int main(int argc, char *argv[])
{
// Intialize the R environment.
int r_argc = 2;
char *r_argv[] = { "R", "--silent" };
Rf_initEmbeddedR(r_argc, r_argv);
int arg[] = { 1, 2, 3, 4, 5 };
// Invoke a function in R
source("func.R");
R_add1(5, arg);
// Release R environment
Rf_endEmbeddedR(0);
return(0);
}
int64_t R_bns_fasta2bntseq(gzFile fp_fa, const char *prefix)
{
// extern void seq_reverse(int len, ubyte_t *seq, int is_comp); // in bwaseqio.c
kseq_t *seq;
char name[1024];
bntseq_t *bns;
uint8_t *pac = 0;
uint8_t *reverse_pac = NULL;
int32_t m_seqs, m_holes;
int64_t ret = -1, m_pac, l, m_r_pac;
bntamb1_t *q;
FILE *fp, *fp_r;
int i;
// initialization
seq = kseq_init(fp_fa);
bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
bns->seed = 11; // fixed seed for random generator
srand48(bns->seed);
m_seqs = m_holes = 8; m_pac = 0x10000;
bns->anns = (bntann1_t*)calloc(m_seqs, sizeof(bntann1_t));
bns->ambs = (bntamb1_t*)calloc(m_holes, sizeof(bntamb1_t));
pac = calloc(m_pac/NT_PER_BYTE, 1);
q = bns->ambs;
strcpy(name, prefix); strcat(name, ".pac");
fp = xopen(name, "wb");
memset(name, '\0', 1024);strcpy(name, prefix); strcat(name, ".rpac");
fp_r = xopen(name, "wb");
// read sequences
while (kseq_read(seq) >= 0) pac = R_add1(seq, bns, pac, &m_pac, &m_seqs, &m_holes, &q);
// add the reverse complemented sequence
ret = bns->l_pac;
fprintf(stderr, "[R_bns_fasta2bntseq]:reverse_pac!\n");
m_r_pac = (bns->l_pac +NT_PER_BYTE-1)/NT_PER_BYTE *NT_PER_BYTE;
reverse_pac = calloc(m_r_pac/NT_PER_BYTE, sizeof(uint8_t));
for(l = bns->l_pac-1, i =0; l>=0, i < bns->l_pac; --l, ++i)
{
_set_pac(reverse_pac, i, _get_pac(pac, l));
}
ubyte_t ct;
{ // finalize .pac and file
fwrite(pac, 1, (bns->l_pac>>1) + ((bns->l_pac&1) == 0? 0 : 1), fp);
// the following codes make the pac file size always (l_pac/4+1+1)
if (bns->l_pac % NT_PER_BYTE == 0) {
ct = 0;
fwrite(&ct, 1, 1, fp);
}
ct = bns->l_pac % NT_PER_BYTE;
fwrite(&ct, 1, 1, fp);
// close .pac file
fclose(fp);
}
{ // finalize .rpac and file
fwrite(reverse_pac, 1, (bns->l_pac>>1) + ((bns->l_pac&1) == 0? 0 : 1), fp_r);
// the following codes make the pac file size always (l_pac/4+1+1)
if (bns->l_pac % NT_PER_BYTE == 0) {
ct = 0;
fwrite(&ct, 1, 1, fp_r);
}
ct = bns->l_pac % NT_PER_BYTE;
fwrite(&ct, 1, 1, fp_r);
// close .rpac file
fclose(fp_r);
}
bns_dump(bns, prefix);
bns_destroy(bns);
kseq_destroy(seq);
free(pac);
free(reverse_pac);
return ret;
}
