SYMBOL INDEX (151 symbols across 3 files)

FILE: Genrich.c
  function printVersion (line 25) | void printVersion(void) {
  function usage (line 34) | void usage(void) {
  function error (line 78) | int error(const char* msg, enum errCode err) {
  function getFloat (line 106) | float getFloat(char* in) {
  function getInt (line 117) | int getInt(char* in) {
  function getLong (line 128) | uint64_t getLong(char* in) {
  function swapFloat (line 154) | void swapFloat(float* a, float* b) {
  function swapInt (line 159) | void swapInt(uint64_t* a, uint64_t* b) {
  function partition (line 164) | int64_t partition(float* pVal, uint64_t* pEnd,
  function quickSort (line 181) | void quickSort(float* pVal, uint64_t* pEnd,
  function lookup (line 196) | float lookup(float* pVal, uint64_t low, uint64_t high,
  function saveQval (line 212) | void saveQval(Chrom* chrom, int chromLen, int n,
  function jenkins_one_at_a_time_hash (line 259) | uint32_t jenkins_one_at_a_time_hash(float f) {
  function recordPval (line 277) | int recordPval(Hash** table, float p, uint32_t length) {
  function Hash (line 300) | Hash** hashPval(Chrom* chrom, int chromLen, int n,
  function computeQval (line 352) | void computeQval(Chrom* chrom, int chromLen,
  function bd0 (line 412) | double bd0(double x, double np) {
  function stirlerr (line 436) | double stirlerr(double n) {
  function dpois (line 474) | double dpois(double x, double lambda) {
  function pd_upper_series (line 482) | double pd_upper_series(double x, double alph) {
  function pd_lower_series (line 496) | double pd_lower_series(double lambda, double y) {
  function pgamma_smallx (line 509) | double pgamma_smallx(double x, double alph) {
  function pgamma (line 528) | double pgamma(double x, double alph) {
  function pchisq (line 555) | double pchisq(double x, int df) {
  function multPval (line 567) | float multPval(Pileup** pval, int n, uint32_t idx[]) {
  function countIntervals2 (line 589) | uint32_t countIntervals2(Chrom* c, int n) {
  function combinePval (line 612) | void combinePval(Chrom* chrom, int chromLen, int n) {
  function printLogHeader (line 674) | void printLogHeader(File log, bool gzOut, int n,
  function printIntervalN (line 724) | void printIntervalN(File out, bool gzOut, char* name,
  function printInterval (line 770) | void printInterval(File out, bool gzOut, char* name,
  function printLog (line 808) | void printLog(File log, bool gzOut, Chrom* chr,
  function logIntervals (line 837) | void logIntervals(File log, bool gzOut, Chrom* chrom,
  function printPeak (line 885) | void printPeak(File out, bool gzOut, char* name,
  function checkPeak (line 916) | void checkPeak(File out, bool gzOut, char* name,
  function resetVars (line 932) | void resetVars(int64_t* peakStart, float* summitVal,
  function updatePeak (line 943) | void updatePeak(int64_t* peakStart, int64_t* peakEnd,
  function callPeaks (line 977) | int callPeaks(File out, File log, bool logOpt, bool gzOut,
  function findPeaks (line 1076) | void findPeaks(File out, File log, bool logOpt, bool gzOut,
  function saveXBed (line 1144) | void saveXBed(char* name, uint32_t len, int* bedLen,
  function checkChrom (line 1212) | bool checkChrom(char* chr, int xcount, char** xchrList) {
  function getIdx (line 1224) | int getIdx(File in, bool gz, char* line, bool qvalOpt,
  function loadBDG (line 1252) | void loadBDG(char* line, char** chr, uint32_t* start,
  function callPeaksLog (line 1277) | void callPeaksLog(File in, bool gz, File out, bool gzOut,
  function do_del (line 1497) | double do_del(double y, double temp, bool ret) {
  function pnorm (line 1509) | double pnorm(double x) {
  function plnorm (line 1617) | double plnorm(double x, double meanlog, double sdlog) {
  function calcPval (line 1628) | float calcPval(float exptVal, float ctrlVal) {
  function countIntervals (line 1661) | uint32_t countIntervals(Chrom* chr) {
  function printPileHeader (line 1680) | void printPileHeader(File pile, char* exptName,
  function printPile (line 1697) | void printPile(File pile, char* name, uint32_t start,
