Alignment	SalmonQuantify.cpp	126
Alignment::Alignment	SalmonQuantify.cpp	/^        Alignment(TranscriptID transcriptIDIn, uin/
Alignment::kmerCount	SalmonQuantify.cpp	132
Alignment::logProb	SalmonQuantify.cpp	133
Alignment::transcriptID	SalmonQuantify.cpp	/^        inline TranscriptID transcriptID() { retur/
Alignment::transcriptID_	SalmonQuantify.cpp	136
AlignmentBatch	TestBAMParser.cpp	54
BamTools::BamAlignment	MultithreadedBAMParser.cpp	39
BamTools::BamReader	MultithreadedBAMParser.cpp	38
ClusterForest	TestBAMParser.cpp	163
ClusterForest::ClusterForest	TestBAMParser.cpp	/^    ClusterForest(size_t numTranscripts, std::vect/
ClusterForest::boost::disjoint_sets	TestBAMParser.cpp	255
ClusterForest::clusterMutex_	TestBAMParser.cpp	257
ClusterForest::clusters_	TestBAMParser.cpp	256
ClusterForest::disjointSets_	TestBAMParser.cpp	255
ClusterForest::getClusters	TestBAMParser.cpp	/^    std::vector<TranscriptCluster*> getClusters() /
ClusterForest::mergeClusters	TestBAMParser.cpp	/^    void mergeClusters(typename AlignmentBatch<Fra/
ClusterForest::parent_	TestBAMParser.cpp	254
ClusterForest::rank_	TestBAMParser.cpp	253
ClusterForest::updateCluster	TestBAMParser.cpp	/^    void updateCluster(size_t memberTranscript, si/
ContainingTranscript	BuildLUT.cpp	74
ContainingTranscript::kmerID	BuildLUT.cpp	75
ContainingTranscript::transcriptID	BuildLUT.cpp	76
DEFAULT_BOOTSTRAP	PerformBiasCorrection.cpp	62
DEFAULT_BOOTSTRAP	PerformBiasCorrection_old.cpp	57
DEFAULT_COMPUTE_IMPORTANCE	PerformBiasCorrection.cpp	63
DEFAULT_COMPUTE_IMPORTANCE	PerformBiasCorrection_old.cpp	58
DEFAULT_LEARN_RATE	PerformBiasCorrection.cpp	59
DEFAULT_LEARN_RATE	PerformBiasCorrection_old.cpp	54
DEFAULT_LOSS	PerformBiasCorrection.cpp	58
DEFAULT_LOSS	PerformBiasCorrection_old.cpp	53
DEFAULT_MAX_DEPTH	PerformBiasCorrection.cpp	55
DEFAULT_MAX_DEPTH	PerformBiasCorrection_old.cpp	50
DEFAULT_MAX_FEATURES_RATIO	PerformBiasCorrection.cpp	53
DEFAULT_MAX_FEATURES_RATIO	PerformBiasCorrection_old.cpp	48
DEFAULT_MIN_SAMPLE_LEAF	PerformBiasCorrection.cpp	54
DEFAULT_MIN_SAMPLE_LEAF	PerformBiasCorrection_old.cpp	49
DEFAULT_N_JOBS	PerformBiasCorrection.cpp	52
DEFAULT_N_JOBS	PerformBiasCorrection_old.cpp	47
DEFAULT_N_TREES	PerformBiasCorrection.cpp	51
DEFAULT_N_TREES	PerformBiasCorrection_old.cpp	46
DEFAULT_OOB	PerformBiasCorrection.cpp	60
DEFAULT_OOB	PerformBiasCorrection_old.cpp	55
DEFAULT_SPLIT_CRITERION	PerformBiasCorrection.cpp	57
DEFAULT_SPLIT_CRITERION	PerformBiasCorrection_old.cpp	52
DEFAULT_SUBSAMPLE	PerformBiasCorrection.cpp	56
DEFAULT_SUBSAMPLE	PerformBiasCorrection_old.cpp	51
DEFAULT_VERBOSE	PerformBiasCorrection.cpp	61
DEFAULT_VERBOSE	PerformBiasCorrection_old.cpp	56
ErrorModel::ErrorModel	ErrorModel.cpp	/^ErrorModel::ErrorModel(double alpha) :$/
ErrorModel::burnedIn	ErrorModel.cpp	/^bool ErrorModel::burnedIn() { return burnedIn_; }$/
ErrorModel::burnedIn	ErrorModel.cpp	/^void ErrorModel::burnedIn(bool burnedIn) { burnedI/
ErrorModel::logLikelihood	ErrorModel.cpp	/^double ErrorModel::logLikelihood(bam1_t* read, Tra/
ErrorModel::logLikelihood	ErrorModel.cpp	/^double ErrorModel::logLikelihood(const ReadPair& h/
ErrorModel::logLikelihood	ErrorModel.cpp	/^double ErrorModel::logLikelihood(const UnpairedRea/
ErrorModel::update	ErrorModel.cpp	/^void ErrorModel::update(const UnpairedRead& hit, T/
ErrorModel::update	ErrorModel.cpp	/^void ErrorModel::update(bam1_t* read, Transcript& /
ErrorModel::update	ErrorModel.cpp	/^void ErrorModel::update(const ReadPair& hit, Trans/
ExpressionRecord	SailfishUtils.cpp	544
ExpressionRecord::ExpressionRecord	SailfishUtils.cpp	/^        ExpressionRecord() : name(""), length(0), /
