C++ (Cpp) gbAlignGetMigrateRel Examples

Example #1

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

int main(int argc, char* argv[])
{
char *relName, *updateName, *typeAccPrefix, *database, *sep;
struct gbIndex* index;
struct gbSelect select;
struct gbSelect* prevSelect = NULL;
struct gbAlignInfo alignInfo;
boolean noMigrate;
ZeroVar(&select);

optionInit(&argc, argv, optionSpecs);
if (argc != 5)
    usage();
maxFaSize = optionInt("fasize", -1);
workDir = optionVal("workdir", "work/align");
noMigrate = optionExists("noMigrate");
createPolyASizes = optionExists("polyASizes");
gbVerbInit(optionInt("verbose", 0));
relName = argv[1];
updateName = argv[2];
typeAccPrefix = argv[3];
database = argv[4];

/* parse typeAccPrefix */
sep = strchr(typeAccPrefix, '.');
if (sep != NULL)
    *sep = '\0';
select.type = gbParseType(typeAccPrefix);
if (sep != NULL)
    {
    select.accPrefix = sep+1;
    *sep = '.';
    }
select.orgCats = gbParseOrgCat(optionVal("orgCats", "native,xeno"));

index = gbIndexNew(database, NULL);
select.release = gbIndexMustFindRelease(index, relName);
select.update = gbReleaseMustFindUpdate(select.release, updateName);
gbVerbMsg(0, "gbAlignGet: %s/%s/%s/%s", select.release->name,
          select.release->genome->database, select.update->name,
          typeAccPrefix);

/* Get the release to migrate, if applicable */
if (!noMigrate)
    prevSelect = gbAlignGetMigrateRel(&select);

alignInfo = gbAlignGet(&select, prevSelect);

/* always print stats */
fprintf(stderr, "gbAlignGet: %s/%s/%s/%s: align=%d, migrate=%d\n",
        select.release->name, select.release->genome->database,
        select.update->name, typeAccPrefix,
        alignInfo.align.accTotalCnt, alignInfo.migrate.accTotalCnt);
gbIndexFree(&index);

/* print alignment and migrate count, which is read by the driver program */
printf("alignCnt: %d %d\n", alignInfo.align.accTotalCnt, alignInfo.migrate.accTotalCnt);
return 0;
}

Example #2

File: gbAlignInstall.c Project: davidhoover/kent

int main(int argc, char* argv[])
{
char *relName, *updateName, *typeAccPrefix, *database, *sep;
struct gbIndex* index;
struct gbSelect select;
struct gbSelect* prevSelect = NULL;
boolean noMigrate;
ZeroVar(&select);

optionInit(&argc, argv, optionSpecs);
if (argc != 5)
    usage();
gWorkDir = optionVal("workdir", "work/align");
gSortTmp = optionVal("sortTmp", NULL);
noMigrate = optionExists("noMigrate");
gbVerbInit(optionInt("verbose", 0));
relName = argv[1];
updateName = argv[2];
typeAccPrefix = argv[3];
database = argv[4];

/* parse typeAccPrefix */
sep = strchr(typeAccPrefix, '.');
if (sep != NULL)
    *sep = '\0';
select.type = gbParseType(typeAccPrefix);
if (sep != NULL)
    {
    select.accPrefix = sep+1;
    *sep = '.';
    }

index = gbIndexNew(database, NULL);
select.release = gbIndexMustFindRelease(index, relName);
select.update = gbReleaseMustFindUpdate(select.release, updateName);
select.orgCats = gbParseOrgCat(optionVal("orgCats", "native,xeno"));

gbVerbMsg(0, "gbAlignInstall: %s/%s/%s/%s", select.release->name,
          select.release->genome->database, select.update->name,
          typeAccPrefix);

/* Get the release to migrate, if applicable */
if (!noMigrate)
    prevSelect = gbAlignGetMigrateRel(&select);

gbAlignInstall(&select, prevSelect);

/* must go to stderr to be logged */
gbVerbMsg(0, "gbAlignInstall: complete");
    
gbIndexFree(&index);
return 0;
}