  function savePval (line 1720) | void savePval(Chrom* chrom, int chromLen, int n,
  function saveConst (line 1801) | void saveConst(Pileup* p, uint32_t* size, uint32_t* mem,
  function calcLambda (line 1817) | float calcLambda(Chrom* chrom, int chromLen,
  function saveLambda (line 1838) | void saveLambda(Chrom* chr, float lambda) {
  function savePileupNoCtrl (line 1883) | void savePileupNoCtrl(Chrom* chrom, int chromLen,
  function getVal (line 1902) | float getVal(int32_t cov, uint8_t frac) {
  function updateVal (line 1915) | float updateVal(int16_t dCov, uint8_t dFrac, int32_t* cov,
  function calcFactor (line 1980) | float calcFactor(Chrom* chrom, int chromLen,
  function savePileupCtrl (line 2052) | void savePileupCtrl(Chrom* chrom, int chromLen,
  function savePileupExpt (line 2168) | double savePileupExpt(Chrom* chrom, int chromLen) {
  function addFrac (line 2311) | void addFrac(int16_t* cov, uint8_t* frac, uint8_t count) {
  function subFrac (line 2412) | void subFrac(int16_t* cov, uint8_t* frac, uint8_t count) {
  function printBED (line 2497) | void printBED(File bed, bool gzOut, char* chr,
  function saveInterval (line 2516) | uint32_t saveInterval(Chrom* c, int64_t start, int64_t end,
  function calcAvgLen (line 2597) | int calcAvgLen(double totalLen, uint64_t pairedPr,
  function processAvgExt (line 2614) | void processAvgExt(Aln** unpair, int unpairIdx,
  function saveAvgExt (line 2654) | void saveAvgExt(char* qname, Aln* b, uint8_t count,
  function saveUnpair (line 2689) | void saveUnpair(char* qname, Aln* a, uint8_t count,
  function saveFragAtac (line 2728) | uint32_t saveFragAtac(Chrom* c, uint32_t start,
  function saveFragment (line 2754) | uint32_t saveFragment(char* qname, Aln* a, uint8_t count,
  function Read (line 2782) | Read* createRead(Read*** read, int* readIdx,
  function copyAlns (line 2815) | void copyAlns(Aln* aln, int alnLen, float score,
  function saveAlnsSingle (line 2856) | void saveAlnsSingle(char* qname, Aln* aln, int alnLen,
  function saveAlnsDiscord (line 2874) | void saveAlnsDiscord(char* qname, Aln* aln, int alnLen,
  function saveAlnsPair (line 2890) | void saveAlnsPair(char* qname, Aln* aln, int alnLen,
  function saveAlns (line 2942) | void saveAlns(char* qname, Aln* aln, int alnLen, bool pair,
  function subsampleSingle (line 2985) | void subsampleSingle(Aln* aln, int alnLen, bool first,
  function processSingle (line 3019) | int processSingle(char* qname, Aln* aln, int alnLen,
  function subsamplePair (line 3089) | void subsamplePair(Aln* aln, int alnLen, uint8_t* count,
  function processPair (line 3122) | int processPair(char* qname, Aln* aln, int alnLen,
  function processAlns (line 3187) | void processAlns(char* qname, Aln* aln, int alnLen,
  function johnPartition (line 3274) | uint32_t johnPartition(uint16_t* qual, uint32_t* order,
  function johnSort (line 3337) | void johnSort(uint16_t* qual, uint32_t* order,
  function sortReads (line 3363) | void sortReads(Read** arr, uint32_t count, uint32_t* order,
  function calcHashSize (line 3390) | uint32_t calcHashSize(uint32_t count) {
  function jenkins_hash_aln (line 3408) | uint32_t jenkins_hash_aln(Chrom* chrom, Chrom* chrom1,
  function addToHash (line 3457) | void addToHash(Chrom* chrom, Chrom* chrom1, uint32_t pos,
  function HashAln (line 3481) | HashAln* checkHash(Chrom* chrom, Chrom* chrom1,
  function checkAndAdd (line 3514) | void checkAndAdd(HashAln** tableSn, uint32_t hashSizeSn,
  function logDup (line 3528) | void logDup(File dups, bool gzOut, char* name,
  function addHashPr (line 3569) | void addHashPr(Read* r, HashAln** table,
  function checkHashPr (line 3593) | bool checkHashPr(Read* r, HashAln** table,
  function findDupsPr (line 3616) | void findDupsPr(Read** readPr, int readIdxPr,
  function addHashDc (line 3689) | void addHashDc(Read* r, HashAln** table,
  function checkHashDc (line 3720) | bool checkHashDc(Read* r, HashAln** table,
  function findDupsDc (line 3761) | void findDupsDc(Read** readDc, int readIdxDc,