ExpressionRecord::length	SailfishUtils.cpp	548
ExpressionRecord::name	SailfishUtils.cpp	547
ExpressionRecord::quants	SailfishUtils.cpp	549
ExpressionResults	PerformBiasCorrection.cpp	104
ExpressionResults	PerformBiasCorrection_old.cpp	101
ExpressionResults::comments	PerformBiasCorrection.cpp	105
ExpressionResults::comments	PerformBiasCorrection_old.cpp	102
ExpressionResults::expressions	PerformBiasCorrection.cpp	106
ExpressionResults::expressions	PerformBiasCorrection_old.cpp	103
ExpressionResults::std::unordered_map	PerformBiasCorrection.cpp	106
ExpressionResults::std::unordered_map	PerformBiasCorrection_old.cpp	103
FASTAParser::populateTargets	FASTAParser.cpp	/^void FASTAParser::populateTargets(std::vector<Tran/
FragmentLengthDistribution::FragmentLengthDistribution	FragmentLengthDistribution.cpp	/^FragmentLengthDistribution::FragmentLengthDistribu/
FragmentLengthDistribution::addVal	FragmentLengthDistribution.cpp	/^void FragmentLengthDistribution::addVal(size_t len/
FragmentLengthDistribution::cmf	FragmentLengthDistribution.cpp	/^double FragmentLengthDistribution::cmf(size_t len)/
FragmentLengthDistribution::cmf	FragmentLengthDistribution.cpp	/^vector<double> FragmentLengthDistribution::cmf() c/
FragmentLengthDistribution::maxVal	FragmentLengthDistribution.cpp	/^size_t FragmentLengthDistribution::maxVal() const /
FragmentLengthDistribution::mean	FragmentLengthDistribution.cpp	/^double FragmentLengthDistribution::mean() const {$/
FragmentLengthDistribution::minVal	FragmentLengthDistribution.cpp	/^size_t FragmentLengthDistribution::minVal() const /
FragmentLengthDistribution::pmf	FragmentLengthDistribution.cpp	/^double FragmentLengthDistribution::pmf(size_t len)/
FragmentLengthDistribution::totMass	FragmentLengthDistribution.cpp	/^double FragmentLengthDistribution::totMass() const/
FragmentList::FragmentList	FragmentList.cpp	/^FragmentList::FragmentList(){$/
FragmentList::addFragMatch	FragmentList.cpp	/^    void FragmentList::addFragMatch(uint32_t refSt/
FragmentList::addFragMatch	FragmentList.cpp	/^    void FragmentList::addFragMatch(uint32_t refSt/
FragmentList::addFragMatchRC	FragmentList.cpp	/^    void FragmentList::addFragMatchRC(uint32_t ref/
FragmentList::addFragMatchRC	FragmentList.cpp	/^    void FragmentList::addFragMatchRC(uint32_t ref/
FragmentList::computeBestChain	FragmentList.cpp	/^    void FragmentList::computeBestChain() {$/
FragmentList::computeBestChain_	FragmentList.cpp	/^void FragmentList::computeBestChain_(Container* fr/
FragmentList::freeFragList	FragmentList.cpp	/^void FragmentList::freeFragList(Container* frags) /
FragmentList::~FragmentList	FragmentList.cpp	/^FragmentList::~FragmentList() {$/
HeptamerIndex::HeptamerIndex	HeptamerIndex.cpp	/^HeptamerIndex::HeptamerIndex() :$/
HeptamerIndex::incHeptamer	HeptamerIndex.cpp	/^HeptamerIndex::incHeptamer(uint64_t heptamer) {$/
HeptamerIndex::index	HeptamerIndex.cpp	/^std::size_t HeptamerIndex::index(uint64_t heptamer/
IndexPair	PartitionRefiner.cpp	84
IndexPair::newIndex	PartitionRefiner.cpp	84
IndexPair::oldIndex	PartitionRefiner.cpp	84
K	cokus.cpp	59
KSEQ_INIT	FASTAParser.cpp	/^KSEQ_INIT(int, read)$/
Kmer	ComputeBiasFeatures.cpp	46
Kmer	PerformBiasCorrection.cpp	66
Kmer	PerformBiasCorrection_old.cpp	61
KmerID	BuildLUT.cpp	69
KmerIDMap	AnalyzeKmerTradeoff.cpp	59
KmerIDMap	SalmonQuantify.cpp	113
KmerVote	SalmonQuantify.cpp	289
KmerVote::KmerVote	SalmonQuantify.cpp	/^        KmerVote(uint32_t vp, uint32_t rp, uint32_/
KmerVote::readPos	SalmonQuantify.cpp	293
KmerVote::voteLen	SalmonQuantify.cpp	294
KmerVote::votePos	SalmonQuantify.cpp	292
LIN	FragmentList.cpp	21
LUTTools	LookUpTableUtils.cpp	47
