int main(int argc, char* argv[])
{
char histoneFileName[1000],chromFileName[1000],projectName[1000];
int binsize;
int count=0;
if (argc!=5)
{
printf("Usage: <Histone File Name> <Chromosome Description File Name> <bin size> <cell-type name>\n");
return 0;
}
strcpy(histoneFileName,argv[1]);
strcpy(chromFileName,argv[2]);
binsize=atoi(argv[3]);
strcpy(projectName,argv[4]);
//Read chromosome description file
if (!GetChromInfo(chromFileName))
{
printf("chromosome description file is not valid\n");
return 0;
}
//Read tag files of L1 and L2, and define the histone modification regions
float **binrpkm;
int i,j;
ReadHistoneFile(histoneFileName,projectName,binsize);
return 0;
}
int main(int argc, char* argv[])
{
char lib1FileName[1000], lib2FileName[1000], chromFileName[1000],configFileName[2000], projectName[1000];
CONFIG_STRUCT config;
CHROM_INFO chroms[MAX_CHROM_NUM];
int chromNum;
double noiseRate, l1Ratio, l2Ratio;
int maxL1Count, maxL2Count;
int i;
if (argc!=6)
{
printf("Usage: <library 1 tag file name> <library 2 tag file name> <chromosome length file name> <config file name> <project name>\n");
return 0;
}
strcpy(lib1FileName, argv[1]);
strcpy(lib2FileName, argv[2]);
strcpy(chromFileName, argv[3]);
strcpy(configFileName, argv[4]);
strcpy(projectName, argv[5]);
chromNum = GetChromInfo(chromFileName, chroms);
if (chromNum<=0)
{
return 0;
}
printf("chromosome length information read. chromNum = %d!\n", chromNum);
for (i=0;i<chromNum;i++)
{
chroms[i].l1PosTagNum = 0;
chroms[i].l2PosTagNum = 0;
chroms[i].l1NegTagNum = 0;
chroms[i].l2NegTagNum = 0;
chroms[i].l1PeakNum = 0;
chroms[i].l2PeakNum = 0;
}
if (ReadConfigFile(configFileName, &config)<0)
{
printf("config file not complet. Default setting used.\n");
}
printf("config file read.\n");
printf("fragmentSize = %d\n", config.fragmentSize);
printf("isStrandSensitiveMode = %d\n", config.isStrandSensitiveMode);
printf("slidingWinSize = %d\n", config.slidingWinSize);
printf("movingStep = %d\n", config.movingStep);
printf("outputNum = %d\n", config.outputNum);
printf("minCount = %d\n", config.minCount);
printf("minScore = %f\n", config.minScore);
printf("bootstrapPass = %d\n", config.bootstrapPass);
printf("randSeed = %d\n", config.randomSeed);
printf("reading tag files......\n");
if (!GetTags(lib1FileName, lib2FileName, chroms, chromNum))
{
printf("tag file error!\n");
return 0;
}
printf("tag file read.\n");
printf("pre-processing......\n");
if (PreProcessing(chroms, chromNum)<0)
{
printf("Preprocessing failed!\n CCAT aborted!\n");
return -1;
}
printf("pre-processing finished.\n");
printf("estimating noise rate......\n");
srand(config.randomSeed);
noiseRate = ComputeNoiseRate(chroms,chromNum, &l1Ratio,&l2Ratio, config);
printf("noise rate = %f\n", noiseRate);
printf("peak-finding......\n");
if (PeakFinding(chroms,chromNum,l1Ratio,l2Ratio, &maxL1Count, &maxL2Count, config)<=0)
{
return -1;
}
printf("peak-finding finished.\n");
printf("Significance Analysis......\n");
if (SignificanceAnalysis(chroms, chromNum, l1Ratio, l2Ratio, maxL1Count, maxL2Count, config)<0)
{
printf("DPS paramter esitmation failed!\n");
return -1;
}
printf("Significance analysis finished.\n");
printf("saving results.......\n");
OutputFiles(chroms, chromNum, projectName, config);
printf("results saved.\n");
FreeChromMem(chroms,chromNum);
printf("CCAT process completed!\n");
return 0;
}