  function addHashSn (line 3845) | void addHashSn(Read* r, HashAln** table,
  function checkHashSn (line 3861) | bool checkHashSn(Read* r, HashAln** table,
  function findDupsSn (line 3886) | void findDupsSn(Read** readSn, int readIdxSn,
  function findDups (line 3949) | void findDups(Read** readPr, int readIdxPr, int readLenPr,
  function updatePairedAln (line 4049) | void updatePairedAln(Aln* a, uint16_t flag,
  function savePairedAln (line 4066) | bool savePairedAln(Aln** aln, int* alnLen,
  function saveSingleAln (line 4102) | bool saveSingleAln(Aln** aln, int* alnLen,
  function sumQual (line 4127) | uint16_t sumQual(char* qual, int len, int offset) {
  function parseAlign (line 4141) | bool parseAlign(Aln** aln, int* alnLen, uint16_t flag,
  function saveChrom (line 4220) | int saveChrom(char* name, uint32_t len, int* chromLen,
  function loadChrom (line 4275) | void loadChrom(char* line, int* chromLen, Chrom** chrom,
  function checkHeader (line 4307) | void checkHeader(char* line, int* chromLen, Chrom** chrom,
  function loadFields (line 4350) | bool loadFields(uint16_t* flag, char** rname, uint32_t* pos,
  function getScore (line 4383) | float getScore(char* extra) {
  function parseCigar (line 4408) | int parseCigar(char* cigar, int* offset) {
  function calcDist (line 4451) | int calcDist(char* qname, char* seq, char* cigar) {
  function readSAM (line 4468) | uint64_t readSAM(File in, bool gz, char* line, Aln** aln,
  function readInt32 (line 4633) | int32_t readInt32(gzFile in, bool end) {
  function loadInt32 (line 4652) | int32_t loadInt32(char** block) {
  function loadBAMfields (line 4665) | void loadBAMfields(char** block, int32_t* refID, int32_t* pos,
  function calcDistBAM (line 4697) | int calcDistBAM(int32_t l_seq, uint16_t n_cigar_op,
  function arrayLen (line 4715) | int arrayLen(char* extra) {
  function loadInt (line 4740) | int64_t loadInt(char* block, size_t size) {
  function getBAMscore (line 4751) | float getBAMscore(char* extra, int len) {
  function parseBAM (line 4826) | uint64_t parseBAM(gzFile in, char* line, Aln** aln,
  function readBAM (line 4983) | uint64_t readBAM(gzFile in, char* line, Aln** aln,
  function openWrite (line 5076) | void openWrite(char* outFile, File* out, bool gz) {
  function checkBAM (line 5107) | bool checkBAM(File in, bool gz) {
  function openRead (line 5132) | bool openRead(char* inFile, File* in) {
  function loadBED (line 5187) | int loadBED(char* xFile, char* line, Bed** xBed) {
  function findPeaksOnly (line 5243) | void findPeaksOnly(char* logFile, char* outFile,
  function logCounts (line 5295) | void logCounts(uint64_t count, uint64_t unmapped,
  function runProgram (line 5386) | void runProgram(char* inFile, char* ctrlFile, char* outFile,
  function saveXChrom (line 5701) | int saveXChrom(char* xchrom, char*** xchrList) {
  function getArgs (line 5718) | void getArgs(int argc, char** argv) {
  function main (line 5832) | int main(int argc, char* argv[]) {

FILE: Genrich.h
  type sam (line 39) | enum sam { NIL, QNAME, FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT,
  type alignType (line 46) | enum alignType { PAIRED, SINGLE, DISCORD }
  type bedGraph (line 49) | enum bedGraph { CHR, START, END }
  type option (line 89) | struct option
  type errCode (line 97) | enum errCode { ERRFILE, ERROPEN, ERROPENW, ERRCLOSE,
  type File (line 157) | typedef union file {
  type Bed (line 162) | typedef struct bed {
  type Hash (line 167) | typedef struct hash {
  type Pileup (line 173) | typedef struct pileup {
  type Diff (line 178) | typedef struct diff {
  type Chrom (line 183) | typedef struct chrom {
  type Aln (line 203) | typedef struct aln {
  type HashAln (line 216) | typedef struct hashAln {
  type Read (line 227) | typedef struct read {

FILE: findNs.py
  function openRead (line 11) | def openRead(filename):
  function openWrite (line 28) | def openWrite(filename):
  function printNs (line 45) | def printNs(fOut, head, seq, minLen):
  function parseFasta (line 70) | def parseFasta(fIn, fOut, minLen):
  function main (line 110) | def main():