int
main(void) {
setvbuf(stdin, 0, _IOFBF, 1024*1024);
long stdin_size = get_file_size(stdin);
uint8_t *buffer = calloc(stdin_size + LINE_LENGTH, 1);
assert(buffer);
lookup_t lookup;
pthread_mutex_t mutex;
job_t *job = 0;
init_lookup(
(const uint8_t *)"acbdghkmnsrutwvy",
(const uint8_t *)"TGVHCDMKNSYAAWBR",
&lookup);
pthread_mutex_init(&mutex, 0);
uint8_t *current = buffer;
uint8_t *end = buffer + stdin_size;
uint8_t *header_begin = 0;
uint8_t *header_end = 0;
uint8_t *body_begin = 0;
while (fgets_unlocked((char *)current, end - current, stdin)) {
if (current[0] == '>') {
if (body_begin != 0) {
job = do_process_block(
header_begin, header_end,
body_begin, current,
&lookup,
&mutex,
job);
}
size_t len = strlen((const char *)current);
header_begin = current;
header_end = current + len;
current += len;
body_begin = current;
} else {
if (current[LINE_LENGTH] == '\n') {
current += LINE_LENGTH;
} else {
size_t len = strlen((const char *)current);
if (current[len - 1] == '\n') {
--len;
}
current += len;
}
}
}
if (body_begin != 0) {
job = do_process_block(
header_begin, header_end,
body_begin, current,
&lookup,
&mutex,
job);
}
while (job) {
pthread_join(job->thread, 0);
if (job->free_buffer) {
free(job->buffer);
}
job = job->prev_job;
}
free(buffer);
return 0;
}
int revcomp_main(void) {
//setvbuf(input_file, 0, _IOFBF, 1024*1024);
//long stdin_size = get_file_size(input_file);
long lSize;
size_t result;
struct rqst_struct rqst;
rqst.bytes = MAXSIZE;
rqst.pid = PROC_ID;
rqst.id = CHUNK_ID;
lSize = rqst.bytes;
fprintf(stdout, "entering revcomp_main \n");
// copy the file into the buffer:
uint8_t *buffer = pnvread(lSize,&rqst);
//uint8_t *buffer = calloc(stdin_size + LINE_LENGTH, 1);
assert(buffer);
lookup_t lookup;
pthread_mutex_t mutex;
job_t *job = 0;
init_lookup(
(const uint8_t *)"acbdghkmnsrutwvy",
(const uint8_t *)"TGVHCDMKNSYAAWBR",
&lookup);
pthread_mutex_init(&mutex, 0);
uint8_t *current = buffer;
uint8_t *end = buffer + lSize;
uint8_t *header_begin = 0;
uint8_t *header_end = 0;
uint8_t *body_begin = 0;
fprintf(stderr,"Current %s \n",current);
if (current[0] == '>') {
if (body_begin != 0) {
job = do_process_block(
header_begin, header_end,
body_begin, current,
&lookup,
&mutex,
job);
}
size_t len = strlen((const char *)current);
header_begin = current;
header_end = current + len;
current += len;
body_begin = current;
} else {
if (current[LINE_LENGTH] == '\n') {
current += LINE_LENGTH;
} else {
size_t len = strlen((const char *)current);
if (current[len - 1] == '\n') {
--len;
}
current += len;
}
}
if (body_begin != 0) {
job = do_process_block(
header_begin, header_end,
body_begin, current,
&lookup,
&mutex,
job);
}
while (job) {
pthread_join(job->thread, 0);
if (job->free_buffer) {
nv_free(job->buffer);
}
job = job->prev_job;
}
fprintf(stdout, "revcomp main returning \n");
/*free(buffer);*/
return 0;
}
