilder.SamBuilder method)
U
unpaired_penalty (samwell.sam.bwa_mem.ScoringOptions attribute)
Unsorted (samwell.sam.SamOrder attribute)
V
verbosity (samwell.sam.bwa_mem.InputOutputOptions attribute)
W
writer() (in module samwell.sam)
X
X (samwell.sam.CigarOp attribute)
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