LUTTools::dumpKmerEquivClasses	LookUpTableUtils.cpp	/^void dumpKmerEquivClasses($/
Length	BuildLUT.cpp	71
LibraryFormat::LibraryFormat	LibraryFormat.cpp	/^LibraryFormat::LibraryFormat(ReadType type_in, Rea/
LibraryFormat::check	LibraryFormat.cpp	/^bool LibraryFormat::check() {$/
M	cokus.cpp	58
MAnalyzeKmerTradeoff.cpp	AnalyzeKmerTradeoff.cpp	/^int main(int argc, char* argv[]) {$/
MBiasCorrectionDriver.cpp	BiasCorrectionDriver.cpp	/^int main(int argc, char* argv[]) {$/
MBuildTranscriptMap.cpp	BuildTranscriptMap.cpp	/^int main(int argc, char* argv[] ) {$/
MPerformBiasCorrection_old.cpp	PerformBiasCorrection_old.cpp	/^int main(int argc, char* argv[]) {$/
MSailfish.cpp	Sailfish.cpp	/^int main( int argc, char* argv[] ) {$/
MSalmon.cpp	Salmon.cpp	/^int main( int argc, char* argv[] ) {$/
MTestBAMParser.cpp	TestBAMParser.cpp	/^int main(int argc, char* argv[]) {$/
MTestHeptamerIndex.cpp	TestHeptamerIndex.cpp	/^int main(int argc, char* argv[]) {$/
MTestUtils.cpp	TestUtils.cpp	/^int main(int argc, char* argv[]) {$/
MatchFragment	SalmonQuantify.cpp	297
MatchFragment::MatchFragment	SalmonQuantify.cpp	/^        MatchFragment(uint32_t refStart_, uint32_t/
MatchFragment::length	SalmonQuantify.cpp	302
MatchFragment::queryStart	SalmonQuantify.cpp	302
MatchFragment::refStart	SalmonQuantify.cpp	302
MatchFragment::score	SalmonQuantify.cpp	304
MatchFragment::weight	SalmonQuantify.cpp	303
MerDirection	IndexedCounter.cpp	67
MerDirection::BOTH	IndexedCounter.cpp	67
MerDirection::FORWARD	IndexedCounter.cpp	67
MerDirection::REVERSE	IndexedCounter.cpp	67
MerIteratorType	JellyfishMerCounter.cpp	151
MiniBatchQueue	TestBAMParser.cpp	57
MultithreadedBAMParser::MultithreadedBAMParser	MultithreadedBAMParser.cpp	/^MultithreadedBAMParser::MultithreadedBAMParser(std/
MultithreadedBAMParser::finishedWithAlignment	MultithreadedBAMParser.cpp	/^void MultithreadedBAMParser::finishedWithAlignment/
MultithreadedBAMParser::nextAlignment	MultithreadedBAMParser.cpp	/^bool MultithreadedBAMParser::nextAlignment(BamAlig/
MultithreadedBAMParser::start	MultithreadedBAMParser.cpp	/^bool MultithreadedBAMParser::start() {$/
MultithreadedBAMParser::~MultithreadedBAMParser	MultithreadedBAMParser.cpp	/^MultithreadedBAMParser::~MultithreadedBAMParser() /
N	cokus.cpp	57
NODEBUG	PCA.cpp	23
OPERATION	JellyfishMerCounter.cpp	150
OPERATION::COUNT	JellyfishMerCounter.cpp	150
OPERATION::PRIME	JellyfishMerCounter.cpp	150
OPERATION::UPDATE	JellyfishMerCounter.cpp	150
ParserT	SalmonQuantify.cpp	702
PartitionRefiner::PartitionRefiner	PartitionRefiner.cpp	/^PartitionRefiner::PartitionRefiner(LUTTools::KmerI/
PartitionRefiner::partitionMembership	PartitionRefiner.cpp	/^const std::vector<LUTTools::KmerID>& PartitionRefi/
PartitionRefiner::relabel	PartitionRefiner.cpp	/^void PartitionRefiner::relabel() {$/
PartitionRefiner::splitWith	PartitionRefiner.cpp	/^void PartitionRefiner::splitWith(std::vector<LUTTo/
PathIterator	JellyfishMerCounter.cpp	151
Pca::Calculate	PCA.cpp	/^int Pca::Calculate(vector<float> &x,$/
Pca::Pca	PCA.cpp	/^Pca::Pca(void) {$/
Pca::cum_prop	PCA.cpp	/^std::vector<float> Pca::cum_prop(void) { return _c/
Pca::eliminated_columns	PCA.cpp	/^std::vector<unsigned int> Pca::eliminated_columns(/
Pca::is_center	PCA.cpp	/^bool Pca::is_center(void) { return _is_center; }$/
Pca::is_scale	PCA.cpp	/^bool Pca::is_scale(void) {  return _is_scale; }$/
Pca::kaiser	PCA.cpp	/^unsigned int Pca::kaiser(void) { return _kaiser; }/
Pca::method	PCA.cpp	/^string Pca::method(void) { return _method; }$/
Pca::ncols	PCA.cpp	/^unsigned int Pca::ncols(void) { return _ncols; }$/
Pca::nrows	PCA.cpp	/^unsigned int Pca::nrows(void) { return _nrows; }$/
Pca::prop_of_var	PCA.cpp	/^std::vector<float> Pca::prop_of_var(void) {return /
