SYMBOL INDEX (1217 symbols across 102 files) FILE: aligner_bt.cpp function main (line 1744) | int main(int argc, char **argv) { FILE: aligner_bt.h function class (line 170) | class BtBranchProblem { function class (line 324) | class BtBranch { function reset (line 348) | void reset() { function isSolution (line 374) | bool isSolution(const BtBranchProblem& prob) const { function isValid (line 382) | bool isValid(const BtBranchProblem& prob) const { function overlap (line 406) | bool overlap(const BtBranchProblem& prob, const BtBranch& bt) const { function endsInFirstRow (line 461) | bool endsInFirstRow() const { function class (line 544) | class BtBranchTracer { FILE: aligner_cache.cpp type option (line 37) | struct option function printUsage (line 42) | static void printUsage(ostream& os) { function add (line 51) | static void add( function aligner_cache_tests (line 64) | static void aligner_cache_tests() { function main (line 164) | int main(int argc, char **argv) { FILE: aligner_cache.h type PListSlice (line 68) | typedef PListSlice TSlice; function QKey (line 73) | struct QKey { function init (line 91) | bool init( function toString (line 122) | void toString(BTDnaString& s) { function reset (line 139) | void reset() { seq = 0; len = 0xffffffff; } function operator (line 144) | bool operator<(const QKey& o) const { function operator (line 151) | bool operator>(const QKey& o) const { function operator (line 158) | bool operator==(const QKey& o) const { function operator (line 166) | bool operator!=(const QKey& o) const { function index_t (line 206) | index_t numRanges() const { function empty (line 224) | bool empty() const { function reset (line 237) | void reset() { function init (line 244) | void init(index_t i, index_t ranges, index_t elts) { function addRange (line 251) | void addRange(index_t numElts) { type QKey (line 275) | typedef QKey SAKey; function valid (line 290) | bool valid() { return len != (index_t)OFF_MASK; } function init (line 303) | void init( function init (line 338) | void init(SAKey k, index_t tf, index_t tb, TSlice o) { function init (line 345) | void init(const SATuple& src, index_t first, index_t last) { function operator (line 370) | bool operator<(const SATuple& o) const { function operator (line 379) | bool operator>(const SATuple& o) const { function operator (line 389) | bool operator==(const SATuple& o) const { function reset (line 393) | void reset() { topf = topb = (index_t)OFF_MASK; offs.reset(); } function setLength (line 398) | void setLength(index_t nlen) { type RedBlackNode (line 435) | typedef RedBlackNode > QNode; type RedBlackNode (line 436) | typedef RedBlackNode > SANode; type PList (line 438) | typedef PList TQList; type PList (line 439) | typedef PList TSAList; function empty (line 507) | bool empty() const { function MUTEX_T (line 600) | MUTEX_T* lockPtr() const { function nextRead (line 808) | void nextRead() { function clear (line 824) | void clear() { function AlignmentCache (line 875) | const AlignmentCache* currentCache() const { return current_; } function AlignmentCache (line 898) | const AlignmentCache& current() { FILE: aligner_metrics.h function class (line 35) | class RunningStat { function class (line 91) | class AlignerMetrics { function nextRead (line 194) | void nextRead(const BTDnaString& read) { function setReadHasRange (line 217) | void setReadHasRange() { function finishRead (line 224) | void finishRead() { FILE: aligner_result.h type TAlScore (line 34) | typedef int64_t TAlScore; function class (line 51) | class AlnScore { function reset (line 74) | void reset() { function AlnScore (line 81) | inline static AlnScore INVALID() { function invalidate (line 98) | inline void invalidate() { function o (line 107) | inline bool operator==(const AlnScore& o) const { function o (line 115) | inline bool operator!=(const AlnScore& o) const { function o (line 122) | inline bool operator>=(const AlnScore& o) const { function o (line 141) | inline bool operator<(const AlnScore& o) const { function o (line 148) | inline bool operator<=(const AlnScore& o) const { function o (line 155) | inline bool operator>(const AlnScore& o) const { function class (line 205) | class AlnRes { function reset (line 244) | void reset() { function setScore (line 257) | void setScore(TAlScore score) { function readPositions (line 270) | uint32_t> readPositions(size_t i) const { return readPositions_[i]; } function printSeq (line 280) | void printSeq( function printQuals (line 304) | void printQuals( function init (line 321) | void init( type TNumAlns (line 353) | typedef uint64_t TNumAlns; function class (line 360) | class AlnSetSumm { FILE: aligner_seed.cpp function Constraint (line 30) | Constraint Constraint::exact() { function Constraint (line 40) | Constraint Constraint::penaltyBased(int pen) { function Constraint (line 50) | Constraint Constraint::penaltyFuncBased(const SimpleFunc& f) { function Constraint (line 60) | Constraint Constraint::mmBased(int mms) { function Constraint (line 71) | Constraint Constraint::editBased(int edits) { function parseInt (line 348) | static int parseInt(const char *errmsg, const char *arg) { type option (line 371) | struct option function printUsage (line 384) | static void printUsage(ostream& os) { function main (line 416) | int main(int argc, char **argv) { FILE: aligner_seed.h function init (line 50) | struct Constraint { function mustMatch (line 68) | bool mustMatch() { function canMismatch (line 78) | bool canMismatch(int q, const Scoring& cm) { function canN (line 87) | bool canN(int q, const Scoring& cm) { function canMismatch (line 97) | bool canMismatch() { function canN (line 106) | bool canN() { function canDelete (line 115) | bool canDelete(int ex, const Scoring& cm) { function canDelete (line 124) | bool canDelete() { function canInsert (line 134) | bool canInsert(int ex, const Scoring& cm) { function canInsert (line 143) | bool canInsert() { function canGap (line 152) | bool canGap() { function chargeMismatch (line 160) | void chargeMismatch(int q, const Scoring& cm) { function chargeN (line 173) | void chargeN(int q, const Scoring& cm) { function chargeDelete (line 186) | void chargeDelete(int ex, const Scoring& cm) { function chargeInsert (line 199) | void chargeInsert(int ex, const Scoring& cm) { function acceptable (line 216) | bool acceptable() { function instantiate (line 229) | static int instantiate(size_t rdlen, const SimpleFunc& func) { function instantiate (line 236) | void instantiate(size_t rdlen) { type InstantiatedSeed (line 310) | struct InstantiatedSeed function Seed (line 321) | struct Seed { function init (line 339) | void init(int ln, int ty, Constraint* oc) { function acceptable (line 359) | bool acceptable() { function mmSeeds (line 386) | static void mmSeeds( type InstantiatedSeed (line 410) | struct InstantiatedSeed { function reset (line 486) | void reset() { function init (line 494) | void init( function ns (line 529) | int ns() const { function operator (line 564) | bool operator<(const EEHit& o) const { function repOk (line 577) | bool repOk(const Read& rd) const { function nextRead (line 638) | void nextRead(const Read& read) { function add (line 647) | void add( function reset (line 683) | void reset( function clearSeeds (line 716) | void clearSeeds() { function clear (line 743) | void clear() { function uniquenessFactor (line 791) | double uniquenessFactor() const { function index_t (line 843) | index_t idx2off(size_t off) const { function QVal (line 856) | const QVal& hitsAtOffIdx(bool fw, size_t seedoffidx) const { function rankSeedHits (line 924) | void rankSeedHits(RandomSource& rnd) { function index_t (line 995) | index_t fewestEditsEE(bool fw, int seedlen, int per) const { function QVal (line 1032) | const QVal& hitsByRank( function BTDnaString (line 1061) | const BTDnaString& seqByRank(index_t r) { function BTString (line 1070) | const BTString& qualByRank(index_t r) { function sort1mmEe (line 1107) | void sort1mmEe(RandomSource& rnd) { function add1mmEe (line 1132) | void add1mmEe( function addExactEeFw (line 1148) | void addExactEeFw( function addExactEeRc (line 1162) | void addExactEeRc( function clearExactE2eHits (line 1176) | void clearExactE2eHits() { function clear1mmE2eHits (line 1184) | void clear1mmE2eHits() { type SeedSearchMetrics (line 1276) | struct SeedSearchMetrics { function reset (line 1305) | void reset() { FILE: aligner_seed_policy.cpp function parseFuncType (line 30) | static int parseFuncType(const std::string& otype) { function main (line 648) | int main() { FILE: aligner_seed_policy.h function class (line 39) | class SeedAlignmentPolicy { FILE: aligner_sw.cpp type option (line 937) | struct option function printUsage (line 945) | static void printUsage(ostream& os) { function T (line 958) | T parse(const char *s) { function doTestCase (line 979) | static void doTestCase( function doTestCase2 (line 1097) | static void doTestCase2( function doTestCase3 (line 1142) | static void doTestCase3( function doTestCase4 (line 1194) | static void doTestCase4( function doTests (line 1246) | static void doTests() { function doLocalTests (line 2505) | static void doLocalTests() { function main (line 2840) | int main(int argc, char **argv) { FILE: aligner_sw.h function class (line 192) | class SwAligner { function backtrace (line 544) | bool backtrace( FILE: aligner_sw_common.h type SwResult (line 40) | struct SwResult { FILE: aligner_sw_nuc.h type DpNucFrame (line 40) | struct DpNucFrame { function DpBtCandidate (line 93) | struct DpBtCandidate { function reset (line 101) | void reset() { init(0, 0, 0); } function init (line 103) | void init(size_t row_, size_t col_, TAlScore score_) { function dominatedBy (line 119) | inline bool dominatedBy(const DpBtCandidate& o) { function repOk (line 174) | bool repOk() const { FILE: aligner_swsse.h function clear (line 32) | struct SSEMetrics { function reset (line 37) | void reset() { type SSEMatrix (line 99) | struct SSEMatrix { function __m128i (line 134) | inline __m128i* evecUnsafe(size_t row, size_t col) { function __m128i (line 146) | inline __m128i* fvec(size_t row, size_t col) { function __m128i (line 158) | inline __m128i* hvec(size_t row, size_t col) { function __m128i (line 170) | inline __m128i* tmpvec(size_t row, size_t col) { function __m128i (line 182) | inline __m128i* tmpvecUnsafe(size_t row, size_t col) { function elt (line 222) | inline int elt(size_t row, size_t col, size_t mat) const { function eelt (line 243) | inline int eelt(size_t row, size_t col) const { function felt (line 250) | inline int felt(size_t row, size_t col) const { function helt (line 257) | inline int helt(size_t row, size_t col) const { function reportedThrough (line 264) | inline bool reportedThrough( function setReportedThrough (line 274) | inline void setReportedThrough( function resetRow (line 381) | void resetRow(size_t i) { type SSEData (line 408) | struct SSEData { function isHMaskSet (line 425) | inline bool SSEMatrix::isHMaskSet( function hMaskSet (line 437) | inline void SSEMatrix::hMaskSet( function isEMaskSet (line 450) | inline bool SSEMatrix::isEMaskSet( function eMaskSet (line 462) | inline void SSEMatrix::eMaskSet( function isFMaskSet (line 475) | inline bool SSEMatrix::isFMaskSet( function fMaskSet (line 487) | inline void SSEMatrix::fMaskSet( FILE: aligner_swsse_ee_i16.cpp function cellOkEnd2EndI16 (line 154) | static bool cellOkEnd2EndI16( function TAlScore (line 297) | TAlScore SwAligner::alignGatherEE16(int& flag, bool debug) { function TAlScore (line 793) | TAlScore SwAligner::alignNucleotidesEnd2EndSseI16(int& flag, bool debug) { FILE: aligner_swsse_ee_u8.cpp function cellOkEnd2EndU8 (line 151) | static bool cellOkEnd2EndU8( function TAlScore (line 298) | TAlScore SwAligner::alignGatherEE8(int& flag, bool debug) { function TAlScore (line 791) | TAlScore SwAligner::alignNucleotidesEnd2EndSseU8(int& flag, bool debug) { FILE: aligner_swsse_loc_i16.cpp function cellOkLocalI16 (line 152) | static bool cellOkLocalI16( function TAlScore (line 295) | TAlScore SwAligner::alignGatherLoc16(int& flag, bool debug) { function TAlScore (line 967) | TAlScore SwAligner::alignNucleotidesLocalSseI16(int& flag, bool debug) { FILE: aligner_swsse_loc_u8.cpp function cellOkLocalU8 (line 166) | static bool cellOkLocalU8( function TAlScore (line 307) | TAlScore SwAligner::alignGatherLoc8(int& flag, bool debug) { function TAlScore (line 973) | TAlScore SwAligner::alignNucleotidesLocalSseU8(int& flag, bool debug) { FILE: aln_sink.h type ReadCounts (line 45) | struct ReadCounts { type SpeciesMetrics (line 56) | struct SpeciesMetrics { function reset (line 84) | void reset() { function init (line 93) | void init( function addSpeciesCounts (line 142) | void addSpeciesCounts( function addAllKmers (line 174) | void addAllKmers( function nDistinctKmers (line 192) | size_t nDistinctKmers(uint64_t taxID) { function EM (line 196) | static void EM( function calculateAbundance (line 274) | void calculateAbundance(const Ebwt& ebwt, uint8_t rank) function reset (line 515) | struct ReportingMetrics { function init (line 525) | void init( type THitInt (line 567) | typedef int64_t THitInt; function init (line 573) | struct ReportingParams { function class (line 624) | class ReportingState { type EList (line 762) | typedef EList StrList; function finish (line 880) | void finish( function ReportingParams (line 1213) | const ReportingParams& reportingParams() { return rp_;} function getPair (line 1287) | void getPair(const EList*& rs) const { rs = &rs_; } type EList (line 1367) | typedef EList StrList; function virtual (line 1384) | virtual ~AlnSinkSam() { } function std (line 1436) | static inline std::ostream& printPct( function AlnSetSumm (line 1696) | AlnSetSumm concordSumm(rd1_, rd2_, &rs_); function printUptoWs (line 2070) | inline void printUptoWs( function appendReadID (line 2202) | inline function appendSeqID (line 2219) | inline function appendTaxID (line 2236) | inline type FIELD_DEF (line 2253) | enum FIELD_DEF { function nextRead (line 2369) | void ReportingState::nextRead(bool paired) { function foundConcordant (line 2382) | bool ReportingState::foundConcordant() { function foundUnpaired (line 2400) | bool ReportingState::foundUnpaired(bool mate1) { function finish (line 2410) | void ReportingState::finish() { function getReport (line 2442) | void ReportingState::getReport(uint64_t& nconcordAln) const // # concord... function areDone (line 2466) | inline void ReportingState::areDone( FILE: alphabet.cpp function setIupacsCat (line 280) | void setIupacsCat(uint8_t cat) { FILE: alphabet.h function isDna (line 89) | static inline bool isDna(char c) { function isColor (line 96) | static inline bool isColor(char c) { function isAmbigNuc (line 103) | static inline bool isAmbigNuc(char c) { function isAmbigColor (line 110) | static inline bool isAmbigColor(char c) { function isAmbig (line 117) | static inline bool isAmbig(char c, bool color) { function isUnambigNuc (line 124) | static inline bool isUnambigNuc(char c) { function comp (line 131) | static inline char comp(char c) { function compDna (line 148) | static inline int compDna(int c) { function isUnambigDna (line 156) | static inline bool isUnambigDna(char c) { function isUnambigColor (line 163) | static inline bool isUnambigColor(char c) { function decodeNuc (line 173) | static inline void decodeNuc(char c , int& num, int *alts) { FILE: assert_helpers.h function class (line 31) | class ReleaseAssertException : public std::runtime_error { function assert_in2 (line 245) | static inline void assert_in2(char c, const char *str, const char *file,... function assert_range_helper (line 262) | static void assert_range_helper(const T& begin, FILE: binary_sa_search.h function TIndexOffU (line 47) | TIndexOffU binarySASearch( FILE: bitpack.h function pack_2b_in_8b (line 31) | static inline void pack_2b_in_8b(const int two, uint8_t& eight, const in... function unpack_2b_from_8b (line 37) | static inline int unpack_2b_from_8b(const uint8_t eight, const int off) { function pack_2b_in_32b (line 42) | static inline void pack_2b_in_32b(const int two, uint32_t& thirty2, cons... function unpack_2b_from_32b (line 48) | static inline int unpack_2b_from_32b(const uint32_t thirty2, const int o... FILE: blockwise_sa.h function hasMoreSuffixes (line 99) | bool hasMoreSuffixes() { function resetSuffixItr (line 114) | void resetSuffixItr() { function suffixItrIsReset (line 127) | bool suffixItrIsReset() { function virtual (line 154) | virtual bool hasMoreBlocks() const = 0; function simulateAllocs (line 233) | static size_t simulateAllocs(const TStr& text, TIndexOffU bucketSz) { function nextBlock_Worker (line 242) | static void nextBlock_Worker(void *vp) { function virtual (line 277) | virtual TIndexOffU nextSuffix() { function virtual (line 369) | virtual bool isReset() { function qsort (line 472) | inline void KarkkainenBlockwiseSA::qsort( function BinarySorting_worker (line 506) | void BinarySorting_worker(void *vp) function TIndexOffU (line 730) | static TIndexOffU suffixLcp(const T& t, TIndexOffU aOff, TIndexOffU bOff) { function TIndexOffU (line 787) | TIndexOffU lookupSuffixZ( FILE: bt2_idx.cpp function string (line 38) | string adjustEbwtBase(const string& cmdline, FILE: bt2_idx.h type EBWT_FLAGS (line 99) | enum EBWT_FLAGS { function init (line 133) | void init( function setOffRate (line 200) | void setOffRate(int __offRate) { function print (line 225) | void print(ostream& out) const { function class (line 283) | class EbwtFileOpenException : public std::runtime_error { function fileSize (line 292) | static inline int64_t fileSize(const char* name) { function initFromTopBot (line 326) | static void initFromTopBot( function initFromRow (line 355) | void initFromRow(index_t row, const EbwtParams& ep, const uint8... function nextSide (line 376) | void nextSide(const EbwtParams& ep) { function repOk (line 404) | bool repOk(const EbwtParams& ep) const { function invalidate (line 414) | void invalidate() { type USE_POPCNT_GENERIC (line 471) | struct USE_POPCNT_GENERIC { function countInU64 (line 505) | inline static int countInU64(int c, uint64_t dw) { function isPacked (line 1193) | bool isPacked() { return packed_; } function index_t (line 1614) | index_t joinedLen(EList& szs) { function index_t (line 1652) | inline index_t* fchr() { return _fchr.get(); } function index_t (line 1653) | inline index_t* ftab() { return _ftab.get(); } function index_t (line 1654) | inline index_t* eftab() { return _eftab.get(); } function index_t (line 1657) | inline index_t* plen() { return _plen.get(); } function index_t (line 1658) | inline index_t* rstarts() { return _rstarts.get(); } function index_t (line 1660) | inline const index_t* fchr() const { return _fchr.get(); } function index_t (line 1661) | inline const index_t* ftab() const { return _ftab.get(); } function index_t (line 1662) | inline const index_t* eftab() const { return _eftab.get(); } function index_t (line 1665) | inline const index_t* plen() const { return _plen.get(); } function index_t (line 1666) | inline const index_t* rstarts() const { return _rstarts.get(); } function saGenomeBoundaryHas (line 1679) | inline const bool saGenomeBoundaryHas( uint64_t key ) const { retur... function saGenomeBoundaryVal (line 1680) | inline const uint32_t saGenomeBoundaryVal( uint64_t key ) const { return... function loadIntoMemory (line 1748) | void loadIntoMemory( function evictFromMemory (line 1773) | void evictFromMemory() { function index_t (line 1794) | index_t ftabSeqToInt( function index_t (line 1823) | index_t ftabHi(index_t i) const { function index_t (line 1842) | static index_t ftabHi( function index_t (line 1863) | index_t ftabLo(index_t i) const { function index_t (line 1876) | index_t ftabLo(const BTDnaString& seq, index_t off) const { function index_t (line 1883) | index_t ftabHi(const BTDnaString& seq, index_t off) const { function ftabLoHi (line 1894) | bool function index_t (line 1921) | static index_t ftabLo( function index_t (line 1944) | index_t tryOffset(index_t elt) const { function index_t (line 1985) | index_t tryOffset( function postReadInit (line 2028) | void postReadInit(EbwtParams& eh) { function print (line 2048) | void print(ostream& out) const { function print (line 2056) | void print(ostream& out, const EbwtParams& eh) const { function index_t (line 2156) | inline index_t countBt2Side(const SideLocus& l, int c) const { function countBt2SideRange (line 2202) | inline void countBt2SideRange( function countBt2SideEx (line 2285) | inline void countBt2SideEx(const SideLocus& l, index_t* arrs) c... function index_t (line 2328) | inline index_t countUpTo(const SideLocus& l, int c) const { function index_t (line 2396) | inline index_t countDownTo(const SideLocus& l, int