/* Unpack the full instruction */
void unpack_instruction(struct Instruction* c)
{
unpack_byte(c->raw0, &(c->operation[0]));
unpack_byte(c->raw1, &(c->operation[2]));
unpack_byte(c->raw2, &(c->operation[4]));
unpack_byte(c->raw3, &(c->operation[6]));
c->opcode[0] = c->operation[0];
c->opcode[1] = c->operation[1];
}
int
msa_recv_pkt(msa_pkt_t *pkt, int sfd)
{
byte_t *dt = 0;
byte_t st_u = 0;
size_t st_sz = 0, id_sz = 0, sz_sz = 0;
unsigned int id_u = 0, sz_u = 0;
assert(sfd >= 0);
st_sz = sizeof(byte_t);
id_sz = sizeof(int);
sz_sz = sizeof(int);
dt = malloc(st_sz);
msa_recv_all(sfd, dt, st_sz);
st_u = unpack_byte(dt);
pkt->st = st_u;
free(dt); dt = 0;
dt = malloc(id_sz);
msa_recv_all(sfd, dt, id_sz);
id_u = unpack_int(dt);
pkt->id = id_u;
free(dt); dt = 0;
dt = malloc(sz_sz);
msa_recv_all(sfd, dt, sz_sz);
sz_u = unpack_int(dt);
pkt->sz = sz_u;
free(dt); dt = 0;
if (sz_u != 0) {
dt = malloc(sz_u * sizeof(char));
msa_recv_all(sfd, dt, sz_u * sizeof(char));
pkt->da = unpack_str(dt, sz_u * sizeof(char));
free(dt); dt = 0;
} else {
pkt->da = 0;
}
return 0; /* do some error checking? */
}
// the packed reference sequence is read from the PAC file, uncompressed,
// concatenated with its reverse complement, and stored into seq
void pac2seq(const char *pacFname, unsigned char** seq, bwtint_t *totalSeqLen) {
FILE* pacFile = (FILE*) fopen(pacFname, "rb");
if (pacFile == NULL) {
printf("pac2seq: Cannot open PAC file %s!\n", pacFname);
exit(1);
}
fseek(pacFile, -1, SEEK_END);
// position in the file (# bytes from the beginning of file)
bwtint_t pacFileLen = ftell(pacFile);
if (pacFileLen < 0) {
printf("pac2seq: Cannot determine the length of the PAC file!\n");
exit(1);
}
unsigned char endByte;
if(fread(&endByte, sizeof(unsigned char), 1, pacFile) < 1) {
printf("pac2seq: Cannot read the PAC file!\n");
exit(1);
}
bwtint_t seqLength = pacFileLen*CHARS_PER_BYTE - endByte;
// read the packed sequence
fseek(pacFile, 0, SEEK_SET);
unsigned char* packedSeq = (unsigned char*) malloc(sizeof(char) * pacFileLen);
if(fread(packedSeq, 1, pacFileLen, pacFile) < pacFileLen) {
printf("pac2seq: Could not read the expected length of the PAC file!\n");
exit(1);
}
fclose(pacFile);
// unpack the sequence
*seq = (unsigned char*) malloc(sizeof(char) * (2*seqLength + 1));
unpack_byte(packedSeq, *seq, seqLength);
// add the reverse complement
for(bwtint_t i = 0; i < seqLength; i++) {
(*seq)[2*seqLength-i-1] = iupacCompl[(int) (*seq)[i]];
}
(*totalSeqLen) = 2*seqLength;
free(packedSeq);
}