Pca::scores	PCA.cpp	/^std::vector<float> Pca::scores(void) { return _sco/
Pca::sd	PCA.cpp	/^std::vector<float> Pca::sd(void) { return _sd; };$/
Pca::thresh95	PCA.cpp	/^unsigned int Pca::thresh95(void) { return _thresh9/
Pca::~Pca	PCA.cpp	/^Pca::~Pca(void) {$/
PosteriorAbundanceVector	TestBAMParser.cpp	60
PriorAbundanceVector	TestBAMParser.cpp	59
ReadLength	BuildLUT.cpp	70
RefSeq	TestBAMParser.cpp	62
RefSeq::RefLength	TestBAMParser.cpp	65
RefSeq::RefName	TestBAMParser.cpp	64
RefSeq::RefSeq	TestBAMParser.cpp	/^    RefSeq(char* name, uint32_t len) : RefName(nam/
SOP	FragmentList.cpp	20
Sailfish::TranscriptFeatures	ComputeBiasFeatures.cpp	47
Sailfish::TranscriptFeatures	PerformBiasCorrection.cpp	67
StrandHasher	IndexedCounter.cpp	431
StrandHasher::operator()	IndexedCounter.cpp	/^              size_t operator()(const ReadStranded/
StreamingReadParser::StreamingReadParser	StreamingSequenceParser.cpp	/^StreamingReadParser::StreamingReadParser( std::vec/
StreamingReadParser::finishedWithRead	StreamingSequenceParser.cpp	/^void StreamingReadParser::finishedWithRead(ReadSeq/
StreamingReadParser::nextRead	StreamingSequenceParser.cpp	/^bool StreamingReadParser::nextRead(ReadSeq*& seq) /
StreamingReadParser::start	StreamingSequenceParser.cpp	/^bool StreamingReadParser::start() {$/
StreamingReadParser::~StreamingReadParser	StreamingSequenceParser.cpp	/^StreamingReadParser::~StreamingReadParser() {$/
TranscriptCluster	TestBAMParser.cpp	76
TranscriptCluster::TranscriptCluster	TestBAMParser.cpp	/^    TranscriptCluster() : members_(std::list<size_/
TranscriptCluster::TranscriptCluster	TestBAMParser.cpp	/^    TranscriptCluster(size_t initialMember) : memb/
TranscriptCluster::active_	TestBAMParser.cpp	/^    TranscriptCluster() : members_(std::list<size_/
TranscriptCluster::active_	TestBAMParser.cpp	/^                                              logM/
TranscriptCluster::active_	TestBAMParser.cpp	159
TranscriptCluster::addMass	TestBAMParser.cpp	/^    void addMass(double logNewMass) { logMass_ = l/
TranscriptCluster::count_	TestBAMParser.cpp	157
TranscriptCluster::deactivate	TestBAMParser.cpp	/^    void deactivate() { active_ = false; }$/
TranscriptCluster::incrementCount	TestBAMParser.cpp	/^    void incrementCount(size_t num) { count_ += nu/
TranscriptCluster::isActive	TestBAMParser.cpp	/^    bool isActive() { return active_; }$/
TranscriptCluster::logMass	TestBAMParser.cpp	/^    double logMass() { return logMass_; }$/
TranscriptCluster::logMass_	TestBAMParser.cpp	/^    TranscriptCluster() : members_(std::list<size_/
TranscriptCluster::logMass_	TestBAMParser.cpp	/^                                              logM/
TranscriptCluster::logMass_	TestBAMParser.cpp	158
TranscriptCluster::members	TestBAMParser.cpp	/^    std::list<size_t>& members() { return members_/
TranscriptCluster::members_	TestBAMParser.cpp	156
TranscriptCluster::merge	TestBAMParser.cpp	/^    void merge(TranscriptCluster& other) {$/
TranscriptCluster::numHits	TestBAMParser.cpp	/^    size_t numHits() { return count_.load(); }$/
TranscriptCluster::projectToPolytope	TestBAMParser.cpp	/^    void projectToPolytope(std::vector<Transcript>/
TranscriptFeatures	PerformBiasCorrection_old.cpp	63
TranscriptFeatures::diNucleotides	PerformBiasCorrection_old.cpp	67
TranscriptFeatures::gcContent	PerformBiasCorrection_old.cpp	66
TranscriptFeatures::length	PerformBiasCorrection_old.cpp	65
TranscriptFeatures::name	PerformBiasCorrection_old.cpp	64
TranscriptFeatures::std::array	PerformBiasCorrection_old.cpp	67
TranscriptHitList	SalmonQuantify.cpp	313
TranscriptHitList::VoteInfo	SalmonQuantify.cpp	337
