Index

_ | A | B | C | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W

_

__contains__ (pysam.FastaFile attribute)
(pysam.VariantHeaderRecord attribute)
__copy__() (pysam.AlignedSegment method)
__deepcopy__() (pysam.AlignedSegment method)
__enter__() (pysam.AlignmentFile method)
(pysam.FastaFile method)
(pysam.FastxFile method)
__eq__ (pysam.AlignedSegment attribute)
__exit__() (pysam.AlignmentFile method)
(pysam.FastaFile method)
(pysam.FastxFile method)
__ge__ (pysam.AlignedSegment attribute)
__getitem__ (pysam.FastaFile attribute)
(pysam.VariantHeaderRecord attribute)
__gt__ (pysam.AlignedSegment attribute)
__hash__ (pysam.AlignedSegment attribute)
__iter__ (pysam.AlignmentFile attribute)
(pysam.FastxFile attribute)
(pysam.VariantFile attribute)
(pysam.VariantHeaderRecord attribute)
__le__ (pysam.AlignedSegment attribute)
__len__ (pysam.FastaFile attribute)
(pysam.VariantHeaderRecord attribute)
__lt__ (pysam.AlignedSegment attribute)
__ne__ (pysam.AlignedSegment attribute)
__next__() (pysam.FastxFile method)
__nonzero__ (pysam.VariantHeader attribute)
(pysam.VariantHeaderRecord attribute)
__str__ (pysam.AlignedSegment attribute)
(pysam.FastqProxy attribute)
(pysam.PileupColumn attribute)
(pysam.PileupRead attribute)
(pysam.VariantHeader attribute)
(pysam.VariantHeaderRecord attribute)
(pysam.VariantRecord attribute)

A

add_line() (pysam.VariantHeader method)
add_meta() (pysam.VariantHeader method)
add_record() (pysam.VariantHeader method)
add_sample() (pysam.VariantHeader method)
aend (pysam.AlignedSegment attribute)
alen (pysam.AlignedSegment attribute)
aligned_pairs (pysam.AlignedSegment attribute)
AlignedSegment (class in pysam)
alignment (pysam.PileupRead attribute)
AlignmentFile (class in pysam)
alleles (pysam.VariantRecord attribute)
alts (pysam.VariantHeader attribute)
(pysam.VariantRecord attribute)
asBed (class in pysam)
asGTF (class in pysam)
asTuple (class in pysam)
asVCF (class in pysam)
attrs (pysam.VariantHeaderRecord attribute)

B

BAM
BCF
bgzip
bin (pysam.AlignedSegment attribute)
blocks (pysam.AlignedSegment attribute)
build() (pysam.IndexedReads method)

C

check_index() (pysam.AlignmentFile method)
chrom (pysam.VariantRecord attribute)
cigar
(pysam.AlignedSegment attribute)
cigarstring (pysam.AlignedSegment attribute)
cigartuples (pysam.AlignedSegment attribute)
close() (pysam.AlignmentFile method)
(pysam.FastaFile method)
(pysam.FastxFile method)
(pysam.TabixFile method)
(pysam.VariantFile method)
closed (pysam.FastaFile attribute)
(pysam.FastxFile attribute)
column
compare() (pysam.AlignedSegment method)
contig (pysam.VariantRecord attribute)
contigs (pysam.TabixFile attribute)
(pysam.VariantHeader attribute)
copy() (pysam.VariantFile method)
(pysam.VariantHeader method)
(pysam.VariantRecord method)
count() (pysam.AlignmentFile method)
count_coverage() (pysam.AlignmentFile method)
csamtools

F

faidx
FastaFile (class in pysam)
FastqProxy (class in pysam)
FastxFile (class in pysam)
fetch() (pysam.AlignmentFile method)
(pysam.FastaFile method)
(pysam.TabixFile method)
(pysam.VariantFile method)
fetching
filename (pysam.FastaFile attribute)
(pysam.FastxFile attribute)
filter (pysam.VariantRecord attribute)
filters (pysam.VariantHeader attribute)
find() (pysam.IndexedReads method)
find_introns() (pysam.AlignmentFile method)
flag (pysam.AlignedSegment attribute)
format (pysam.VariantRecord attribute)
formats (pysam.VariantHeader attribute)

