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);
}
extern int
main(int argc, char* argv[]) {
int i, n;
char pathBuf[512];
FileStream *in;
UNewDataMemory *out;
UErrorCode errorCode=U_ZERO_ERROR;
U_MAIN_INIT_ARGS(argc, argv);
/* preset then read command line options */
options[DESTDIR].value=options[SOURCEDIR].value=u_getDataDirectory();
argc=u_parseArgs(argc, argv, sizeof(options)/sizeof(options[0]), options);
/* error handling, printing usage message */
if(argc<0) {
fprintf(stderr,
"error in command line argument \"%s\"\n",
argv[-argc]);
}
if(argc<0 || options[HELP1].doesOccur || options[HELP2].doesOccur) {
fprintf(stderr,
"usage: %s [-options] [convrtrs.txt]\n"
"\tread convrtrs.txt and create " U_ICUDATA_NAME "_" DATA_NAME "." DATA_TYPE "\n"
"options:\n"
"\t-h or -? or --help this usage text\n"
"\t-v or --verbose prints out extra information about the alias table\n"
"\t-q or --quiet do not display warnings and progress\n"
"\t-c or --copyright include a copyright notice\n"
"\t-d or --destdir destination directory, followed by the path\n"
"\t-s or --sourcedir source directory, followed by the path\n",
argv[0]);
return argc<0 ? U_ILLEGAL_ARGUMENT_ERROR : U_ZERO_ERROR;
}
if(options[VERBOSE].doesOccur) {
verbose = TRUE;
}
if(options[QUIET].doesOccur) {
quiet = TRUE;
}
if(argc>=2) {
path=argv[1];
} else {
path=options[SOURCEDIR].value;
if(path!=NULL && *path!=0) {
char *end;
uprv_strcpy(pathBuf, path);
end = uprv_strchr(pathBuf, 0);
if(*(end-1)!=U_FILE_SEP_CHAR) {
*(end++)=U_FILE_SEP_CHAR;
}
uprv_strcpy(end, "convrtrs.txt");
path=pathBuf;
} else {
path = "convrtrs.txt";
}
}
uprv_memset(stringStore, 0, sizeof(stringStore));
uprv_memset(tagStore, 0, sizeof(tagStore));
uprv_memset(converters, 0, sizeof(converters));
uprv_memset(tags, 0, sizeof(tags));
uprv_memset(aliasLists, 0, sizeof(aliasLists));
uprv_memset(knownAliases, 0, sizeof(aliasLists));
in=T_FileStream_open(path, "r");
if(in==NULL) {
fprintf(stderr, "gencnval: unable to open input file %s\n", path);
exit(U_FILE_ACCESS_ERROR);
}
parseFile(in);
T_FileStream_close(in);
/* create the output file */
out=udata_create(options[DESTDIR].value, DATA_TYPE, DATA_NAME, &dataInfo,
options[COPYRIGHT].doesOccur ? U_COPYRIGHT_STRING : NULL, &errorCode);
if(U_FAILURE(errorCode)) {
fprintf(stderr, "gencnval: unable to open output file - error %s\n", u_errorName(errorCode));
exit(errorCode);
}
/* write the table of aliases based on a tag/converter name combination */
writeAliasTable(out);
/* finish */
udata_finish(out, &errorCode);
if(U_FAILURE(errorCode)) {
fprintf(stderr, "gencnval: error finishing output file - %s\n", u_errorName(errorCode));
exit(errorCode);
}
/* clean up tags */
for (i = 0; i < MAX_TAG_COUNT; i++) {
for (n = 0; n < MAX_CONV_COUNT; n++) {
if (tags[i].aliasList[n].aliases!=NULL) {
uprv_free(tags[i].aliasList[n].aliases);
}
}
}
return 0;
}
