buffer get_weather(char * cmd, int sockfd){
int numbytes;
char version[50];
char cmd1[8];
struct timeval timeout;
buffer ret;
memcpy (cmd1,cmd,6);
cmd1[6]='\n';
cmd1[7]='\0';
do{
ret = write_read("VER\n",4,sockfd);
}while (ret.error <= 0);
//printf("appeared to have gotten the version. packet length %d\n",ret.len);
memcpy (version,ret.data,ret.len);
version[ret.len] = '\0';
//printf("version is %s",version);
//printf("sending cmd %s",cmd1);
do{
ret = write_read(cmd1,7,sockfd);
//printf("code is %d\n",ret.error);
}while(ret.error<=0);
//printf("recieved %d bytes\n",ret.len);
return ret;
}
static int fusecow_read(const char *path, char *buf, size_t size,
off64_t offset, struct fuse_file_info *fi)
{
int res;
long long int block_number = offset / block_size;
if(offset + size > (block_number+1)*block_size) {
size = (block_number+1)*block_size - offset; // read only one block
}
if(write_map_get(block_number)) {
res=pread64(fd_write, buf, size, offset);
} else if(read_map_get(block_number)) {
res=pread64(fd_read, buf, size, offset);
} else {
res=pread64(fd, buf, size, offset);
// Data was never read yet, write to copy-on-read file.
if (res != write_read(buf, size, offset) && read_only)
res = -errno;
}
if (res == -1)
res = -errno;
return res;
}
bool setProtocolISO_EIC_15693BM019(BM019_PROTOCOL_ISO_IEC_15693_BYTE_0 configuration)
{
if(stateBM019 < BM019_STATE_ANSWERING) {
DEBUG("SETTING Protocol failed, bm019 not answering\n");
return false;
}
DEBUG("SETTING Protocol to iso/iec 15693: %#x\n",configuration);
int len = BM019_CMD_PROTOCOL_START[0]+BM019_CMD_PROTOCOL_ISO_IEC_15693[0];
uint8_t iso[BM019_CMD_PROTOCOL_START[0]+BM019_CMD_PROTOCOL_ISO_IEC_15693[0]];
memcpy(iso,&BM019_CMD_PROTOCOL_START[1],BM019_CMD_PROTOCOL_START[0]);
memcpy(&iso[BM019_CMD_PROTOCOL_START[0]],&BM019_CMD_PROTOCOL_ISO_IEC_15693[1],BM019_CMD_PROTOCOL_ISO_IEC_15693[0]);
iso[len-1] = configuration;
int recieved = write_read(iso,len,20);
if(recieved >= 2 && rxBuffer[0] == 0x00 && rxBuffer[1] == 0x00) {
stateBM019 = stateBM019 > BM019_STATE_PROTOCOL ? stateBM019 : BM019_STATE_PROTOCOL;
return true;
} else {
DEBUG("SETTING Protocol failed: %#x\n",rxBuffer[0]);
stateBM019 = BM019_STATE_UNKNOWN;
return false;
}
}
bool idnBM019(BM019_IDN *idn)
{
if(stateBM019 < BM019_STATE_ANSWERING) {
DEBUG("IDN failed, bm019 not answering\n");
return false;
}
int len = write_read(&BM019_CMD_IDN[1],BM019_CMD_IDN[0]);
if(len == 17) {
memcpy(idn->deviceID,(const void *)&rxBuffer[2],13);
memcpy(idn->romCRC,(const void *)&rxBuffer[15],2);
return true;
}
return false;
}
bool inventoryISO_IES_15693BM019(BM019_TAG *tag, int timeout)
{
if(stateBM019 < BM019_STATE_PROTOCOL) {
DEBUG("inventory failed, bm019 not in protocol\n");
return false;
}
DEBUG("inventory..");
int len = write_read(&BM019_CMD_ISO_IEC_15693_INVENTORY[1],BM019_CMD_ISO_IEC_15693_INVENTORY[0]);
DEBUG("got answer len()=%d\n",len);
for(int i = 0; i < len; i++) {
DEBUG("%#04x ",rxBuffer[i]);
}
DEBUG("\n");
if(rxBuffer[0] != EFrameRecvOK) {
DEBUG("got error %#04x\n",rxBuffer[0]);
return false;
}
int tlen = rxBuffer[1];
if(tlen < 11) {
DEBUG("to few bytes recieved \n");
return false;
}
/* this does not work very good, maybe something misinterpreted from docs
if(rxBuffer[tlen-1] & 0x01) {
DEBUG("got collision \n");
return false;
}
if(rxBuffer[tlen-1] & 0x02) {
DEBUG("got bad crc \n");
return false;
}*/
