void HiRes5Engine::initGameState() {
_state.vars.resize(40);
insertDisk(2);
StreamPtr stream(_disk->createReadStream(0x5, 0x1, 0x00, 3));
loadItems(*stream);
// A combined total of 1213 rooms
static const byte rooms[kRegions] = {
6, 16, 24, 57, 40, 30, 76, 40,
54, 38, 44, 21, 26, 42, 49, 32,
59, 69, 1, 1, 1, 1, 1, 18,
25, 13, 28, 28, 11, 23, 9, 31,
6, 29, 29, 34, 9, 10, 95, 86,
1
};
initRegions(rooms, kRegions);
loadRegion(1);
_state.room = 5;
_doAnimation = false;
}
int main(int argc, char *argv[])
{
if(argc != 5){
printf("Usage: gregions mode distance regionsfile.prof \n");
printf("\t mode = 0 -> ASCII candidates \n");
printf("\t mode = 1 -> Reference Candidates \n");
printf("example: bin/gregions 1 1.2 input/regions-score.1M.prof input/human_genome.fasta \n");
exit(0);
}
regions_t *regions;
sequences_t *genome;
seq_format_t candidatesMode = SEQ_ASCII, queriesMode = SEQ_ASCII;
uint32_t mode = atof(argv[1]);
float distance = atof(argv[2]);
char *profileFile = argv[3], *genomeFile = argv[4];
char regionsFile[512];
FILE *fp = NULL;
const uint32_t numGenomes = 1;
uint32_t *h_genomePositionCandidates = NULL, *h_regionsProfiledScores = NULL;
uint32_t numQueries = 0, totalSizeQueries = 0, numCandidates = 0, totalSizeCandidates = 0;
if(mode == 1) candidatesMode |= SEQ_REF_POS;
fp = fopen(profileFile, "rb");
if (fp == NULL) return(E_OPENING_FILE);
PSA_ERROR(countRegionsProfile(fp, distance, &numQueries, &totalSizeQueries, &numCandidates, &totalSizeCandidates));
PSA_ERROR(initRegions(®ions, numQueries, numCandidates, numCandidates));
PSA_ERROR(allocateRegions(regions, distance, totalSizeQueries, queriesMode, totalSizeCandidates, candidatesMode));
h_genomePositionCandidates = (uint32_t *) malloc(numCandidates * sizeof(uint32_t));
if (h_genomePositionCandidates == NULL) PSA_ERROR(E_ALLOCATE_MEM);
h_regionsProfiledScores = (uint32_t *) malloc(numCandidates * sizeof(uint32_t));
if (h_regionsProfiledScores == NULL) PSA_ERROR(E_ALLOCATE_MEM);
rewind(fp);
if(mode == 1) PSA_ERROR(loadRegionsProfile(fp, regions->queries->h_ASCII, regions->queries->h_size, regions->queries->h_ASCIIposition,
regions->candidates->h_refPosition, regions->alignments->h_info, h_regionsProfiledScores));
else PSA_ERROR(loadRegionsProfile(fp, regions->queries->h_ASCII, regions->queries->h_size, regions->queries->h_ASCIIposition,
h_genomePositionCandidates, regions->alignments->h_info, h_regionsProfiledScores));
regions->queries->formats |= queriesMode;
fclose(fp);
fp = fopen(genomeFile, "rb");
if (fp == NULL) return(E_OPENING_FILE);
PSA_ERROR(initSequences(&genome, numGenomes));
PSA_ERROR(loadSequenceMFASTA(fp, &genome->h_size, &genome->h_ASCII, &genome->h_ASCIIposition, &genome->formats));
fclose(fp);
/* recover the candidates from genome in ASCII rep */
if (mode == 1) PSA_ERROR(gatherCandidatesASCIIReference(regions, genome));
else PSA_ERROR(gatherCandidatesASCIIStream(regions, h_genomePositionCandidates, genome));
regions->candidates->formats |= candidatesMode;
/* DEBUG REGIONS*/
#if defined(DEBUG)
PSA_ERROR(printRegions(regions, 4, 1));
#endif
if (mode == 1) sprintf(regionsFile, "%s.%u.%u.%u.ref.regions", profileFile, regions->queries->num, regions->averageSizeQuery, regions->averageCandidatesPerQuery);\
else sprintf(regionsFile, "%s.%u.%u.%u.regions", profileFile, regions->queries->num, regions->averageSizeQuery, regions->averageCandidatesPerQuery);
fp = fopen(regionsFile, "wb");
if (fp == NULL) return(E_OPENING_FILE);
PSA_ERROR(saveRegions(fp, regions));
fclose(fp);
PSA_ERROR(freeRegions(®ions));
free(h_genomePositionCandidates);
free(h_regionsProfiledScores);
return (SUCCESS);
}