TranscriptHitList::VoteInfo::coverage	SalmonQuantify.cpp	338
TranscriptHitList::VoteInfo::rightmostBase	SalmonQuantify.cpp	339
TranscriptHitList::addFragMatch	SalmonQuantify.cpp	/^        void addFragMatch(uint32_t tpos, uint32_t /
TranscriptHitList::addFragMatchRC	SalmonQuantify.cpp	/^        void addFragMatchRC(uint32_t tpos, uint32_/
TranscriptHitList::bestHitPos	SalmonQuantify.cpp	315
TranscriptHitList::bestHitScore	SalmonQuantify.cpp	316
TranscriptHitList::computeBestChain	SalmonQuantify.cpp	/^        bool computeBestChain() {$/
TranscriptHitList::computeBestLoc_	SalmonQuantify.cpp	/^        void computeBestLoc_(std::vector<KmerVote>/
TranscriptHitList::rcVotes	SalmonQuantify.cpp	319
TranscriptHitList::targetID	SalmonQuantify.cpp	321
TranscriptHitList::totalNumHits	SalmonQuantify.cpp	/^        uint32_t totalNumHits() { return std::max(/
TranscriptHitList::votes	SalmonQuantify.cpp	318
TranscriptID	AnalyzeKmerTradeoff.cpp	57
TranscriptID	BuildLUT.cpp	68
TranscriptID	SalmonQuantify.cpp	111
TranscriptIDVector	AnalyzeKmerTradeoff.cpp	58
TranscriptIDVector	SalmonQuantify.cpp	112
TranscriptKey	SailfishUtils.cpp	336
TranscriptKey::DYNAMIC	SailfishUtils.cpp	336
TranscriptKey::GENE_ID	SailfishUtils.cpp	336
TranscriptKey::GENE_NAME	SailfishUtils.cpp	336
TranscriptKeyPair	SailfishUtils.cpp	327
TranscriptKeyPair::TranscriptKeyPair	SailfishUtils.cpp	/^        TranscriptKeyPair(const char* t, const cha/
TranscriptKeyPair::key	SailfishUtils.cpp	329
TranscriptKeyPair::transcript_id	SailfishUtils.cpp	328
TranscriptList	BuildLUT.cpp	72
TranscriptResult	PerformBiasCorrection.cpp	95
TranscriptResult	PerformBiasCorrection_old.cpp	95
TranscriptResult::approxCount	PerformBiasCorrection.cpp	101
TranscriptResult::approxKmerCount	PerformBiasCorrection.cpp	100
TranscriptResult::kpkm	PerformBiasCorrection.cpp	99
TranscriptResult::length	PerformBiasCorrection.cpp	96
TranscriptResult::length	PerformBiasCorrection_old.cpp	96
TranscriptResult::rpkm	PerformBiasCorrection.cpp	98
TranscriptResult::rpkm	PerformBiasCorrection_old.cpp	98
TranscriptResult::tpm	PerformBiasCorrection.cpp	97
TranscriptResult::tpm	PerformBiasCorrection_old.cpp	97
VersionChecker::VersionChecker	VersionChecker.cpp	/^VersionChecker::VersionChecker(boost::asio::io_ser/
VersionChecker::cancel_upgrade_check	VersionChecker.cpp	/^void VersionChecker::cancel_upgrade_check(const bo/
VersionChecker::handle_connect	VersionChecker.cpp	/^void VersionChecker::handle_connect(const boost::s/
VersionChecker::handle_read_content	VersionChecker.cpp	/^void VersionChecker::handle_read_content(const boo/
VersionChecker::handle_read_headers	VersionChecker.cpp	/^void VersionChecker::handle_read_headers(const boo/
VersionChecker::handle_read_status_line	VersionChecker.cpp	/^void VersionChecker::handle_read_status_line(const/
VersionChecker::handle_resolve	VersionChecker.cpp	/^void VersionChecker::handle_resolve(const boost::s/
VersionChecker::handle_write_request	VersionChecker.cpp	/^void VersionChecker::handle_write_request(const bo/
VersionChecker::message	VersionChecker.cpp	/^std::string VersionChecker::message() {$/
_GNU_SOURCE	IndexedCounter.cpp	48
aggregateEstimatesToGeneLevel	SailfishUtils.cpp	/^void aggregateEstimatesToGeneLevel(TranscriptGeneM/
args	JellyfishMerCounter.cpp	73
as_seconds	JellyfishMerCounter.cpp	/^inline double as_seconds(DtnType dtn) { return dur/
assert_file_good	PCAUtils.cpp	/^void assert_file_good(const bool& is_file_good, co/
basesCovered	SalmonQuantify.cpp	/^uint32_t basesCovered(std::vector<uint32_t>& kmerH/
basesCovered	SalmonQuantify.cpp	/^uint32_t basesCovered(std::vector<uint32_t>& posLe/
boost::asio::ip::tcp	VersionChecker.cpp	14