tag->crc[0] = rxBuffer[tlen-2];
tag->crc[1] = rxBuffer[tlen-3];
for(int i = 0; i < 9; i++) {
tag->uid[i] = rxBuffer[11-i];
}
return true;
}
bool echoBM019(int timeout, bool log)
{
if(log) {
DEBUG("BM019: echo\n");
}
int len = write_read(&BM019_CMD_ECHO[1],BM019_CMD_ECHO[0], timeout);
if(len>=1 && rxBuffer[0] == 0x55) {
stateBM019 = stateBM019 > BM019_STATE_ANSWERING ? stateBM019 : BM019_STATE_ANSWERING;
return true;
} else {
if(log) {
DEBUG("recievedlen: %d \n",len);
for(int i = 0; i < len; i++)
DEBUG("rx[%d]: %#x\n",i,rxBuffer[i]);
}
}
stateBM019 = BM019_STATE_UNKNOWN;
return false;
}
bool setProtocolOFF()
{
if(stateBM019 < BM019_STATE_ANSWERING) {
DEBUG("SETTING Protocol failed, bm019 not answering\n");
return false;
}
DEBUG("SETTING Protocol to OFF\n");
int len = BM019_CMD_PROTOCOL_START[0]+BM019_CMD_PROTOCOL_OFF[0];
uint8_t off[BM019_CMD_PROTOCOL_START[0]+BM019_CMD_PROTOCOL_OFF[0]];
memcpy(off,&BM019_CMD_PROTOCOL_START[1],BM019_CMD_PROTOCOL_START[0]);
memcpy(&off[BM019_CMD_PROTOCOL_START[0]],&BM019_CMD_PROTOCOL_OFF[1],BM019_CMD_PROTOCOL_OFF[0]);
int recieved = write_read(off,len,20);
if(recieved >= 2 && rxBuffer[0] == 0x00 && rxBuffer[1] == 0x00) {
stateBM019 = BM019_STATE_ANSWERING;
return true;
} else {
DEBUG("SETTING Protocol failed: %#x\n",rxBuffer[0]);
stateBM019 = BM019_STATE_UNKNOWN;
return false;
}
}
int readMultiBM019(uint8_t adr, int count, uint8_t *buf, int len, int timeout)
{
if(stateBM019 < BM019_STATE_PROTOCOL) {
DEBUG("multi read failed, bm019 not in protocol\n");
return -1;
}
uint8_t cmd[BM019_CMD_READ_MULTI[0]];
memcpy(cmd,&BM019_CMD_READ_MULTI[1],BM019_CMD_READ_MULTI[0]);
cmd[BM019_CMD_READ_MULTI[0]-2] = adr & 0xFF;
cmd[BM019_CMD_READ_MULTI[0]-1] = (count-1) & 0xFF;
DEBUG("multi read at %#4X for %d..\n",adr, count & 0xFF);
for(int i = 0; i < BM019_CMD_READ_MULTI[0]; i++) {
DEBUG("%#04x ",cmd[i]);
}
int tx = write_read(cmd,BM019_CMD_READ_MULTI[0]);
DEBUG("got answer len()=%d\n",tx);
for(int i = 0; i < tx; i++) {
DEBUG("%02x ",rxBuffer[i]);
}
DEBUG("\n");
if(rxBuffer[0] != EFrameRecvOK) {
DEBUG("got error %#04x\n",rxBuffer[0]);
return -1;
}
DEBUG("flags: %#04x\n",rxBuffer[2]);
int tlen = rxBuffer[1]-4;
if(tlen <=0)
return -1;
DEBUG("read resultet in %d bytes, copying %d bytes\n",rxBuffer[1],(tlen < len ? tlen : len));
tlen = (tlen < len ? tlen : len);
memcpy(buf,(const void *)&rxBuffer[3],tlen);
return tlen;
}
void map_reads(gzFile *output_files, gzFile multi_out_file,
gzFile unmapped_out_file, gzFile reads_f, Mapper *mapper,
int reads_format, int output_type) {
FastqRead fastq_read;
MapRead map_read;
long warn_count, n_fastq_rec, n_fastq_err;
long n_map_uniq, n_map_multi, n_map_none;
map_read.fwd_nucs = my_new(unsigned char, FASTQ_MAX_LINE);
map_read.rev_nucs = my_new(unsigned char, FASTQ_MAX_LINE);
n_map_uniq = n_map_multi = n_map_none = 0;
warn_count = n_fastq_err = n_fastq_rec = 0;
/* loop over all records in FASTQ file */
while(TRUE) {
long r = 0;
/* read fastq record from file */
if(reads_format == READS_FORMAT_FASTQ) {
r = fastq_parse_read(&fastq_read, reads_f);
}
else if(reads_format == READS_FORMAT_QSEQ) {
r = fastq_parse_qseq_read(&fastq_read, reads_f);
}
else {
my_err("%s:%d: unknown read format", __FILE__, __LINE__);
}
if(r == FASTQ_END) {
/* we have reached the end of the file */
break;
}
if(r == FASTQ_ERR) {
/* this fastq record contains an error */
if(warn_count < FASTQ_MAX_WARN) {
