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discoal.h
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// discoal.h
// defs, headers, etc for discoal.c
#ifndef __DISCOAL_GLOBALS__
#define __DISCOAL_GLOBALS__
/******************************************************************************/
/* here are just some defines to allocate initial global arrays and stuff */
/* like that */
#define MAXNODES 20000000
#define MAXSITES 220020
#define SMALLCHUNKS 100000
#define MAXBREAKS 1000000
#define MAXMUTS 40000
#define MAXTIME 100000.0
#define MAXPOPS 121
#define MAX(a, b) (((a) > (b)) ? (a) : (b))
#define MIN(a, b) (((a) > (b)) ? (b) : (a))
#define MAXEVENTS 250
#define MAXLEAFS 200
/******************************************************************************/
/******************************************************************************/
/* A "rootedNode" is just a node in a coalescent graph. Since recombination */
/* is possible, each node has a left and a right parent as well as 2 children */
/* Nodes also keep track of their time in the tree and their mutations (which */
/* they pass on to their children) as well as the number of descendents */
/* at each site */
/* Nodes are used to build the coalescent tree and place mutations */
typedef struct rootedNode
{
struct rootedNode *leftParent, *rightParent, *leftChild, *rightChild;
double time, branchLength, blProb;
double muts[MAXMUTS];
#ifdef BIG
uint16_t ancSites[MAXSITES];
#else
uint8_t ancSites[MAXSITES];
#endif
int nancSites, lLim, rLim;
int id, mutationNumber, population, sweepPopn;
int ndes[2],*leafs;
double times[2];
}
rootedNode;
/******************************************************************************/
/******************************************************************************/
/* Here is the event object used to keep track of demographic changes */
typedef struct event
{
double time, popnSize;
char type;
int popID, popID2, popID3; //some events like splits involve two populations, admixture is 3
int lineageNumber; //some events involve a specified number of lineages, like ancient samples
double admixProp; // admixture proportion from population popID2
}
event;
/******************************************************************************/
/******************************************************************************/
/* here are all the global variables that are needed in the program. Most of */
/* these have to do with storage for the coalescent graph and the chunks of */
/* ancestral dna. There are also parameters controlling the coalescent */
/* process */
rootedNode *nodes[MAXNODES], *allNodes[MAXNODES];
int activeMaterial[MAXSITES];
int sampleSize, sampleNumber, breakNumber, segSites,alleleNumber, \
totNodeNumber, totChunkNumber, npops, eventFlag, nSites, activeSites,\
mask, finiteOutputFlag, outputStyle, effectiveSampleSize, runMode, gcMean,\
breakPoints[MAXBREAKS],sampleSizes[MAXPOPS];
double leftRho, rho, theta, tDiv, alpha, sweepSite, tau, my_gamma, \
lambda, timeRecovery,bottleNeckRatio, bottleNeckDuration, \
ancestralSizeRatio, sweepLeft, sweepRight, thetas[MAXPOPS];
double mig[MAXPOPS];
int sampleS, sampleFD, sampleHaps, rejectCount, sampleRMin, offset, winNumber, \
popnSizes[MAXPOPS],sweepPopnSizes[MAXPOPS];
const char *mFile;
char sweepMode, windowMode;
double coaltime, currentTime, pAccept;
int mn, eventNumber, migFlag, currentEventNumber;
double SweepStartingFrequency, f0;
double uA;
double gammaCoRatio, gammaCoRatioMode;
int priorTheta, priorRho, priorAlpha, priorTau, priorX, priorF0, priorE1, priorE2, priorUA, priorC;
double gammaCoRatioMode, gammaCoRatio;
double pThetaUp, pThetaLow,pRhoMean,pRhoUp,pRhoLow,pAlphaUp,pAlphaLow,pTauUp,pTauLow,pXUp,pXLow,pF0Up,pF0Low,pUALow,pUAUp,pCUp,pCLow;
double pE2TLow,pE1TLow, pE2THigh, pE1THigh, pE1SLow, pE1SHigh, pE2SLow,pE2SHigh;
double migMat[MAXPOPS][MAXPOPS], migMatConst[MAXPOPS][MAXPOPS];
double recurSweepRate;
int EFFECTIVE_POPN_SIZE;
#define TRAJSTEPSTART 500000000
long int maxTrajSteps;
float *currentTrajectory;
long int currentTrajectoryStep, totalTrajectorySteps;
struct event events[MAXEVENTS];
int lSpot, rSpot, condRecMode;
int condRecMet;
int activeSweepFlag;
int recurSweepMode;
int partialSweepMode,softSweepMode;
double partialSweepFinalFreq;
double deltaTMod;
int treeOutputMode;
int ancSampleSize, ancPopID, ancSampleFlag;
int ancSampleTime;
int hidePartialSNP;
#endif