buildLUTs	BuildLUT.cpp	/^int buildLUTs($/
buildPerfectHashIndex	PerfectHashIndexer.cpp	/^void buildPerfectHashIndex(bool canonical, std::ve/
buildTLUTIndex	LookUpTableUtils.cpp	/^std::vector<Offset> buildTLUTIndex(const std::stri/
bwa_pg	SalmonQuantify.cpp	105
computeBiasFeatures	ComputeBiasFeatures.cpp	/^int computeBiasFeatures($/
computeBiasFeaturesHelper	ComputeBiasFeatures.cpp	/^bool computeBiasFeaturesHelper(ParserT& parser,$/
compute_column_means	PCAUtils.cpp	/^arma::Col<double> compute_column_means(const arma:/
compute_column_rms	PCAUtils.cpp	/^arma::Col<double> compute_column_rms(const arma::M/
countKmers	IndexedCounter.cpp	/^bool countKmers(std::vector<std::string> readFiles/
dumpKmerLUT	LookUpTableUtils.cpp	/^void dumpKmerLUT($/
eigen_pair	PCA.cpp	198
encode	SailfishUtils.cpp	/^uint64_t encode(uint64_t tid, uint64_t offset) {$/
enforce_positive_sign_by_column	PCAUtils.cpp	/^void enforce_positive_sign_by_column(arma::Mat<dou/
extractReadLibraries	SailfishUtils.cpp	/^std::vector<ReadLibrary> extractReadLibraries(boos/
extract_column_vector	PCAUtils.cpp	/^std::vector<double> extract_column_vector(const ar/
extract_row_vector	PCAUtils.cpp	/^std::vector<double> extract_row_vector(const arma:/
fifoRead	StreamingSequenceParser.cpp	/^int fifoRead(int f, void* buf, int n) {$/
file_vector	JellyfishMerCounter.cpp	85
file_vector::const_iterator	JellyfishMerCounter.cpp	209
file_vector::const_iterator	JellyfishMerCounter.cpp	210
filter	JellyfishMerCounter.cpp	116
filter::and_res	JellyfishMerCounter.cpp	/^  bool and_res(bool r, const mer_dna& x) const {$/
filter::filter	JellyfishMerCounter.cpp	/^  filter(filter* prev = 0) : prev_(prev) { }$/
filter::operator()	JellyfishMerCounter.cpp	/^  virtual bool operator()(const mer_dna& x) { retu/
filter::prev_	JellyfishMerCounter.cpp	117
filter::~filter	JellyfishMerCounter.cpp	/^  virtual ~filter() { }$/
filter_bc	JellyfishMerCounter.cpp	126
filter_bc::counter_	JellyfishMerCounter.cpp	127
filter_bc::filter_bc	JellyfishMerCounter.cpp	/^  filter_bc(const mer_dna_bloom_counter& counter, /
filter_bc::operator()	JellyfishMerCounter.cpp	/^  bool operator()(const mer_dna& m) {$/
filter_bf	JellyfishMerCounter.cpp	138
filter_bf::bf_	JellyfishMerCounter.cpp	139
filter_bf::filter_bf	JellyfishMerCounter.cpp	/^  filter_bf(mer_dna_bloom_filter& bf, filter* prev/
filter_bf::operator()	JellyfishMerCounter.cpp	/^  bool operator()(const mer_dna& m) {$/
futureIsReady	IndexedCounter.cpp	/^bool futureIsReady(std::future<R>& f) {$/
getHitsForFragment	SalmonQuantify.cpp	/^void getHitsForFragment(std::pair<header_sequence_/
getHitsForFragment	SalmonQuantify.cpp	/^void getHitsForFragment(jellyfish::header_sequence/
getVersionMessage	VersionChecker.cpp	/^std::string getVersionMessage() {$/
get_mean	PCAUtils.cpp	/^double get_mean(const std::vector<double>& iter) {/
get_sigma	PCAUtils.cpp	/^double get_sigma(const std::vector<double>& iter) /
help	Sailfish.cpp	/^int help(int argc, char* argv[]) {$/
help	Salmon.cpp	/^int help(int argc, char* argv[]) {$/
hiBit	cokus.cpp	/^#define hiBit(u)       ((u) & 0x80000000U)   \/\/ ma/
jellyfish::mer_dna	JellyfishMerCounter.cpp	82
jellyfish::mer_dna_bloom_counter	JellyfishMerCounter.cpp	83
jellyfish::mer_dna_bloom_filter	JellyfishMerCounter.cpp	84
jellyfish_count_main	JellyfishMerCounter.cpp	/^int jellyfish_count_main(int argc, char *argv[])$/
left	cokus.cpp	67
loBit	cokus.cpp	/^#define loBit(u)       ((u) & 0x00000001U)   \/\/ ma/
loBits	cokus.cpp	/^#define loBits(u)      ((u) & 0x7FFFFFFFU)   \/\/ ma/
load_bloom_filter	JellyfishMerCounter.cpp	/^mer_dna_bloom_counter* load_bloom_filter(const cha/
mainBuildLUT	BuildLUT.cpp	/^int mainBuildLUT(int argc, char* argv[] ) {$/
