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restructure bns_fasta2bntseq() for further changes

This commit is contained in:
Heng Li 2011-10-20 11:53:44 -04:00
parent b7e8c4c5aa
commit 70da24e177
1 changed files with 52 additions and 48 deletions
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100
bntseq.c
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@ -163,16 +163,63 @@ void bns_destroy(bntseq_t *bns)
}
}
static void add1(const kseq_t *seq, bntseq_t *bns, FILE *fp, uint8_t *buf, int *l_buf, int *m_seqs, int *m_holes, bntamb1_t **q)
{
bntann1_t *p;
int i, lasts;
if (bns->n_seqs == *m_seqs) {
*m_seqs <<= 1;
bns->anns = (bntann1_t*)realloc(bns->anns, *m_seqs * sizeof(bntann1_t));
}
p = bns->anns + bns->n_seqs;
p->name = strdup((char*)seq->name.s);
p->anno = seq->comment.s? strdup((char*)seq->comment.s) : strdup("(null)");
p->gi = 0; p->len = seq->seq.l;
p->offset = (bns->n_seqs == 0)? 0 : (p-1)->offset + (p-1)->len;
p->n_ambs = 0;
for (i = lasts = 0; i < seq->seq.l; ++i) {
int c = nst_nt4_table[(int)seq->seq.s[i]];
if (c >= 4) { // N
if (lasts == seq->seq.s[i]) { // contiguous N
++(*q)->len;
} else {
if (bns->n_holes == *m_holes) {
(*m_holes) <<= 1;
bns->ambs = (bntamb1_t*)realloc(bns->ambs, (*m_holes) * sizeof(bntamb1_t));
}
*q = bns->ambs + bns->n_holes;
(*q)->len = 1;
(*q)->offset = p->offset + i;
(*q)->amb = seq->seq.s[i];
++p->n_ambs;
++bns->n_holes;
}
}
lasts = seq->seq.s[i];
{ // fill buffer
if (c >= 4) c = lrand48()&0x3;
if (*l_buf == 0x40000) {
fwrite(buf, 1, 0x10000, fp);
memset(buf, 0, 0x10000);
*l_buf = 0;
}
buf[*l_buf>>2] |= c << ((3 - (*l_buf&3)) << 1);
++(*l_buf);
}
}
++bns->n_seqs;
bns->l_pac += seq->seq.l;
}
int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix)
{
kseq_t *seq;
char name[1024];
bntseq_t *bns;
bntamb1_t *q;
int l_buf;
unsigned char buf[0x10000];
int32_t m_seqs, m_holes, l, i;
int32_t l_buf, m_seqs, m_holes;
int64_t ret = -1;
bntamb1_t *q;
FILE *fp;
// initialization
@ -189,51 +236,8 @@ int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix)
fp = xopen(name, "wb");
memset(buf, 0, 0x10000);
// read sequences
while ((l = kseq_read(seq)) >= 0) {
bntann1_t *p;
int lasts;
if (bns->n_seqs == m_seqs) {
m_seqs <<= 1;
bns->anns = (bntann1_t*)realloc(bns->anns, m_seqs * sizeof(bntann1_t));
}
p = bns->anns + bns->n_seqs;
p->name = strdup((char*)seq->name.s);
p->anno = seq->comment.s? strdup((char*)seq->comment.s) : strdup("(null)");
p->gi = 0; p->len = l;
p->offset = (bns->n_seqs == 0)? 0 : (p-1)->offset + (p-1)->len;
p->n_ambs = 0;
for (i = 0, lasts = 0; i < l; ++i) {
int c = nst_nt4_table[(int)seq->seq.s[i]];
if (c >= 4) { // N
if (lasts == seq->seq.s[i]) { // contiguous N
++q->len;
} else {
if (bns->n_holes == m_holes) {
m_holes <<= 1;
bns->ambs = (bntamb1_t*)realloc(bns->ambs, m_holes * sizeof(bntamb1_t));
}
q = bns->ambs + bns->n_holes;
q->len = 1;
q->offset = p->offset + i;
q->amb = seq->seq.s[i];
++p->n_ambs;
++bns->n_holes;
}
}
lasts = seq->seq.s[i];
{ // fill buffer
if (c >= 4) c = lrand48()&0x3;
if (l_buf == 0x40000) {
fwrite(buf, 1, 0x10000, fp);
memset(buf, 0, 0x10000);
l_buf = 0;
}
buf[l_buf>>2] |= c << ((3 - (l_buf&3)) << 1);
++l_buf;
}
}
++bns->n_seqs;
bns->l_pac += seq->seq.l;
while (kseq_read(seq) >= 0) {
add1(seq, bns, fp, buf, &l_buf, &m_seqs, &m_holes, &q);
}
xassert(bns->l_pac, "zero length sequence.");
ret = bns->l_pac;