c) const { function countInU64Ex (line 2441) | inline static void countInU64Ex(uint64_t dw, index_t* arrs) { function countUpToEx (line 2496) | inline void countUpToEx(const SideLocus& l, index_t* arrs) const { function index_t (line 2631) | inline index_t countBt2SideRange2( function rowL (line 2701) | inline int rowL(const SideLocus& l) const { function rowL (line 2711) | inline int rowL(index_t i) const { function inMemoryRepOk (line 2932) | bool inMemoryRepOk(const EbwtParams& eh) const { function repOk (line 2949) | bool repOk(const EbwtParams& eh) const { function string (line 2963) | string get_uid(const string& header) { function get_tid (line 2975) | uint64_t get_tid(const string& stid) { function verbose (line 3074) | void verbose(const string& s) const { function is_read_err (line 3821) | inline bool is_read_err(int fdesc, ssize_t ret, size_t count) { function is_fread_err (line 3832) | inline bool is_fread_err(FILE* file_hd, size_t ret, size_t count) { FILE: bt2_io.h type stat (line 90) | struct stat function else (line 120) | else if(_useMm && !justHeader) { function readEbwtColor (line 821) | bool function readEntireReverse (line 835) | bool FILE: btypes.h type TIndexOffU (line 30) | typedef uint64_t TIndexOffU; type TIndexOff (line 31) | typedef int64_t TIndexOff; type TIndexOffU (line 39) | typedef uint32_t TIndexOffU; type TIndexOff (line 40) | typedef int TIndexOff; FILE: ccnt_lut.cpp function countCnt (line 27) | int countCnt(int by, int c, uint8_t str) { function countCnt_rev (line 39) | int countCnt_rev(int by, int c, uint8_t str) { function initializeCntLut (line 51) | void initializeCntLut() { FILE: centrifuge.cpp function parse_col_fmt (line 268) | static void parse_col_fmt(const string arg, EList& tab_fmt_cols_... function resetOptions (line 285) | static void resetOptions() { type option (line 532) | struct option function printArgDesc (line 701) | static void printArgDesc(ostream& out) { function printUsage (line 737) | static void printUsage(ostream& out) { function parseInt (line 869) | static int parseInt(int lower, int upper, const char *errmsg, const char... function parseInt (line 890) | static int parseInt(int lower, const char *errmsg, const char *arg) { function T (line 898) | T parse(const char *s) { function parsePair (line 909) | pair parsePair(const char *str, char delim) { function parseTuple (line 923) | void parseTuple(const char *str, char delim, EList& ret) { function string (line 932) | static string applyPreset(const string& sorig, Presets& presets) { function parseOption (line 959) | static void parseOption(int next_option, const char *arg) { function parseOptions (line 1495) | static void parseOptions(int argc, const char **argv) { function PatternSourcePerThreadFactory (line 1665) | static PatternSourcePerThreadFactory* type OuterLoopMetrics (line 1690) | struct OuterLoopMetrics { method OuterLoopMetrics (line 1692) | OuterLoopMetrics() { method reset (line 1699) | void reset() { method merge (line 1709) | void merge( type PerfMetrics (line 1739) | struct PerfMetrics { method PerfMetrics (line 1741) | PerfMetrics() : first(true) { reset(); } method reset (line 1746) | void reset() { method merge (line 1769) | void merge( method reportInterval (line 1807) | void reportInterval( method mergeIncrementals (line 2184) | void mergeIncrementals() { function printMmsSkipMsg (line 2232) | static inline void printMmsSkipMsg( function printLenSkipMsg (line 2252) | static inline void printLenSkipMsg( function printLocalScoreMsg (line 2269) | static inline void printLocalScoreMsg( function printEEScoreMsg (line 2288) | static inline void printEEScoreMsg( function multiseedSearchWorker (line 2342) | static void multiseedSearchWorker(void *vp) { function multiseedSearch (line 2762) | static void multiseedSearch( function driver (line 2826) | static void driver( function centrifuge (line 3345) | int centrifuge(int argc, const char **argv) { FILE: centrifuge_build.cpp function resetOptions (line 79) | static void resetOptions() { function printUsage (line 143) | static void printUsage(ostream& out) { type option (line 193) | struct option function T (line 238) | static T parseNumber(T lower, const char *errmsg) { function parseOptions (line 258) | static void parseOptions(int argc, const char **argv) { function deleteIdxFiles (line 379) | static void deleteIdxFiles( function driver (line 399) | static void driver( function centrifuge_build (line 554) | int centrifuge_build(int argc, const char **argv) { FILE: centrifuge_build_main.cpp function main (line 43) | int main(int argc, const char **argv) { FILE: centrifuge_compress.cpp function resetOptions (line 77) | static void resetOptions() { function printUsage (line 134) | static void printUsage(ostream& out) { type option (line 187) | struct option function parseNumber (line 229) | static int parseNumber(T lower, const char *errmsg) { function parseOptions (line 249) | static void parseOptions(int argc, const char **argv) { function print_fasta_record (line 353) | static void print_fasta_record( type RegionSimilar (line 392) | struct RegionSimilar { method reset (line 400) | void reset() { type Region (line 412) | struct Region { method match_size (line 421) | uint32_t match_size() { method reset (line 426) | void reset() { type RegionToMerge (line 436) | struct RegionToMerge { method reset (line 440) | void reset() { function driver (line 450) | static void driver( function centrifuge_compress (line 1271) | int centrifuge_compress(int argc, const char **argv) { function main (line 1406) | int main(int argc, const char **argv) { FILE: centrifuge_inspect.cpp type option (line 62) | struct option function printUsage (line 83) | static void printUsage(ostream& out) { function parseInt (line 124) | static int parseInt(int lower, const char *errmsg) { function parseOptions (line 145) | static void parseOptions(int argc, char **argv) { function print_fasta_record (line 191) | static void print_fasta_record( function count_idx_kmers (line 218) | static uint64_t count_idx_kmers ( Ebwt& ebwt) function print_ref_sequence (line 301) | static void print_ref_sequence( function print_ref_sequences (line 334) | static void print_ref_sequences( function print_index_sequences (line 369) | static void print_index_sequences(ostream& fout, Ebwt& ebwt) function print_index_sequence_names (line 434) | static void print_index_sequence_names(const string& fname, ostream& fout) function print_index_summary (line 447) | static void print_index_summary( function driver (line 487) | static void driver( function main (line 609) | int main(int argc, char **argv) { FILE: centrifuge_main.cpp function main (line 42) | int main(int argc, const char **argv) { FILE: centrifuge_report.cpp function printUsage (line 36) | static void printUsage(ostream& out) { class Pair2ndComparator (line 48) | class Pair2ndComparator{ function driver (line 57) | static void driver( function main (line 167) | int main(int argc, const char **argv) { FILE: classifier.h function reset (line 47) | void reset() { function finalize (line 86) | void finalize( function virtual (line 211) | virtual function getGenomeIdx (line 573) | bool getGenomeIdx( function reportUnclassified (line 619) | void reportUnclassified( AlnSinkWrap& sink ) function searchForwardAndReverse (line 646) | void searchForwardAndReverse( function addHitToHitMap (line 982) | size_t addHitToHitMap( type compareBWTHits (line 1058) | struct compareBWTHits { FILE: diff_sample.cpp type sampleEntry (line 22) | struct sampleEntry FILE: diff_sample.h type sampleEntry (line 61) | struct sampleEntry { type sampleEntry (line 69) | struct sampleEntry function dcRepOk (line 77) | bool dcRepOk(T v, EList& ds) { function increasing (line 109) | bool increasing(T* ts, size_t limit) { function hasDifference (line 121) | inline bool hasDifference(T *ds, T d, T v, T diff) { function popCount (line 414) | unsigned int popCount(T i) { function myLog2 (line 427) | unsigned int myLog2(T i) { function simulateAllocs (line 480) | static size_t simulateAllocs(const TStr& text, uint32_t v) { function modv (line 493) | uint32_t modv(TIndexOffU i) const { return (uint32_t)(i & ~_vmask); } function TIndexOffU (line 494) | TIndexOffU divv(TIndexOffU i) const { return i >> _log2v; } function print (line 513) | void print(ostream& out) { function verbose (line 536) | void verbose(const string& s) const { function suffixSameUpTo (line 661) | inline bool suffixSameUpTo( function VSorting_worker (line 690) | void VSorting_worker(void *vp) FILE: dp_framer.cpp function testCaseFindMateAnchorLeft (line 364) | static void testCaseFindMateAnchorLeft( function testCaseFindMateAnchorRight (line 424) | static void testCaseFindMateAnchorRight( function main (line 483) | int main(void) { FILE: dp_framer.h type DPRect (line 59) | struct DPRect { function entirelyTrimmed (line 94) | bool entirelyTrimmed() const { function initIval (line 112) | void initIval(Interval& iv) { function class (line 122) | class DynProgFramer { FILE: ds.cpp function main (line 57) | int main(void) { FILE: ds.h function class (line 37) | class MemoryTally { function xfer (line 394) | void xfer(EList& o) { function ensure (line 440) | inline void ensure(size_t thresh) { function reserveExact (line 450) | inline void reserveExact(size_t newsz) { function push_back (line 469) | void push_back(const T& el) { function expand (line 478) | void expand() { function fill (line 487) | void fill(size_t begin, size_t end, const T& v) { function fill (line 498) | void fill(const T& v) { function fillZero (line 507) | void fillZero(size_t begin, size_t end) { function fillZero (line 515) | void fillZero() { function resizeNoCopy (line 523) | void resizeNoCopy(size_t sz) { function resize (line 537) | void resize(size_t sz) { function resizeExact (line 553) | void resizeExact(size_t sz) { function erase (line 566) | void erase(size_t idx) { function erase (line 577) | void erase(size_t idx, size_t len) { function insert (line 592) | void insert(const T& el, size_t idx) { function insert (line 606) | void insert(const EList& l, size_t idx) { function pop_back (line 623) | void pop_back() { function clear (line 631) | void clear() { function T (line 639) | inline T& back() { function reverse (line 647) | void reverse() { function T (line 661) | inline const T& back() const { function isSuperset (line 699) | bool isSuperset(const EList& o) const { function T (line 724) | inline T& operator[](size_t i) { function T (line 732) | inline const T& operator[](size_t i) const { function T (line 740) | inline T& get(size_t i) { function T (line 747) | inline const T& get(size_t i) const { function T (line 763) | const T& getSlow(size_t i) const { function sortPortion (line 770) | void sortPortion(size_t begin, size_t num) { function shufflePortion (line 784) | void shufflePortion(size_t begin, size_t num, RandomSource& rnd) { function sort (line 800) | void sort() { function remove (line 825) | void remove(size_t idx) { function T (line 837) | T *ptr() { return list_; } function T (line 842) | const T *ptr() const { return list_; } function setCat (line 847) | void setCat(int cat) { function bsearchLoBound (line 863) | size_t bsearchLoBound(const T& el) const { function lazyInitExact (line 896) | void lazyInitExact(size_t sz) { function T (line 907) | T *alloc(size_t sz) { function free (line 919) | void free() { function expandCopy (line 935) | void expandCopy(size_t thresh) { function expandCopyExact (line 946) | void expandCopyExact(size_t newsz) { function expandNoCopy (line 968) | void expandNoCopy(size_t thresh) { function expandNoCopyExact (line 980) | void expandNoCopyExact(size_t newsz) { function xfer (line 1096) | void xfer(ELList& o) { function expand (line 1123) | void expand() { function resize (line 1133) | void resize(size_t sz) { function clear (line 1148) | void clear() { function setCat (line 1236) | void setCat(int cat) { function free (line 1283) | void free() { function expandCopy (line 1296) | void expandCopy(size_t thresh) { function expandNoCopy (line 1318) | void expandNoCopy(size_t thresh) { function xfer (line 1434) | void xfer(ELLList& o) { function expand (line 1461) | void expand() { function resize (line 1471) | void resize(size_t sz) { function clear (line 1484) | void clear() { function setCat (line 1572) | void setCat(int cat) { function free (line 1619) | void free() { function expandCopy (line 1632) | void expandCopy(size_t thresh) { function expandNoCopy (line 1654) | void expandNoCopy(size_t thresh) { function insert (line 1776) | bool insert(const T& el) { function contains (line 1797) | bool contains(const T& el) const { function remove (line 1818) | void remove(const T& el) { function resize (line 1835) | void resize(size_t sz) { function clear (line 1843) | void clear() { cur_ = 0; } function setCat (line 1853) | void setCat(int cat) { function xfer (line 1862) | void xfer(ESet& o) { function T (line 1877) | T *ptr() { return list_; } function T (line 1882) | const T *ptr() const { return list_; } function free (line 1901) | void free() { function scanLoBound (line 1914) | size_t scanLoBound(const T& el) const { function bsearchLoBound (line 1928) | size_t bsearchLoBound(const T& el) const { function insert (line 1977) | void insert(const T& el, size_t idx) { function erase (line 1994) | void erase(size_t idx) { function expandCopy (line 2007) | void expandCopy(size_t thresh) { function xfer (line 2107) | void xfer(ELSet& o) { function expand (line 2134) | void expand() { function resize (line 2144) | void resize(size_t sz) { function clear (line 2159) | void clear() { function ESet (line 2167) | inline ESet& back() { function ESet (line 2175) | inline const ESet& back() const { function ESet (line 2235) | const ESet& getSlow(size_t i) const { function ESet (line 2247) | const ESet *ptr() const { return list_; } function setCat (line 2252) | void setCat(int cat) { function free (line 2299) | void free() { function expandCopy (line 2312) | void expandCopy(size_t thresh) { function expandNoCopy (line 2334) | void expandNoCopy(size_t thresh) { function list_ (line 2392) | list_(NULL) { function insert (line 2444) | bool insert(const std::pair& el) { function contains (line 2465) | bool contains(const K& el) const { function containsEx (line 2482) | bool containsEx(const K& el, size_t& i) const { function remove (line 2501) | void remove(const K& el) { function resize (line 2518) | void resize(size_t sz) { function clear (line 2541) | void clear() { cur_ = 0; } function free (line 2560) | void free() { function scanLoBound (line 2573) | size_t scanLoBound(const K& el) const { function bsearchLoBound (line 2587) | size_t bsearchLoBound(const K& el) const { function insert (line 2635) | void insert(const std::pair& el, size_t idx) { function erase (line 2652) | void erase(size_t idx) { function expandCopy (line 2665) | void expandCopy(size_t thresh) { function clear (line 2702) | void clear() { function alloc (line 2709) | size_t alloc() { function resize (line 2738) | void resize(size_t sz) { function pop (line 2753) | void pop() { function T (line 2767) | const T& operator[](size_t off) const { function clear (line 2791) | void clear() { function reset (line 2798) | void reset() { function set (line 2806) | void set(size_t off) { function test (line 2817) | bool test(size_t off) const { function resize (line 2834) | void resize(size_t off) { function T (line 2885) | T top() { function T (line 2893) | T pop() { function T (line 2964) | const T& operator[](size_t i) const { function repOkNode (line 2980) | bool repOkNode(size_t cur) const { function clear (line 3001) | void clear() { function class (line 3015) | class Pool { function full (line 3055) | bool full() { return cur_ == pages_.size(); } function clear (line 3060) | void clear() { function free (line 3068) | void free() { function add (line 3132) | bool add(Pool& p, const EList& os) { function copy (line 3150) | bool copy( function addFill (line 3173) | bool addFill(Pool& p, size_t num, const T& o) { function clear (line 3191) | void clear() { function T (line 3224) | inline const T& getConst(size_t i) const { function T (line 3234) | inline T& get(size_t i) { function T (line 3246) | inline T& back() { function T (line 3257) | inline const T& back() const { function ensure (line 3284) | bool ensure(Pool& p, size_t num) { function init (line 3352) | void init(const EListSlice& sl, size_t first, size_t last) { function reset (line 3363) | void reset() { function T (line 3371) | inline const T& get(size_t i) const { function T (line 3380) | inline T& get(size_t i) { function T (line 3389) | inline T& operator[](size_t i) { function T (line 3398) | inline const T& operator[](size_t i) const { function setLength (line 3449) | void setLength(size_t nlen) { function init (line 3484) | void init(const PListSlice& sl, size_t first, size_t last) { function reset (line 3495) | void reset() { function T (line 3503) | inline const T& get(size_t i) const { function T (line 3512) | inline T& get(size_t i) { function T (line 3521) | inline T& operator[](size_t i) { function T (line 3530) | inline const T& operator[](size_t i) const { function setLength (line 3581) | void setLength(size_t nlen) { type RedBlackNode (line 3599) | typedef RedBlackNode TNode; function RedBlackNode (line 3612) | RedBlackNode *grandparent() { function RedBlackNode (line 3619) | RedBlackNode *uncle() { function replaceChild (line 3638) | void replaceChild(RedBlackNode* ol, RedBlackNode* nw) { function operator (line 3669) | bool operator<(const TNode& o) const { return key < o.key; } function operator (line 3674) | bool operator>(const TNode& o) const { return key > o.key; } function operator (line 3679) | bool operator==(const TNode& o) const { return key == o.key; } function operator (line 3684) | bool operator<(const K& okey) const { return key < okey; } function operator (line 3689) | bool operator>(const K& okey) const { return key > okey; } function operator (line 3694) | bool operator==(const K& okey) const { return key == okey; } type RedBlackNode (line 3707) | typedef RedBlackNode TNode; function TNode (line 3721) | inline TNode* lookup(const K& key) const { function clear (line 3806) | void clear() { function addNode (line 3833) | bool addNode(Pool& p, TNode*& node) { function TNode (line 3861) | const TNode* root() const { return root_; } function redBlackRepOk (line 3869) | bool redBlackRepOk(TNode* n) { function redBlackRepOk (line 3899) | bool redBlackRepOk( function leftRotate (line 3950) | void leftRotate(TNode* n) { function rightRotate (line 3977) | void rightRotate(TNode* n) { function addNode (line 4002) | void addNode(TNode* n, TNode* parent, bool leftChild) { function toList (line 4111) | void toList(EList& l) { function operator (line 4142) | bool operator==(const Pair& o) const { function operator (line 4146) | bool operator<(const Pair& o) const { function operator (line 4167) | bool operator==(const Triple& o) const { function operator (line 4171) | bool operator<(const Triple& o) const { function init (line 4201) | void init( function operator (line 4210) | bool operator==(const Quad& o) const { function operator (line 4214) | bool operator<(const Quad& o) const { function head (line 4249) | head(NULL) { function delete_node (line 4282) | void delete_node(LinkedEListNode *node) { FILE: edit.cpp function ostream (line 31) | ostream& operator<< (ostream& os, const Edit& e) { FILE: edit.h type Edit (line 65) | struct Edit { function reset (line 95) | void reset() { function hasN (line 171) | bool hasN() const { function operator (line 195) | int operator== (const Edit &rhs) const { function isReadGap (line 210) | bool isReadGap() const { function isGap (line 227) | bool isGap() const { function numGaps (line 240) | static size_t numGaps(const EList& es) { FILE: endian_swap.h function currentlyBigEndian (line 29) | static inline bool currentlyBigEndian() { function endianSwapU16 (line 37) | static inline uint16_t endianSwapU16(uint16_t u) { function endianSwapU32 (line 47) | static inline uint32_t endianSwapU32(uint32_t u) { function endianSwapU64 (line 59) | static inline uint64_t endianSwapU64(uint64_t u) { function index_t (line 76) | inline index_t endianSwapIndex(index_t u) { function endianSwapI16 (line 89) | static inline int16_t endianSwapI16(int16_t i) { function endianizeU16 (line 100) | static inline uint16_t endianizeU16(uint16_t u, bool toBig) { function endianizeI16 (line 111) | static inline int16_t endianizeI16(int16_t i, bool toBig) { function endianSwapI32 (line 121) | static inline int32_t endianSwapI32(int32_t i) { function endianizeU32 (line 134) | static inline uint32_t endianizeU32(uint32_t u, bool