mainCount	IndexedCounter.cpp	/^int mainCount( uint32_t numThreads,$/
mainIndex	PerfectHashIndexer.cpp	/^int mainIndex( int argc, char *argv[] ) {$/
mainQuantify	QuantificationDriver.cpp	/^int mainQuantify( int argc, char *argv[] ) {$/
mainSailfish	Sailfish.cpp	/^int mainSailfish(int argc, char* argv[]) {$/
make_shuffled_matrix	PCAUtils.cpp	/^arma::Mat<double> make_shuffled_matrix(const arma:/
manager_pid	JellyfishMerCounter.cpp	230
mer_counter	JellyfishMerCounter.cpp	209
mer_counter_base	JellyfishMerCounter.cpp	152
mer_counter_base::ary_	JellyfishMerCounter.cpp	154
mer_counter_base::filter_	JellyfishMerCounter.cpp	157
mer_counter_base::mer_counter_base	JellyfishMerCounter.cpp	/^  mer_counter_base(int nb_threads, mer_hash& ary,$/
mer_counter_base::nb_threads_	JellyfishMerCounter.cpp	153
mer_counter_base::op_	JellyfishMerCounter.cpp	158
mer_counter_base::parser_	JellyfishMerCounter.cpp	156
mer_counter_base::start	JellyfishMerCounter.cpp	/^  virtual void start(int thid) {$/
mer_counter_base::streams_	JellyfishMerCounter.cpp	155
mer_iterator	JellyfishMerCounter.cpp	89
mer_iterator	JellyfishMerCounter.cpp	209
mer_qual_counter	JellyfishMerCounter.cpp	210
mer_qual_iterator	JellyfishMerCounter.cpp	105
mer_qual_iterator	JellyfishMerCounter.cpp	210
mer_qual_iterator::mer_qual_iterator	JellyfishMerCounter.cpp	/^  mer_qual_iterator(sequence_qual_parser& parser, /
mer_qual_iterator::sequence_qual_parser	JellyfishMerCounter.cpp	106
mer_qual_iterator::super	JellyfishMerCounter.cpp	106
mixBits	cokus.cpp	/^#define mixBits(u, v)  (hiBit(u)|loBits(v))  \/\/ mo/
mpdec	PerformBiasCorrection.cpp	68
mute	FragmentList.cpp	23
my_mer	BuildSalmonIndex.cpp	58
my_mer	SalmonQuantify.cpp	114
next	cokus.cpp	66
normalize_by_column	PCAUtils.cpp	/^void normalize_by_column(arma::Mat<double>& data, /
numberOfReadsInFastaFile	SailfishUtils.cpp	/^size_t numberOfReadsInFastaFile(const std::string&/
offset	SailfishUtils.cpp	/^uint32_t offset(uint64_t enc) {$/
offset	SalmonQuantify.cpp	/^uint32_t offset(uint64_t enc) {$/
operator<<	GenomicFeature.cpp	/^std::ostream& operator<< ( std::ostream& out, cons/
operator<<	GenomicFeature.cpp	/^std::ostream& operator<< ( std::ostream& out, cons/
operator<<	LibraryFormat.cpp	/^std::ostream& operator<<(std::ostream& os, Library/
operator>>	GenomicFeature.cpp	/^std::istream& operator>> ( std::istream& in, Genom/
overlap	SailfishUtils.cpp	/^bool overlap( const S<T> &a, const S<T> &b ) {$/
paired_parser	SalmonQuantify.cpp	107
parseExpressionRecord	SailfishUtils.cpp	/^ExpressionRecord parseExpressionRecord(std::string/
parseFeature	PerformBiasCorrection.cpp	/^TranscriptFeatures parseFeature(std::ifstream& ifs/
parseFeature	PerformBiasCorrection_old.cpp	/^TranscriptFeatures parseFeature(std::ifstream& ifs/
parseFeatureFile	PerformBiasCorrection.cpp	/^std::vector<TranscriptFeatures> parseFeatureFile(c/
parseFeatureFile	PerformBiasCorrection_old.cpp	/^std::vector<TranscriptFeatures> parseFeatureFile(c/
parseLibraryFormatString	SailfishUtils.cpp	/^LibraryFormat parseLibraryFormatString(std::string/
parseLibraryFormatString	TestBAMParser.cpp	/^LibraryFormat parseLibraryFormatString(std::string/
parseSailfishFile	PerformBiasCorrection.cpp	/^ExpressionResults parseSailfishFile(const bfs::pat/
parseSailfishFile	PerformBiasCorrection_old.cpp	/^ExpressionResults parseSailfishFile(const bfs::pat/
parseTranscripts	BuildTranscriptMap.cpp	/^bool parseTranscripts(boost::filesystem::path& tpa/
performBiasCorrection	PerformBiasCorrection.cpp	/^int performBiasCorrection($/
populateFromTPMs	PerformBiasCorrection.cpp	/^void populateFromTPMs(vector<mpdec>& tpms,$/