warn_count += 1;
my_warn("%s:%d: skipping invalid fastq record:\n",
__FILE__, __LINE__);
fprintf(stderr, " %s\n %s\n %s\n %s\n", fastq_read.line1,
fastq_read.line2, fastq_read.line3, fastq_read.line4);
}
n_fastq_err += 1;
}
else if(fastq_read.read_len != mapper->seed_finder_fwd->read_len) {
/* check that read length is correct */
warn_count += 1;
my_warn("%s:%d: specified read length is %u, but got %d, "
"skipping read\n", __FILE__, __LINE__,
mapper->seed_finder_fwd->read_len, fastq_read.read_len);
n_fastq_err += 1;
}
else if(r == FASTQ_OK) {
n_fastq_rec += 1;
read_from_fastq_record(&map_read, &fastq_read);
if((n_fastq_rec % 1000000) == 0) {
fprintf(stderr, ".");
}
/* try to map this read to genome */
mapper_map_one_read(mapper, &map_read);
if(map_read.map_code == MAP_CODE_NONE) {
/* read does not map to genome */
n_map_none += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_unmapped_read(output_files[0], &map_read);
} else {
write_unmapped_read(unmapped_out_file, &map_read);
}
}
else if(map_read.map_code == MAP_CODE_MULTI) {
/* read maps to multiple genomic locations */
n_map_multi += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_read(output_files, mapper->chr_tab, &map_read, FALSE);
} else {
write_read(&multi_out_file, mapper->chr_tab, &map_read, FALSE);
}
}
else if(map_read.map_code == MAP_CODE_UNIQUE) {
/* read maps to single genomic location */
n_map_uniq += 1;
if(output_type == OUTPUT_TYPE_SINGLE) {
write_read(output_files, mapper->chr_tab, &map_read, FALSE);
} else {
write_read(output_files, mapper->chr_tab, &map_read, TRUE);
}
}
else {
my_err("%s:%d: unknown mapping code", __FILE__, __LINE__);
}
} else {
my_err("%s:%d: unknown fastq status", __FILE__, __LINE__);
}
}
fprintf(stderr, "\ndone\n");
fprintf(stderr, "fastq errors: %ld\n", n_fastq_err);
fprintf(stderr, "fastq records (without errors): %ld\n", n_fastq_rec);
fprintf(stderr, "unmapped reads: %ld\n", n_map_none);
fprintf(stderr, "uniquely mapping reads: %ld\n", n_map_uniq);
fprintf(stderr, "multiply mapping reads: %ld\n", n_map_multi);
my_free(map_read.fwd_nucs);
my_free(map_read.rev_nucs);
}
/* main */
int main(int argc, char **argv)
{
off_t seek_pt;
int fd;
int c;
uint64_t i;
uint64_t node = 0;
long int random_tmp;
/* initialize */
seek_max = 0x7FFFFFFFFFFULL - IO_SIZE;
seek_min = 0;
/* option proc */
if (argc < 3) {
usage();
}
while ((c = getopt(argc, argv, "r:")) != EOF) {
switch (c) {
case 'r':
node = (uint64_t)strtoull(optarg, &optarg, 16);
seek_max = (node + 1) * IO_SIZE * IO_POINT - IO_SIZE;
seek_min = node * IO_SIZE * IO_POINT;
break;
default:
usage();
}
}
srand((unsigned int)node + time(NULL));
/* malloc buffer */
buf = (uint64_t *)malloc(IO_SIZE);
if (buf == NULL) {
perror("malloc()");
return TO_RETURN;
}
/* creat data set */
for (i = 0; i < (IO_SIZE / sizeof(uint64_t)); i++) {
buf[i] = i;
}
printf("node %"PRIu64" , start : %"PRIu64" , end : %"PRIu64"\n", node, seek_min, seek_max);
/* open file */
fd = open(FILE_NAME, O_RDWR|O_CREAT, 0666);
if (fd < 0) {
perror("OPEN");
free(buf);
return TO_RETURN;
}
for (;;) {
random_tmp = random() % IO_POINT;
seek_pt = random_tmp * IO_SIZE + seek_min;
if (seek_pt > seek_max) {
continue;
}
if (write_read(seek_pt, fd) < 0) {
if (close(fd) < 0) {
perror("close");
}
free(buf);
return TO_RETURN;
}
}
free(buf);
if (close(fd) < 0) {
perror("close");
return TO_RETURN;
}
return 0;
}