toBig) { function endianizeI32 (line 145) | static inline int32_t endianizeI32(int32_t i, bool toBig) { FILE: evaluation/centrifuge_evaluate.py function read_taxonomy_tree (line 13) | def read_taxonomy_tree(tax_file): function compare_scm (line 26) | def compare_scm(centrifuge_out, true_out, taxonomy_tree, rank): function compare_abundance (line 117) | def compare_abundance(centrifuge_out, true_out, taxonomy_tree, debug): function sql_execute (line 166) | def sql_execute(sql_db, sql_query): function create_sql_db (line 180) | def create_sql_db(sql_db): function write_analysis_data (line 232) | def write_analysis_data(sql_db, genome_name, database_name): function evaluate (line 278) | def evaluate(index_base, FILE: evaluation/centrifuge_simulate_reads.py function reverse_complement (line 30) | def reverse_complement(seq): function get_genome_seq_id (line 58) | def get_genome_seq_id(genome_name): class ErrRandomSource (line 68) | class ErrRandomSource: method __init__ (line 69) | def __init__(self, prob = 0.0, size = 1 << 20): method getRand (line 79) | def getRand(self): function read_genomes (line 88) | def read_genomes(genomes_file, seq2taxID): function read_transcript (line 118) | def read_transcript(genomes_seq, gtf_file, frag_len): function generate_rna_expr_profile (line 183) | def generate_rna_expr_profile(expr_profile_type, num_transcripts = 10000): function generate_dna_expr_profile (line 208) | def generate_dna_expr_profile(expr_profile_type, num_genomes): function getSamAlignment (line 233) | def getSamAlignment(dna, exons, genome_seq, trans_seq, frag_pos, read_le... function samRepOk (line 457) | def samRepOk(genome_seq, read_seq, chr, pos, cigar, XM, NM, MD, Zs, max_... function simulate_reads (line 585) | def simulate_reads(index_fname, base_fname, \ FILE: evaluation/test/centrifuge_evaluate_mason.py function read_taxonomy_tree (line 13) | def read_taxonomy_tree(tax_file): function compare_scm (line 26) | def compare_scm(centrifuge_out, true_out, taxonomy_tree, rank): function evaluate (line 128) | def evaluate(index_base, FILE: fast_mutex.h function lock (line 120) | inline void lock() FILE: filebuf.h function isnewline (line 35) | static inline bool isnewline(int c) { function isspace_notnl (line 43) | static inline bool isspace_notnl(int c) { function class (line 57) | class FileBuf { function isOpen (line 84) | bool isOpen() { function close (line 91) | void close() { function get (line 104) | int get() { function eof (line 117) | bool eof() { function newFile (line 124) | void newFile(FILE *in) { function newFile (line 136) | void newFile(std::ifstream *__inf) { function newFile (line 148) | void newFile(std::istream *__ins) { function reset (line 161) | void reset() { function peek (line 181) | int peek() { function gets (line 222) | size_t gets(char *buf, size_t len) { function get (line 252) | size_t get(char *buf, size_t len) { function getPastWhitespace (line 268) | int getPastWhitespace() { function getPastNewline (line 279) | int getPastNewline() { function peekPastNewline (line 293) | int peekPastNewline() { function peekUptoNewline (line 306) | int peekUptoNewline() { function resetLastN (line 402) | void resetLastN() { function copyLastN (line 410) | size_t copyLastN(char *buf) { function class (line 456) | class BitpairOutFileBuf { function class (line 524) | class OutFileBuf { function write (line 586) | void write(char c) { function writeString (line 595) | void writeString(const std::string& s) { function writeChars (line 640) | void writeChars(const char * s, size_t len) { function writeChars (line 661) | void writeChars(const char * s) { function close (line 668) | void close() { function reset (line 680) | void reset() { function flush (line 685) | void flush() { FILE: formats.h type file_format (line 29) | enum file_format { FILE: group_walk.h function init (line 106) | void init(TIndexOffU tf, size_t len_, const T& o) { function reset (line 113) | void reset() { topf = std::numeric_limits::max(); } function map (line 140) | GroupWalkState(int cat) : map(cat) { type WalkMetrics (line 155) | struct WalkMetrics { function reset (line 177) | void reset() { function reset (line 200) | void reset() { function init (line 208) | void init( function operator (line 226) | bool operator==(const GWElt& o) const { function operator (line 238) | bool operator!=(const GWElt& o) const { function reset (line 261) | void reset() { function init (line 269) | void init( function init (line 313) | void init( function reset (line 333) | void reset() { function repOk (line 350) | bool repOk(const SARangeWithOffs& sa) const { function repOkBasic (line 374) | bool repOkBasic() { function setReported (line 382) | void setReported(index_t i) { function reported (line 392) | bool reported(index_t i) const { function repOk (line 711) | bool repOk( function repOkBasic (line 739) | bool repOkBasic() { function repOkMapInclusive (line 748) | bool repOkMapInclusive(GWHit& hit, index_t range) const { function index_t (line 783) | index_t off( function index_t (line 797) | index_t map(index_t i) const { function setOff (line 830) | void setOff( function reset (line 1021) | void reset() { function initMap (line 1033) | void initMap(size_t newsz) { function doneReporting (line 1045) | bool doneReporting(const GWHit& hit) const { function doneResolving (line 1056) | bool doneResolving(const SARangeWithOffs& sa) const { function reset (line 1089) | void reset() { function init (line 1097) | void init( function advanceElement (line 1154) | bool advanceElement( function repOk (line 1220) | bool repOk(const SARangeWithOffs& sa) const { FILE: hi_aligner.h function reset (line 63) | void reset() { function init (line 73) | void init( function operator (line 103) | bool operator<(const BWTHit& o) const { function repOk (line 124) | bool repOk(const Read& rd) const { function reset (line 154) | void reset() { function init (line 164) | void init( function done (line 178) | bool done() { function done (line 188) | void done(bool done) { function offsetSize (line 197) | size_t offsetSize() { return _partialHits.size(); } function numPartialSearch (line 198) | size_t numPartialSearch() { return _numPartialSearch; } function numActualPartialSearch (line 199) | size_t numActualPartialSearch() function width (line 205) | bool width(index_t offset_) { function hasGenomeCoords (line 210) | bool hasGenomeCoords(index_t offset_) { function hasAllGenomeCoords (line 220) | bool hasAllGenomeCoords() { function index_t (line 233) | index_t minWidth(index_t& offset) const { function searchScore (line 252) | int64_t searchScore(index_t minK) { function adjustOffset (line 272) | bool adjustOffset(index_t minK) { function setOffset (line 285) | void setOffset(index_t offset) { function trim5 (line 470) | void trim5(index_t trim5) { _trim5 = trim5; } function trim3 (line 471) | void trim3(index_t trim3) { _trim3 = trim3; } function contains (line 508) | bool contains(const GenomeHit& other) const { function reset (line 639) | struct HIMetrics { function init (line 655) | void init( function initReads (line 765) | void initReads(Read *rds[2], bool nofw[2], bool norc[2], TAlScore minsc[... FILE: hier_idx.h type Ebwt (line 38) | typedef Ebwt PARENT_CLASS; function sanityCheckAll (line 275) | void sanityCheckAll(int reverse) const { type Ebwt (line 1074) | typedef Ebwt PARENT_CLASS; function loadIntoMemory (line 1184) | void loadIntoMemory( function evictFromMemory (line 1222) | void evictFromMemory() { function sanityCheckAll (line 1231) | void sanityCheckAll(int reverse) const { function clearLocalEbwts (line 1270) | void clearLocalEbwts() { type EList (line 1382) | typedef EList EList_RefRecord; type stat (line 1737) | struct stat function else (line 1767) | else if(this->_useMm && !justHeader) { FILE: hyperloglogplus.h function linearCounting (line 47) | double linearCounting(uint32_t m, uint32_t v) { function ranhash (line 60) | inline uint64_t ranhash (uint64_t u) { function murmurhash3_finalizer (line 72) | inline uint64_t murmurhash3_finalizer (uint64_t key) { function alpha (line 87) | double alpha(uint32_t m) { function calculateEstimate (line 103) | double calculateEstimate(vector array) { function countZeros (line 112) | uint32_t countZeros(vector s) { function clz_manual (line 161) | static int clz_manual(uint64_t x) function clz (line 176) | inline uint32_t clz(const uint32_t x) { function clz (line 180) | inline uint32_t clz(const uint64_t x) { function clz_log2 (line 191) | uint32_t clz_log2(const uint64_t w) { type set (line 201) | typedef set SparseListType; type HashSize (line 202) | typedef uint64_t HashSize; type T_KEY (line 209) | typedef uint64_t T_KEY; function add (line 258) | void add(T_KEY item) { function add (line 267) | void add(T_KEY item, size_t size) { function add (line 306) | void add(vector words) { function reset (line 315) | void reset() { function switchToNormalRepresentation (line 324) | void switchToNormalRepresentation() { function addToRegisters (line 343) | void addToRegisters(const SparseListType &sparseList) { function merge (line 362) | void merge(const HyperLogLogPlusMinus* other) { function get_index (line 444) | uint32_t get_index(const T hash_value, const uint8_t p, const uint8_t si... function get_index (line 451) | inline uint32_t get_index(const uint64_t hash_value, const uint8_t p) co... function get_index (line 455) | inline uint32_t get_index(const uint32_t hash_value, const uint8_t p) co... function T (line 460) | T get_trailing_ones(const uint8_t p) const { function get_rank (line 465) | uint8_t get_rank(const T hash_value, const uint8_t p) const { function initRawEstimateData (line 477) | void initRawEstimateData() { function initBiasData (line 498) | void initBiasData() { function getEstimateBias (line 525) | double getEstimateBias(double estimate) { function encodeHashIn32Bit (line 556) | uint32_t encodeHashIn32Bit(uint64_t hash_value) { function else (line 582) | struct idx_n_rank { FILE: ls.cpp function main (line 30) | int main(void) { FILE: ls.h function update_group (line 58) | inline void update_group(T *pl, T *pm) { function select_sort_split (line 73) | inline void select_sort_split(T *p, T n) { function T (line 100) | inline T choose_pivot(T *p, T n) { function sort_split (line 125) | inline void sort_split(T *p, T n) function bucketsort (line 187) | inline void bucketsort(T *x, T *p, T n, T k) function T (line 228) | inline T transform(T *x, T *p, T n, T k, T l, T q) FILE: mask.h function matchesEx (line 37) | static inline int matchesEx(int i, int j) { function matches (line 48) | static inline bool matches(int i, int j) { function randFromMask (line 56) | static inline int randFromMask(RandomSource& rnd, int mask) { FILE: multikey_qsort.h function swap (line 37) | inline void swap(TStr& s, size_t slen, TPos a, TPos b) { function swap (line 47) | inline void swap(TVal* s, size_t slen, TPos a, TPos b) { function vecswap (line 105) | inline void vecswap(TStr& s, size_t slen, TPos i, TPos j, TPos n, TPos b... function vecswap (line 123) | inline void vecswap(TVal *s, size_t slen, TPos i, TPos j, TPos n, TPos b... function vecswap2 (line 147) | inline void vecswap2( function vecswap2 (line 175) | inline void vecswap2(TVal* s, size_t slen, TVal* s2, TPos i, TPos j, TPo... function sanityCheckInputSufs (line 323) | static inline void sanityCheckInputSufs(TIndexOffU *s, size_t slen) { type QSortRange (line 506) | struct QSortRange { function get_uint8 (line 855) | uint8_t get_uint8(const TStr& t, size_t off) { function char_at_suf_u8 (line 874) | inline int char_at_suf_u8( FILE: outq.cpp function main (line 107) | int main(void) { FILE: outq.h function class (line 37) | class OutputQueue { function class (line 123) | class OutputQueueMark { FILE: pat.cpp function PatternSource (line 48) | PatternSource* PatternSource::patsrcFromStrings( function parseQuals (line 650) | int parseQuals( function ASSERT_ONLY (line 986) | ASSERT_ONLY(int pk =) peekToEndOfLine(fb_); function wrongQualityFormat (line 1505) | void wrongQualityFormat(const BTString& read_name) { function tooFewQualities (line 1513) | void tooFewQualities(const BTString& read_name) { function tooManyQualities (line 1519) | void tooManyQualities(const BTString& read_name) { type SRA_Read (line 1527) | struct SRA_Read { method reset (line 1532) | void reset() { type SRA_Data (line 1541) | struct SRA_Data { method SRA_Data (line 1550) | SRA_Data() { method isFull (line 1558) | bool isFull() { method isEmpty (line 1564) | bool isEmpty() { method advanceReadPos (line 1580) | void advanceReadPos() { method advanceWritePos (line 1585) | void advanceWritePos() { function SRA_IO_Worker (line 1591) | static void SRA_IO_Worker(void *vp) FILE: pat.h function genRandSeed (line 55) | static inline uint32_t genRandSeed(const BTDnaString& qry, type PatternParams (line 96) | struct PatternParams { function class (line 141) | class PatternSource { function class (line 279) | class PairedPatternSource { function class (line 344) | class PairedSoloPatternSource : public PairedPatternSource { function class (line 419) | class PairedDualPatternSource : public PairedPatternSource { function class (line 511) | class PatternSourcePerThread { function class (line 559) | class PatternSourcePerThreadFactory { function class (line 590) | class WrappedPatternSourcePerThread : public PatternSourcePerThread { function class (line 617) | class WrappedPatternSourcePerThreadFactory : public PatternSourcePerThre... function getOverNewline (line 649) | static inline int getOverNewline(FileBuf& in) { function peekOverNewline (line 658) | static inline int peekOverNewline(FileBuf& in) { function getToEndOfLine (line 670) | static inline int getToEndOfLine(FileBuf& in) { function peekToEndOfLine (line 685) | static inline int peekToEndOfLine(FileBuf& in) { function class (line 707) | class VectorPatternSource : public PatternSource { function class (line 757) | class BufferedFilePatternSource : public PatternSource { function class (line 936) | class FastaPatternSource : public BufferedFilePatternSource { function tokenizeQualLine (line 1007) | static inline bool tokenizeQualLine( function class (line 1025) | class TabbedPatternSource : public BufferedFilePatternSource { function class (line 1112) | class QseqPatternSource : public BufferedFilePatternSource { function class (line 1214) | class FastaContinuousPatternSource : public BufferedFilePatternSource { function virtual (line 1225) | virtual void reset() { function virtual (line 1330) | virtual void resetForNextFile() { function class (line 1360) | class FastqPatternSource : public BufferedFilePatternSource { function virtual (line 1449) | virtual void resetForNextFile() { function class (line 1478) | class RawPatternSource : public BufferedFilePatternSource { function namespace (line 1624) | namespace ngs { function namespace (line 1629) | namespace tthread { type SRA_Data (line 1633) | struct SRA_Data function class (line 1638) | class SRAPatternSource : public PatternSource { function virtual (line 1734) | virtual void reset() { FILE: pe.cpp function testCaseClassify (line 361) | void testCaseClassify( function testCaseOtherMate (line 401) | void testCaseOtherMate( function main (line 466) | int main(int argc, char **argv) { FILE: pe.h function pePolicyCompat (line 102) | static inline bool pePolicyCompat( function pePolicyMateDir (line 130) | static inline void pePolicyMateDir( function class (line 169) | class PairedEndPolicy { function reset (line 201) | void reset() { function init (line 208) | void init( function peClassifyPair (line 268) | int peClassifyPair( FILE: presets.h function class (line 34) | class Presets { function class (line 52) | class PresetsV0 : public Presets { FILE: processor_support.h type regs_t (line 23) | struct regs_t {unsigned int EAX, EBX, ECX, EDX;} function class (line 26) | class ProcessorSupport { FILE: qual.h function phredcToPhredq (line 31) | static inline uint8_t phredcToPhredq(char c) { function solexaToPhred (line 45) | static inline uint8_t solexaToPhred(int sol) { function class (line 51) | class SimplePhredPenalty { function class (line 64) | class MaqPhredPenalty { function mmPenalty (line 77) | static inline uint8_t mmPenalty(bool maq, uint8_t qual) { function delPenalty (line 85) | static inline uint8_t delPenalty(bool maq, uint8_t qual) { function insPenalty (line 93) | static inline uint8_t insPenalty(bool maq, uint8_t qual_left, uint8_t qu... function charToPhred33 (line 105) | inline static char charToPhred33(char c, bool solQuals, bool phred64Qual... function intToPhred33 (line 152) | inline static char intToPhred33(int iQ, bool solQuals) { function roundPenalty (line 173) | inline static uint8_t roundPenalty(uint8_t p) { function penaltiesAt (line 183) | inline static uint8_t penaltiesAt(size_t off, uint8_t *q, function loPenaltyAt (line 217) | inline static uint8_t loPenaltyAt(size_t off, int alts, FILE: random_source.cpp function main (line 69) | int main(void) { FILE: random_source.h function class (line 34) | class RandomSource { function nextU32 (line 52) | uint32_t nextU32() { function nextU64 (line 63) | uint64_t nextU64() { function nextU32Range (line 75) | uint32_t nextU32Range(uint32_t lo, uint32_t hi) { function nextU2 (line 86) | uint32_t nextU2() { function nextBool (line 99) | bool nextBool() { function nextFromProbs (line 115) | uint32_t nextFromProbs( function nextFloat (line 128) | float nextFloat() { function nextU32 (line 133) | static uint32_t nextU32(uint32_t last, function class (line 154) | class RandomSource { // Mersenne Twister random number generator function reset (line 173) | void reset() { function virtual (line 179) | virtual ~RandomSource() { } function nextBool (line 188) | bool nextBool() { function nextU32 (line 195) | inline uint32_t nextU32() { function nextFloat (line 213) | float nextFloat() { function twiddle (line 229) | uint32_t twiddle(uint32_t u, uint32_t v) { FILE: random_util.h function class (line 32) | class Random1toN { function reset (line 77) | void reset() { function T (line 86) | T next(RandomSource& rnd) { function setDone (line 171) | void setDone() { assert(inited()); cur_ = n_; } FILE: read.h type rna_strandness_format (line 30) | enum rna_strandness_format { type TReadId (line 38) | typedef uint64_t TReadId; type TReadOff (line 39) | typedef size_t TReadOff; type TAlScore (line 40) | typedef int64_t TAlScore; function Read (line 47) | struct Read { function reset (line 53) | void reset() { function finalize (line 85) | void finalize() { function init (line 98) | void init( function constructRevComps (line 138) | void constructRevComps() { function constructReverses (line 156) | void constructReverses() { function fixMateName (line 171) | void fixMateName(int i) { function dump (line 200) | void dump(std::ostream& os) const { function same (line 258) | static bool same( function getc (line 298) | int getc(TReadOff off5p, bool fw) const { function getq (line 307) | int getq(TReadOff off5p) const { type FmStringOp (line 367) | struct FmStringOp { function back (line 378) | struct FmString { function reset (line 432) | struct PerReadMetrics { type timeval (line 463) | struct timeval type timezone (line 464) | struct timezone FILE: read_qseq.cpp function ASSERT_ONLY (line 250) | ASSERT_ONLY(int c =) fb_.get(); FILE: ref_coord.cpp function ostream (line 25) | ostream& operator<<(ostream& out, const Interval& c) { function ostream (line 30) | ostream& operator<<(ostream& out, const Coord& c) { FILE: ref_coord.h type TRefId (line 28) | typedef int64_t TRefId; type TRefOff (line 29) | typedef int64_t TRefOff; function class (line 36) | class Coord { function init (line 49) | void init(TRefId rf, TRefOff of, bool fw) { function init (line 58) | void init(const Coord& c) { function operator (line 67) | bool operator==(const Coord& o) const { function operator (line 78) | bool operator<(const Coord& o) const { function operator (line 91) | bool operator>=(const Coord& o) const { function operator (line 100) | bool operator>(const Coord& o) const { function operator (line 113) | bool operator<=(const Coord& o) const { function reset (line 120) | void reset() { function fw (line 143) | bool fw() const { function within (line 168) | bool within(int64_t len, int64_t inbegin, int64_t inend) const { function setRef (line 176) | inline void setRef(TRefId id) { ref_ = id; } function setOff (line 177) | inline void setOff(TRefOff off) { off_ = off; } function adjustOff (line 179) | inline void adjustOff(TRefOff off) { off_ += off; } function class (line 193) | class Interval { FILE: ref_read.cpp function RefRecord (line 28) | RefRecord fastaRefReadSize( function printRecords (line 198) | static void function