G

get() (pysam.VariantHeaderRecord method)
get_aligned_pairs() (pysam.AlignedSegment method)
get_blocks() (pysam.AlignedSegment method)
get_cigar_stats() (pysam.AlignedSegment method)
get_overlap() (pysam.AlignedSegment method)
get_quality_array() (pysam.FastqProxy method)
get_reference_length() (pysam.FastaFile method)
get_reference_name() (pysam.AlignmentFile method)
get_reference_positions() (pysam.AlignedSegment method)
get_reference_sequence() (pysam.AlignedSegment method)
get_tag() (pysam.AlignedSegment method)
get_tags() (pysam.AlignedSegment method)
get_tid() (pysam.AlignmentFile method)
getrname() (pysam.AlignmentFile method)
gettid() (pysam.AlignmentFile method)

H

hard clipped
hard clipping
has_index() (pysam.AlignmentFile method)
has_tag() (pysam.AlignedSegment method)
head() (pysam.AlignmentFile method)
header (pysam.AlignmentFile attribute)
(pysam.TabixFile attribute)

I

id (pysam.VariantRecord attribute)
indel (pysam.PileupRead attribute)
IndexedReads (class in pysam)
infer_query_length() (pysam.AlignedSegment method)
inferred_length (pysam.AlignedSegment attribute)
info (pysam.VariantHeader attribute)
(pysam.VariantRecord attribute)
is_del (pysam.PileupRead attribute)
is_duplicate (pysam.AlignedSegment attribute)
is_head (pysam.PileupRead attribute)
is_open() (pysam.FastaFile method)
(pysam.FastxFile method)
is_paired (pysam.AlignedSegment attribute)
is_proper_pair (pysam.AlignedSegment attribute)
is_qcfail (pysam.AlignedSegment attribute)
is_read1 (pysam.AlignedSegment attribute)
is_read2 (pysam.AlignedSegment attribute)
is_refskip (pysam.PileupRead attribute)
is_reverse (pysam.AlignedSegment attribute)
is_secondary (pysam.AlignedSegment attribute)
is_supplementary (pysam.AlignedSegment attribute)
is_tail (pysam.PileupRead attribute)
is_unmapped (pysam.AlignedSegment attribute)
isize (pysam.AlignedSegment attribute)
items() (pysam.VariantHeaderRecord method)
iteritems() (pysam.VariantHeaderRecord method)
iterkeys() (pysam.VariantHeaderRecord method)
itervalues() (pysam.VariantHeaderRecord method)

K

key (pysam.VariantHeaderRecord attribute)
keys() (pysam.VariantHeaderRecord method)

L

lengths (pysam.AlignmentFile attribute)
(pysam.FastaFile attribute)
level (pysam.PileupRead attribute)

M

mapped (pysam.AlignmentFile attribute)
mapping_quality (pysam.AlignedSegment attribute)
mapq (pysam.AlignedSegment attribute)
mate() (pysam.AlignmentFile method)
mate_is_reverse (pysam.AlignedSegment attribute)
mate_is_unmapped (pysam.AlignedSegment attribute)
merge() (pysam.VariantHeader method)
mpos (pysam.AlignedSegment attribute)
mrnm (pysam.AlignedSegment attribute)

N

name (pysam.FastqProxy attribute)
new_record() (pysam.VariantFile method)
(pysam.VariantHeader method)
next (pysam.AlignmentFile attribute)
(pysam.FastxFile attribute)
(pysam.VariantFile attribute)
next_reference_id (pysam.AlignedSegment attribute)
next_reference_name (pysam.AlignedSegment attribute)
next_reference_start (pysam.AlignedSegment attribute)
nocoordinate (pysam.AlignmentFile attribute)
nreferences (pysam.AlignmentFile attribute)
(pysam.FastaFile attribute)
nsegments (pysam.PileupColumn attribute)

