C++ (Cpp) readMarkers Examples

Example #1

File: main.c Project: koromo/Distributer

int main(int argv, char** argc)
{
    File* hw;
    Marker* markers;
    Marker* it;
    const char* markersPath;
    const char* hwPath;
    FILE* outFile;

    if (argv != 3)
    {
        printf("Usage: %s markers homeworks\n", argc[0]);
        printf("markers: Markers file path.\n");
        printf("files: HW files path.\n");
        exit(EXIT_FAILURE);
    }

    markersPath = argc[1];
    hwPath = argc[2];

    markers = readMarkers(markersPath);

    srand(time(NULL));
    rand();
    rand();

    hw = makeFileList(hwPath);
    markers = distribute(hw, markers);
    markers = sortMarkers(markers, numMarkers(markers));
    for (it = markers; it; it = it->next)
    {
        it->files = sortFiles(it->files, numFiles(it->files));
    }

    printMarkers(markers);

    for (it = markers; it; it = it->next)
    {
        free((void*)it->name);
    }

    freeMarkers(markers);
    freeFiles(hw);

    return 0;
}

Example #2

File: zfishBacClonesandSts.c Project: CEpBrowser/CEpBrowser--from-UCSC-CGI-BIN

int main(int argc, char *argv[])
{
struct lineFile *cgf, *clf, *mkf, *nmf, *acf, *usf;
FILE *bacAlias, *bacXRef; 
int verb = 0;
char *dir, errorFile[256], aliasFile[256], xRefFile[256];

verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc != 8)
    {
fprintf(stdout, "USAGE: formatZfishSts [-verbose=<level>] <contig file> <clone file> <marker file> <list of BACs and chroms> <accessions> <UniSTS IDs file><output directory>\n");
    return 1;
    }
verb = optionInt("verbose", 0);
verboseSetLevel(verb);

fprintf(stdout, "Opening and reading files ...\n");
cgf = lineFileOpen(argv[1], TRUE );
clf = lineFileOpen(argv[2], TRUE);
mkf = lineFileOpen(argv[3], TRUE);
nmf = lineFileOpen(argv[4], TRUE);
acf = lineFileOpen(argv[5], TRUE);
usf = lineFileOpen(argv[6], TRUE);
dir = cloneString(argv[7]); 

sprintf(errorFile, "%s/error.log", dir);
sprintf(aliasFile, "%s/bacAlias.tab", dir);
sprintf(xRefFile, "%s/bacXRef.tab", dir);

fprintf(stdout, "files are error: %s, alias: %s and xRef: %s \n", errorFile, aliasFile, xRefFile);
stderr = mustOpen(errorFile, "w");
bacAlias = mustOpen(aliasFile, "w");
bacXRef = mustOpen(xRefFile, "w");

/* Read in contigs file with internal name, external name and FPC contig */
verbose(1, "Reading contig names file\n");
readContigs(cgf);

/* Read in internal BAC clone names and Sanger sts names  */
verbose(1, "Reading BAC clone names and Sanger sts names\n");
readCloneNames(clf);

/* Read in BAC clone information: Sanger name, UniSTS ID and aliases */
verbose(1, "Reading markers file\n");
readMarkers(mkf);

/* Read in file of BAC clones names and chroms mapped to by blat */
verbose(1, "Reading file of BAC clone external names\n");
readBacNames(nmf);

/* Read in internal names and corresponding GenBank accessions */
verbose(1, "Reading accessions file\n");
readAccessions(acf);

/*Read file of UniSTS IDs and BAC Clone IDs */
verbose(1, "Reading UniSTS IDs file\n");
readUniStsIds(usf);

/* Print out the STS marker information to a file */
verbose(1, "Creating output file\n");
fprintf(stdout, "Printing tab files for bacCloneAlias and bacCloneXRef tables ...\n");
writeAliasTable(bacAlias);
writeXRefTable(bacXRef);

lineFileClose(&nmf);
lineFileClose(&cgf);
lineFileClose(&clf);
lineFileClose(&mkf);
lineFileClose(&acf);
lineFileClose(&usf);
carefulClose(&bacXRef);
carefulClose(&bacAlias);
carefulClose(&stderr);

freeHashAndVals(&bacHash);
freeHashAndVals(&extNameHash);
freeHashAndVals(&aliasHash);
freeHashAndVals(&sangerByExtNameHash);

return(0);
}