precedes	SalmonQuantify.cpp	/^bool precedes(const MatchFragment& a, const MatchF/
processMiniBatch	SalmonQuantify.cpp	/^void processMiniBatch($/
processMiniBatch	TestBAMParser.cpp	/^void processMiniBatch(MiniBatchQueue<AlignmentGrou/
processReadsMEM	SalmonQuantify.cpp	/^void processReadsMEM(ParserT* parser,$/
quantifyLibrary	TestBAMParser.cpp	/^void quantifyLibrary(LibraryFormat libFmt,$/
randomMT	cokus.cpp	/^uint32 randomMT(void)$/
readKmerEquivClasses	LookUpTableUtils.cpp	/^std::vector<KmerID> readKmerEquivClasses(const std/
readKmerLUT	LookUpTableUtils.cpp	/^void readKmerLUT($/
readKmerOrder	SailfishUtils.cpp	/^bool readKmerOrder( const std::string& fname, std:/
readTranscriptInfo	LookUpTableUtils.cpp	/^std::unique_ptr<TranscriptInfo> readTranscriptInfo/
readTranscriptToGeneMap	SailfishUtils.cpp	/^TranscriptGeneMap readTranscriptToGeneMap( std::if/
reloadMT	cokus.cpp	/^uint32 reloadMT(void)$/
remove_column_means	PCAUtils.cpp	/^void remove_column_means(arma::Mat<double>& data, /
runIterativeOptimizer	QuantificationDriver.cpp	/^int runIterativeOptimizer(int argc, char* argv[] )/
runJellyfish	PerfectHashIndexer.cpp	/^int runJellyfish(bool canonical,$/
runKmerCounter	QuantificationDriver.cpp	/^int runKmerCounter(const std::string& sfCommand,$/
runSailfishEstimation	QuantificationDriver.cpp	/^int runSailfishEstimation(const std::string& sfCom/
sailfish	SailfishUtils.cpp	44
salmon::math::LOG_0	TestBAMParser.cpp	48
salmon::math::LOG_1	TestBAMParser.cpp	49
salmon::math::logAdd	TestBAMParser.cpp	50
salmon::math::logSub	TestBAMParser.cpp	51
salmon::stringtools::encodeSequenceInSAM	SailfishStringUtils.cpp	/^uint8_t* salmon::stringtools::encodeSequenceInSA/
salmon::utils	SailfishUtils.cpp	45
salmon::utils::parseLibraryFormatStringNew	SailfishUtils.cpp	/^LibraryFormat parseLibraryFormatStringNew(std::str/
salmon::utils::std::string	SailfishUtils.cpp	46
salmonIndex	BuildSalmonIndex.cpp	/^int salmonIndex(int argc, char* argv[]) {$/
salmonQuantify	SalmonQuantify.cpp	/^int salmonQuantify(int argc, char *argv[]) {$/
salmonSwim	Salmon.cpp	/^int salmonSwim(int argc, char* argv[]) {$/
scaleBy	TestBAMParser.cpp	/^void scaleBy(std::vector<T>& vec, T scale) {$/
seedMT	cokus.cpp	/^void seedMT(uint32 seed)$/
sequence_parser	BuildSalmonIndex.cpp	61
sequence_parser	JellyfishMerCounter.cpp	88
sequence_parser	JellyfishMerCounter.cpp	89
sequence_qual_parser	JellyfishMerCounter.cpp	93
sequence_qual_parser::StreamIterator	JellyfishMerCounter.cpp	96
sequence_qual_parser::sequence_qual_parser	JellyfishMerCounter.cpp	/^  sequence_qual_parser(uint16_t mer_len, uint32_t /
sequence_qual_parser::super	JellyfishMerCounter.cpp	97
signal_handler	JellyfishMerCounter.cpp	/^static void signal_handler(int sig) {$/
single_parser	SalmonQuantify.cpp	109
state	cokus.cpp	65
stats	PCAUtils.cpp	28
stats::utils	PCAUtils.cpp	29
stats::utils::make_covariance_matrix	PCAUtils.cpp	/^arma::Mat<double> make_covariance_matrix(const arm/
std::chrono::duration	JellyfishMerCounter.cpp	76
std::chrono::duration_cast	JellyfishMerCounter.cpp	77
std::chrono::system_clock	JellyfishMerCounter.cpp	75
std::string	QuantificationDriver.cpp	56
stream_manager	BuildSalmonIndex.cpp	60
stream_manager	SalmonQuantify.cpp	108
transcript	SailfishUtils.cpp	/^uint32_t transcript(uint64_t enc) {$/
transcript	SalmonQuantify.cpp	/^uint32_t transcript(uint64_t enc) {$/
transcriptGeneMapFromGTF	SailfishUtils.cpp	/^TranscriptGeneMap transcriptGeneMapFromGTF(const s/
transcriptToGeneMapFromFasta	SailfishUtils.cpp	/^TranscriptGeneMap transcriptToGeneMapFromFasta( co/
uint32	cokus.cpp	55
writeTranscriptInfo	LookUpTableUtils.cpp	/^void writeTranscriptInfo (TranscriptInfo *ti, std:/