reverseRefRecords (line 210) | void reverseRefRecords( function fastaRefReadSizes (line 277) | std::pair FILE: ref_read.h function class (line 38) | class RefTooLongException : public exception { function write (line 94) | void write(std::ostream& out, bool be) { type RefReadInParams (line 114) | struct RefReadInParams { FILE: reference.cpp type stat (line 74) | struct stat FILE: reference.h function class (line 59) | class BitPairReference { FILE: scoring.cpp function main (line 172) | int main() { FILE: scoring.h function class (line 96) | class Scoring { function setMatchBonus (line 186) | void setMatchBonus(int bonus) { function setMmPen (line 196) | void setMmPen(int mmType_, int mmpMax_, int mmpMin_) { function setNPen (line 206) | void setNPen(int nType, int n) { function linearFunc (line 230) | static float linearFunc(int64_t x, float cnst, float lin) { function mm (line 240) | inline int mm(int rdc, int refm, int q) const { function score (line 249) | inline int score(int rdc, int refm, int q) const { function score (line 266) | inline int score(int rdc, int refm, int q, int& ns) const { function mm (line 284) | inline int mm(int rdc, int q) const { function mm (line 293) | inline int mm(int q) const { function match (line 310) | inline int64_t match(int q) const { function perfectScore (line 318) | inline int64_t perfectScore(size_t rdlen) const { function n (line 337) | inline int n(int q) const { function ins (line 348) | inline int ins(int ext) const { function del (line 359) | inline int del(int ext) const { function Scoring (line 493) | static Scoring base1() { FILE: sequence_io.h function parseFastaLens (line 38) | void parseFastaLens( function parseFasta (line 68) | void parseFasta( function parseFastas (line 108) | void parseFastas( FILE: shmem.cpp function notifySharedMem (line 35) | void notifySharedMem(void *mem, size_t len) { function waitSharedMem (line 43) | void waitSharedMem(void *mem, size_t len) { FILE: simple_func.cpp function SimpleFunc (line 42) | SimpleFunc SimpleFunc::parse( FILE: simple_func.h function class (line 44) | class SimpleFunc { function init (line 54) | void init(int type, double I, double X, double C, double L) { function init (line 58) | void init(int type, double C, double L) { function setType (line 64) | void setType (int type ) { type_ = type; } function setMin (line 65) | void setMin (double mn) { I_ = mn; } function setMax (line 66) | void setMax (double mx) { X_ = mx; } function setConst (line 67) | void setConst(double co) { C_ = co; } function setCoeff (line 68) | void setCoeff(double ce) { L_ = ce; } function mult (line 76) | void mult(double x) { function reset (line 83) | void reset() { type_ = 0; } FILE: sse_util.h function class (line 29) | class EList_m128i { function ensure (line 60) | inline void ensure(size_t thresh) { function reserveExact (line 70) | inline void reserveExact(size_t newsz) { function resize (line 89) | void resize(size_t sz) { function zero (line 104) | void zero() { function resizeNoCopy (line 114) | void resizeNoCopy(size_t sz) { function resizeExact (line 130) | void resizeExact(size_t sz) { function clear (line 143) | void clear() { function __m128i (line 151) | inline __m128i& operator[](size_t i) { function __m128i (line 159) | inline __m128i operator[](size_t i) const { function __m128i (line 167) | inline __m128i& get(size_t i) { function __m128i (line 174) | inline __m128i get(size_t i) const { function __m128i (line 181) | __m128i *ptr() { return list_; } function __m128i (line 186) | const __m128i *ptr() const { return list_; } function lazyInitExact (line 206) | void lazyInitExact(size_t sz) { function __m128i (line 217) | __m128i *alloc(size_t sz) { function free (line 243) | void free() { function expandCopy (line 257) | void expandCopy(size_t thresh) { function expandCopyExact (line 268) | void expandCopyExact(size_t newsz) { function expandNoCopy (line 290) | void expandNoCopy(size_t thresh) { function expandNoCopyExact (line 302) | void expandNoCopyExact(size_t newsz) { function reset (line 320) | struct CpQuad { function operator (line 325) | bool operator==(const CpQuad& o) const { function class (line 339) | class Checkpointer { FILE: sstring.cpp function main (line 29) | int main(void) { FILE: sstring.h function sstr_len (line 82) | static inline size_t sstr_len(const char *s) { function sstr_eq (line 96) | inline bool sstr_eq(const T1& s1, const T2& s2) { function sstr_neq (line 107) | inline bool sstr_neq(const T1& s1, const T2& s2) { function virtual (line 572) | virtual ~SString() { function resize (line 603) | void resize(size_t sz) { function set (line 655) | inline void set(int c, size_t idx) { function T (line 663) | inline const T& operator[](size_t i) const { function T (line 671) | inline T& operator[](size_t i) { function T (line 679) | inline const T& get(size_t i) const { function virtual (line 688) | virtual void install(const T* b, size_t sz) { function virtual (line 698) | virtual void install(const std::basic_string& b) { function install (line 708) | void install(const T* b) { function installReverse (line 716) | void installReverse(const char* b, size_t sz) { function installReverse (line 729) | void installReverse(const SString& b) { function operator (line 736) | bool operator==(const SString& o) { function operator (line 743) | bool operator!=(const SString& o) { function operator (line 750) | bool operator<(const SString& o) { function operator (line 757) | bool operator>(const SString& o) { function operator (line 764) | bool operator<=(const SString& o) { function operator (line 771) | bool operator>=(const SString& o) { function reverse (line 778) | void reverse() { function reverseWindow (line 789) | void reverseWindow(size_t off, size_t len) { function fill (line 803) | void fill(size_t len, const T& el) { function fill (line 813) | void fill(const T& el) { function clear (line 825) | void clear() { len_ = 0; } function virtual (line 856) | virtual const T* toZBuf() const { function T (line 864) | const T* buf() const { return cs_; } function T (line 869) | T* wbuf() { return cs_; } function class (line 883) | class S2bDnaString { function virtual (line 983) | virtual ~S2bDnaString() { function resize (line 1016) | void resize(size_t sz) { function toChar (line 1034) | char toChar(size_t idx) const { function toColor (line 1043) | char toColor(size_t idx) const { function set (line 1094) | void set(int c, size_t idx) { function setChar (line 1106) | void setChar(int c, size_t idx) { function setColor (line 1115) | void setColor(int c, size_t idx) { function setWord (line 1124) | void setWord(uint32_t w, size_t i) { function const (line 1132) | char operator[](size_t i) const { function get (line 1140) | char get(size_t i) const { function install (line 1150) | void install(const uint32_t* b, size_t sz) { function install (line 1160) | void install(const char* b, size_t sz) { function installChars (line 1179) | void installChars(const char* b, size_t sz) { function installColors (line 1200) | void installColors(const char* b, size_t sz) { function install (line 1221) | void install(const char* b) { function installChars (line 1228) | void installChars(const char* b) { function installColors (line 1235) | void installColors(const char* b) { function install (line 1242) | void install(const std::basic_string& b) { function installChars (line 1249) | void installChars(const std::basic_string& b) { function installColors (line 1256) | void installColors(const std::basic_string& b) { function installReverse (line 1264) | void installReverse(const char* b, size_t sz) { function installReverse (line 1285) | void installReverse(const char* b) { function installReverseChars (line 1293) | void installReverseChars(const char* b, size_t sz) { function installReverseChars (line 1317) | void installReverseChars(const char* b) { function installReverseColors (line 1325) | void installReverseColors(const char* b, size_t sz) { function installReverseColors (line 1349) | void installReverseColors(const char* b) { function installReverse (line 1357) | void installReverse(const S2bDnaString& b) { function reverse (line 1426) | void reverse() { function reverseWindow (line 1453) | void reverseWindow(size_t off, size_t len) { function fill (line 1483) | void fill(size_t len, char el) { function fill (line 1515) | void fill(char el) { function clear (line 1576) | void clear() { len_ = 0; } function virtual (line 1698) | virtual ~SStringExpandable() { function insert (line 1762) | void insert(const T& c, size_t idx) { function set (line 1777) | void set(int c, size_t idx) { function append (line 1785) | void append(const T& c) { function remove (line 1793) | void remove(size_t idx) { function T (line 1805) | const T& operator[](size_t i) const { function T (line 1821) | const T& get(size_t i) const { function T (line 1829) | const T* get_ptr(size_t i) const { function virtual (line 1837) | virtual void install(const T* b, size_t sz) { function install (line 1847) | void install(const T* b) { install(b, strlen(b)); } function installReverse (line 1853) | void installReverse(const char* b, size_t sz) { function installReverse (line 1865) | void installReverse(const SStringExpandable& b) { function reverse (line 1918) | void reverse() { function reverseWindow (line 1929) | void reverseWindow(size_t off, size_t len) { function resize (line 1945) | void resize(size_t len) { function resize (line 1954) | void resize(size_t len, const T& el) { function fill (line 1967) | void fill(size_t len, const T& el) { function fill (line 1977) | void fill(const T& el) { function trimBegin (line 1984) | void trimBegin(size_t len) { function trimEnd (line 1998) | void trimEnd(size_t len) { function append (line 2006) | void append(const T* b, size_t sz) { function append (line 2015) | void append(const T* b) { function clear (line 2027) | void clear() { len_ = 0; } function virtual (line 2058) | virtual const T* toZBuf() const { function eq (line 2072) | bool eq(const char *str) const { function T (line 2080) | const T* buf() const { return cs_; } function T (line 2085) | T* wbuf() { return cs_; } function expandNoCopy (line 2113) | void expandNoCopy(size_t sz) { function explicit (line 2156) | explicit SStringFixed(const std::basic_string& str) { function explicit (line 2163) | explicit SStringFixed(const T* b, size_t sz) { function