Index

A | B | C | D | E | F | H | I | L | M | N | P | Q | R | S | T | U | W | X

A

automagic_csfasta() (in module ngs_plumbing.xsq)
automagic_fastq() (in module ngs_plumbing.xsq)

B

bit_encoding (ngs_plumbing.dna.PackedDNABytes attribute)

C

close() (ngs_plumbing.colorspace.FastaqualWriter method)
(ngs_plumbing.colorspace.FastqWriter method)
colour (ngs_plumbing.xsq.ColourQual attribute)
ColourQual (class in ngs_plumbing.xsq)
complemented() (ngs_plumbing.dna.PackedDNABytes method)

D

DataError
ddecode_seq() (in module ngs_plumbing.colorspace)
ddecode_seq_G() (in module ngs_plumbing.colorspace)
ddecode_seq_T() (in module ngs_plumbing.colorspace)
dencode_seq() (in module ngs_plumbing.colorspace)

E

exec_code() (in module ngs_plumbing.colorspace)

F

FastaqualWriter (class in ngs_plumbing.colorspace)
fastqual() (in module ngs_plumbing.xsq)
FastqWriter (class in ngs_plumbing.colorspace)
fileversion (ngs_plumbing.xsq.XSQRunMetadata attribute)
flush() (ngs_plumbing.colorspace.FastaqualWriter method)
(ngs_plumbing.colorspace.FastqWriter method)
FragmentError
fragments() (ngs_plumbing.xsq.XSQLibrary method)
fromxsqfile_toordict() (ngs_plumbing.xsq.XSQInfo class method)

H

hdfversion (ngs_plumbing.xsq.XSQRunMetadata attribute)

I

InvalidXSQError
isbasepresent (ngs_plumbing.xsq.XSQTagDetails attribute)
iter_colourqual() (ngs_plumbing.xsq.XSQLibrary method)
iter_csfasta_reads() (in module ngs_plumbing.xsq)
iter_dnaqual() (ngs_plumbing.xsq.XSQLibrary method)
iter_fastq_reads() (in module ngs_plumbing.xsq)
iter_lib() (ngs_plumbing.xsq.XSQFile method)
iter_reads() (in module ngs_plumbing.xsq)
(ngs_plumbing.xsq.XSQLibrary method)
iter_valuearrays() (in module ngs_plumbing.xsq)

L

lanenumber (ngs_plumbing.xsq.XSQRunMetadata attribute)
library() (ngs_plumbing.xsq.XSQFile method)
library_names (ngs_plumbing.xsq.XSQFile attribute)
librarytype (ngs_plumbing.xsq.XSQRunMetadata attribute)
list_xsq() (in module ngs_plumbing.xsq)

M

make_csfasta() (in module ngs_plumbing.xsq)
make_csfastq() (in module ngs_plumbing.xsq)
make_fastq() (in module ngs_plumbing.xsq)
make_htmlreport() (in module ngs_plumbing.xsq)

N

name (ngs_plumbing.xsq.XSQLibrary attribute)
ngs_plumbing (module)
ngs_plumbing.colorspace (module)
ngs_plumbing.fastq (module)
ngs_plumbing.parsing (module)
ngs_plumbing.xsq (module)
numbasecalls (ngs_plumbing.xsq.XSQTagDetails attribute)

P

PackedDNABytes (class in ngs_plumbing.dna)

Q

qual (ngs_plumbing.xsq.ColourQual attribute)

R

readcount() (ngs_plumbing.xsq.XSQLibrary method)
reversecomplemented() (ngs_plumbing.dna.PackedDNABytes method)
reversed() (ngs_plumbing.dna.PackedDNABytes method)
run_metadata (ngs_plumbing.xsq.XSQFile attribute)
runname (ngs_plumbing.xsq.XSQRunMetadata attribute)

S

seqid_template() (in module ngs_plumbing.xsq)
seqid_template_csfasta() (in module ngs_plumbing.xsq)
sequencingsampledescription (ngs_plumbing.xsq.XSQRunMetadata attribute)
sequencingsamplename (ngs_plumbing.xsq.XSQRunMetadata attribute)

T

tagdetails (ngs_plumbing.xsq.XSQRunMetadata attribute)
tags (ngs_plumbing.xsq.XSQTagDetailsList attribute)
tile_valuearray() (in module ngs_plumbing.xsq)

U

unpack_slice() (ngs_plumbing.dna.PackedDNABytes method)

W

write() (ngs_plumbing.colorspace.FastaqualWriter method)
(ngs_plumbing.colorspace.FastqWriter method)

X

XSQFile (class in ngs_plumbing.xsq)
XSQInfo (class in ngs_plumbing.xsq)
XSQLibrary (class in ngs_plumbing.xsq)
XSQRunMetadata (class in ngs_plumbing.xsq)
XSQTagDetails (class in ngs_plumbing.xsq)
XSQTagDetailsList (class in ngs_plumbing.xsq)