O

open() (pysam.VariantFile method)
opt() (pysam.AlignedSegment method)
overlap() (pysam.AlignedSegment method)

P

parse_region() (pysam.AlignmentFile method)
pileup
pileup() (pysam.AlignmentFile method)
PileupColumn (class in pysam)
PileupRead (class in pysam)
pileups (pysam.PileupColumn attribute)
pnext (pysam.AlignedSegment attribute)
pos (pysam.AlignedSegment attribute)
(pysam.VariantRecord attribute)
positions (pysam.AlignedSegment attribute)

Q

qend (pysam.AlignedSegment attribute)
qlen (pysam.AlignedSegment attribute)
qname (pysam.AlignedSegment attribute)
qqual (pysam.AlignedSegment attribute)
qstart (pysam.AlignedSegment attribute)
qual (pysam.AlignedSegment attribute)
(pysam.VariantRecord attribute)
quality (pysam.FastqProxy attribute)
query (pysam.AlignedSegment attribute)
query_alignment_end (pysam.AlignedSegment attribute)
query_alignment_length (pysam.AlignedSegment attribute)
query_alignment_qualities (pysam.AlignedSegment attribute)
query_alignment_sequence (pysam.AlignedSegment attribute)
query_alignment_start (pysam.AlignedSegment attribute)
query_length (pysam.AlignedSegment attribute)
query_name (pysam.AlignedSegment attribute)
query_position (pysam.PileupRead attribute)
query_position_or_next (pysam.PileupRead attribute)
query_qualities (pysam.AlignedSegment attribute)
query_sequence (pysam.AlignedSegment attribute)

R

records (pysam.VariantHeader attribute)
ref (pysam.VariantRecord attribute)
Reference
reference_end (pysam.AlignedSegment attribute)
reference_id (pysam.AlignedSegment attribute)
(pysam.PileupColumn attribute)
reference_length (pysam.AlignedSegment attribute)
reference_name (pysam.AlignedSegment attribute)
(pysam.PileupColumn attribute)
reference_pos (pysam.PileupColumn attribute)
reference_start (pysam.AlignedSegment attribute)
references (pysam.AlignmentFile attribute)
(pysam.FastaFile attribute)
region
remove() (pysam.VariantHeaderRecord method)
reset() (pysam.VariantFile method)
rid (pysam.VariantRecord attribute)
rlen (pysam.AlignedSegment attribute)
(pysam.VariantRecord attribute)
rname (pysam.AlignedSegment attribute)
rnext (pysam.AlignedSegment attribute)

S

SAM
sam file
samples (pysam.VariantHeader attribute)
(pysam.VariantRecord attribute)
samtools
seq (pysam.AlignedSegment attribute)
sequence (pysam.FastqProxy attribute)
set_tag() (pysam.AlignedSegment method)
set_tags() (pysam.AlignedSegment method)
setTag() (pysam.AlignedSegment method)
soft clipped
soft clipping
start (pysam.VariantRecord attribute)
stop (pysam.VariantRecord attribute)
subset_samples() (pysam.VariantFile method)

T

tabix
tabix file
tabix row
tabix_compress() (in module pysam)
tabix_index() (in module pysam)
tabix_iterator() (in module pysam)
TabixFile (class in pysam)
tags (pysam.AlignedSegment attribute)
TAM
target
template_length (pysam.AlignedSegment attribute)
text (pysam.AlignmentFile attribute)
tid
(pysam.AlignedSegment attribute)
tlen (pysam.AlignedSegment attribute)
tostring() (pysam.AlignedSegment method)
translate() (pysam.VariantRecord method)
type (pysam.VariantHeaderRecord attribute)

U

unmapped (pysam.AlignmentFile attribute)

V

value (pysam.VariantHeaderRecord attribute)
values() (pysam.VariantHeaderRecord method)
VariantFile (class in pysam)
VariantHeader (class in pysam)
VariantHeaderRecord (class in pysam)
VariantRecord (class in pysam)
VCF
version (pysam.VariantHeader attribute)

W

write() (pysam.AlignmentFile method)
(pysam.VariantFile method)