explicit (line 2170) | explicit SStringFixed(const T* b) { function virtual (line 2174) | virtual ~SStringFixed() { } function T (line 2179) | inline const T& operator[](size_t i) const { function T (line 2186) | inline T& operator[](size_t i) { function T (line 2193) | inline const T& get(size_t i) const { function T (line 2201) | inline T& get(size_t i) { function insert (line 2258) | void insert(const T& c, size_t idx) { function set (line 2272) | void set(int c, size_t idx) { function append (line 2280) | void append(const T& c) { function remove (line 2288) | void remove(size_t idx) { function virtual (line 2300) | virtual void install(const T* b, size_t sz) { function install (line 2309) | void install(const T* b) { install(b, strlen(b)); } function installReverse (line 2315) | void installReverse(const char* b, size_t sz) { function installReverse (line 2327) | void installReverse(const SStringFixed& b) { function reverse (line 2380) | void reverse() { function reverseWindow (line 2391) | void reverseWindow(size_t off, size_t len) { function resize (line 2407) | void resize(size_t len) { function resize (line 2416) | void resize(size_t len, const T& el) { function fill (line 2429) | void fill(size_t len, const T& el) { function fill (line 2439) | void fill(const T& el) { function trimBegin (line 2446) | void trimBegin(size_t len) { function trimEnd (line 2460) | void trimEnd(size_t len) { function append (line 2468) | void append(const T* b, size_t sz) { function append (line 2477) | void append(const T* b) { function clear (line 2489) | void clear() { len_ = 0; } function virtual (line 2500) | virtual const T* toZBuf() const { function eq (line 2509) | bool eq(const char *str) const { function T (line 2532) | const T* buf() const { return cs_; } function T (line 2537) | T* wbuf() { return cs_; } function explicit (line 2584) | explicit SDnaStringFixed(const std::basic_string& str) : function explicit (line 2590) | explicit SDnaStringFixed(const char* b, size_t sz) : function virtual (line 2613) | virtual ~SDnaStringFixed() { } function installReverseComp (line 2620) | void installReverseComp(const char* b, size_t sz) { function installReverseComp (line 2633) | void installReverseComp(const SDnaStringFixed& b) { function virtual (line 2667) | virtual void install(const char* b, size_t sz) { function virtual (line 2683) | virtual void installChars(const char* b, size_t sz) { function virtual (line 2698) | virtual void installColors(const char* b, size_t sz) { function virtual (line 2713) | virtual void installChars(const std::basic_string& str) { function virtual (line 2721) | virtual void installColors(const std::basic_string& str) { function set (line 2728) | void set(int c, size_t idx) { function append (line 2738) | void append(const char& c) { function setChar (line 2748) | void setChar(char c, size_t idx) { function appendChar (line 2757) | void appendChar(char c) { function toChar (line 2766) | char toChar(size_t idx) const { function const (line 2775) | const char& operator[](size_t i) const { function get (line 2782) | const char& get(size_t i) const { function virtual (line 2832) | virtual const char* toZBuf() const { return this->toZBufXForm("ACGTN"); } function virtual (line 2908) | virtual ~SDnaStringExpandable() { } function installReverseComp (line 2915) | void installReverseComp(const char* b, size_t sz) { function installReverseComp (line 2928) | void installReverseComp(const SDnaStringExpandable& b) { function virtual (line 2981) | virtual void install(const char* b, size_t sz) { function virtual (line 2996) | virtual void installChars(const char* b, size_t sz) { function virtual (line 3010) | virtual void installColors(const char* b, size_t sz) { function virtual (line 3024) | virtual void installChars(const std::basic_string& str) { function virtual (line 3032) | virtual void installColors(const std::basic_string& str) { function set (line 3039) | void set(int c, size_t idx) { function append (line 3048) | void append(const char& c) { function setChar (line 3059) | void setChar(char c, size_t idx) { function appendChar (line 3068) | void appendChar(char c) { function toChar (line 3079) | char toChar(size_t idx) const { function const (line 3176) | inline const char& operator[](size_t i) const { function get (line 3183) | inline const char& get(size_t i) const { function virtual (line 3232) | virtual const char* toZBuf() const { return this->toZBufXForm("ACGTN"); } function explicit (line 3255) | explicit SDnaMaskString(const std::basic_string& str) : function virtual (line 3277) | virtual ~SDnaMaskString() { } function installReverseComp (line 3284) | void installReverseComp(const char* b, size_t sz) { function installReverseComp (line 3299) | void installReverseComp(const SDnaMaskString& b) { function virtual (line 3335) | virtual void install(const char* b, size_t sz) { function virtual (line 3351) | virtual void installChars(const char* b, size_t sz) { function virtual (line 3367) | virtual void installChars(const std::basic_string& str) { function set (line 3374) | void set(int c, size_t idx) { function append (line 3383) | void append(const char& c) { function setChar (line 3394) | void setChar(char c, size_t idx) { function appendChar (line 3403) | void appendChar(char c) { function toChar (line 3414) | char toChar(size_t idx) const { function const (line 3422) | const char& operator[](size_t i) const { function get (line 3436) | const char& get(size_t i) const { function get (line 3445) | char& get(size_t i) { function virtual (line 3530) | virtual const char* toZBuf() const { return this->toZBufXForm(iupacs); } type SStringExpandable (line 3533) | typedef SStringExpandable BTString; FILE: str_util.h function hash_string (line 28) | static inline int FILE: taxonomy.h type TaxonomyNode (line 51) | struct TaxonomyNode { function getPath (line 151) | void getPath(uint64_t tid, EList& path) const { type std (line 163) | typedef std::map TaxonomyTree; function initial_tax_rank_num (line 165) | inline static void initial_tax_rank_num() { function get_tax_rank_id (line 241) | inline static uint8_t get_tax_rank_id(const char* rank) { function get_taxid_at_parent_rank (line 303) | inline static uint64_t get_taxid_at_parent_rank(const TaxonomyTree& tree... function TaxonomyTree (line 322) | inline static TaxonomyTree read_taxonomy_tree(string taxonomy_fname) { FILE: third_party/MurmurHash3.cpp function rotl32 (line 34) | inline uint32_t rotl32 ( uint32_t x, int8_t r ) function rotl64 (line 39) | inline uint64_t rotl64 ( uint64_t x, int8_t r ) function FORCE_INLINE (line 55) | FORCE_INLINE uint32_t getblock32 ( const uint32_t * p, int i ) function FORCE_INLINE (line 60) | FORCE_INLINE uint64_t getblock64 ( const uint64_t * p, int i ) function FORCE_INLINE (line 68) | FORCE_INLINE uint32_t fmix32 ( uint32_t h ) function FORCE_INLINE (line 81) | FORCE_INLINE uint64_t fmix64 ( uint64_t k ) function MurmurHash3_x86_32 (line 94) | void MurmurHash3_x86_32 ( const void * key, int len, function MurmurHash3_x86_128 (line 150) | void MurmurHash3_x86_128 ( const void * key, const int len, function MurmurHash3_x64_128 (line 255) | void MurmurHash3_x64_128 ( const void * key, const int len, FILE: third_party/cpuid.h function __get_cpuid_max (line 120) | static __inline unsigned int function __get_cpuid (line 175) | static __inline int FILE: threading.h function class (line 37) | class ThreadSafe { FILE: timer.h function class (line 35) | class Timer { FILE: tinythread.cpp type tthread (line 35) | namespace tthread { function _pthread_t_to_ID (line 131) | static thread::id _pthread_t_to_ID(const pthread_t &aHandle) type _thread_start_info (line 150) | struct _thread_start_info { FILE: tinythread.h function class (line 159) | class mutex { function class (line 251) | class recursive_mutex { function explicit (line 350) | explicit lock_guard(mutex_type &aMutex) function class (line 392) | class condition_variable { function class (line 481) | class thread { FILE: tokenize.h function tokenize (line 54) | void tokenize(const std::string& s, char delim, T& ss) { FILE: util.h function extractIDFromRefName (line 57) | inline function string (line 72) | string to_string(T value) { function V (line 83) | V find_or_use_default(const std::map& my_map, const K& query, cons... FILE: word_io.h function writeU32 (line 35) | static inline void writeU32(std::ostream& out, uint32_t x, bool toBigEnd... function writeU32 (line 44) | static inline void writeU32(std::ostream& out, uint32_t x) { function writeI32 (line 53) | static inline void writeI32(std::ostream& out, int32_t x, bool toBigEndi... function writeI32 (line 62) | static inline void writeI32(std::ostream& out, int32_t x) { function writeU16 (line 71) | static inline void writeU16(std::ostream& out, uint16_t x, bool toBigEnd... function writeU16 (line 80) | static inline void writeU16(std::ostream& out, uint16_t x) { function writeI16 (line 89) | static inline void writeI16(std::ostream& out, int16_t x, bool toBigEndi... function writeI16 (line 98) | static inline void writeI16(std::ostream& out, int16_t x) { function readU32 (line 106) | static inline uint32_t readU32(std::istream& in, bool swap) { function readU32 (line 122) | static inline uint32_t readU32(int in, bool swap) { function readU32 (line 139) | static inline uint32_t readU32(FILE* in, bool swap) { function readI32 (line 156) | static inline int32_t readI32(std::istream& in, bool swap) { function readI32 (line 172) | static inline uint32_t readI32(int in, bool swap) { function readI32 (line 189) | static inline uint32_t readI32(FILE* in, bool swap) { function readU16 (line 206) | static inline uint16_t readU16(std::istream& in, bool swap) { function readU16 (line 222) | static inline uint16_t readU16(int in, bool swap) { function readU16 (line 239) | static inline uint16_t readU16(FILE* in, bool swap) { function readI16 (line 256) | static inline int32_t readI16(std::istream& in, bool swap) { function readI16 (line 272) | static inline uint16_t readI16(int in, bool swap) { function readI16 (line 289) | static inline uint16_t readI16(FILE* in, bool swap) { function index_t (line 312) | inline index_t readIndex(std::istream& in, bool swap) { function index_t (line 329) | inline index_t readIndex(int in, bool swap) { function index_t (line 355) | inline index_t readIndex(FILE* in, bool swap) {