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c
d
e
f
g
h
i
l
m
n
o
p
q
r
s
t
u
v
w
~
Here is a list of all class members with links to the classes they belong to:
- c -
clear() :
DuplicateCounter
Clusterer() :
Clusterer< T >
counts_t :
DuplicateCounter
cover() :
ReferenceGenome
coverage :
GenomeLocusMapping
- d -
d_aCount :
ReferenceGenome
d_cCount :
ReferenceGenome
d_clusters :
Clusterer< T >
d_correctMappings :
ReferenceGenome
d_fastqs :
GenomeLocusMapping
d_gcMappings :
ReferenceGenome
d_gCount :
ReferenceGenome
d_header :
FastQRead
d_insertCounts :
ReferenceGenome
d_kmerMappings :
ReferenceGenome
d_locimap :
ReferenceGenome
d_mapping :
ReferenceGenome
d_members :
Clusterer< T >::cluster
d_name :
ReferenceGenome
d_nucleotides :
FastQRead
d_quality :
FastQRead
d_taMappings :
ReferenceGenome
d_tCount :
ReferenceGenome
d_unmRegions :
ReferenceGenome
d_wrongMappings :
ReferenceGenome
DuplicateCounter() :
DuplicateCounter
- e -
exceedsQuality() :
FastQRead
- f -
FastQRead() :
FastQRead
FASTQReader() :
FASTQReader
feed() :
Clusterer< T >
feedString() :
DuplicateCounter
- g -
GeneAnnotationReader() :
GeneAnnotationReader
GenomeLocusMapping() :
GenomeLocusMapping
getAllReadPosBoth() :
ReferenceGenome
getBegin() :
Clusterer< T >::cluster
getCounts() :
DuplicateCounter
getEnd() :
Clusterer< T >::cluster
getGCHisto() :
ReferenceGenome
getMatchingFastQs() :
ReferenceGenome
getMatchingHashes() :
ReferenceGenome
getMiddle() :
Clusterer< T >::cluster
getRead() :
StereoFASTQReader
,
FASTQReader
getReadPair() :
StereoFASTQReader
getReadPosBoth() :
ReferenceGenome
getReadPositions() :
ReferenceGenome
getSangerQualityString() :
FastQRead
- h -
headOrTail :
ReferenceGenome::LociStats::Difference
hits :
Entry16S
- i -
id :
Entry16S
incorrect :
qtally
indel :
FASTQMapping
index() :
ReferenceGenome
- l -
left :
Unmatched
locimap_t :
ReferenceGenome
lookup() :
GeneAnnotationReader
- m -
mapFastQ() :
ReferenceGenome
mean :
VarMeanEstimator
- n -
name :
GeneAnnotation
nucleotide :
ReferenceGenome::LociStats::Difference
- o -
operator()() :
VarMeanEstimator
operator<() :
ReferenceGenome::LociStats::Difference
- p -
pos :
FASTQMapping
,
Unmatched
,
ReferenceGenome::MatchDescriptor
position :
FastQRead
printCoverage() :
ReferenceGenome
printTop() :
Search16S
- q -
qtally() :
qtally
quality :
ReferenceGenome::LociStats::Difference
- r -
ReferenceGenome() :
ReferenceGenome
reverse :
FASTQMapping
,
FastQRead
,
ReferenceGenome::MatchDescriptor
reversed :
FastQRead
right :
Unmatched
- s -
samples :
ReferenceGenome::LociStats
SAMWriter() :
SAMWriter
score() :
Search16S
,
ReferenceGenome::MatchDescriptor
Search16S() :
Search16S
seek() :
FASTQReader
,
StereoFASTQReader
size() :
GeneAnnotationReader
,
ReferenceGenome
snippet() :
ReferenceGenome
startPos :
GeneAnnotation
StereoFASTQReader() :
StereoFASTQReader
stopPos :
GeneAnnotation
strand :
GeneAnnotation
- t -
tag :
GeneAnnotation
topScores() :
Search16S
type :
GeneAnnotation
- u -
unmatched :
Unmatched
- v -
variance :
VarMeanEstimator
VarMeanEstimator() :
VarMeanEstimator
- w -
write() :
SAMWriter
- ~ -
~SAMWriter() :
SAMWriter
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