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/* The MIT License
Copyright (c) 2008 Genome Research Ltd (GRL).
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
/* Contact: Heng Li <lh3@sanger.ac.uk> */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include "bntseq.h"
#include "main.h"
#include "utils.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
unsigned char nst_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
void bns_dump(const bntseq_t *bns, const char *prefix)
{
char str[1024];
FILE *fp;
int i;
{ // dump .ann
strcpy(str, prefix); strcat(str, ".ann");
fp = xopen(str, "w");
fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->seed);
for (i = 0; i != bns->n_seqs; ++i) {
bntann1_t *p = bns->anns + i;
fprintf(fp, "%d %s", p->gi, p->name);
if (p->anno[0]) fprintf(fp, " %s\n", p->anno);
else fprintf(fp, "\n");
fprintf(fp, "%lld %d %d\n", (long long)p->offset, p->len, p->n_ambs);
}
fclose(fp);
}
{ // dump .amb
strcpy(str, prefix); strcat(str, ".amb");
fp = xopen(str, "w");
fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->n_holes);
for (i = 0; i != bns->n_holes; ++i) {
bntamb1_t *p = bns->ambs + i;
fprintf(fp, "%lld %d %c\n", (long long)p->offset, p->len, p->amb);
}
fclose(fp);
}
}
bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename)
{
char str[1024];
FILE *fp;
bntseq_t *bns;
long long xx;
int i;
bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
{ // read .ann
fp = xopen(ann_filename, "r");
fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
bns->l_pac = xx;
bns->anns = (bntann1_t*)calloc(bns->n_seqs, sizeof(bntann1_t));
for (i = 0; i < bns->n_seqs; ++i) {
bntann1_t *p = bns->anns + i;
char *q = str;
int c;
// read gi and sequence name
fscanf(fp, "%u%s", &p->gi, str);
p->name = strdup(str);
// read fasta comments
while ((c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
*q = 0;
if (q - str > 1) p->anno = strdup(str + 1); // skip leading space
else p->anno = strdup("");
// read the rest
fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
p->offset = xx;
}
fclose(fp);
}
{ // read .amb
int64_t l_pac;
int32_t n_seqs;
fp = xopen(amb_filename, "r");
fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
l_pac = xx;
xassert(l_pac == bns->l_pac && n_seqs == bns->n_seqs, "inconsistent .ann and .amb files.");
bns->ambs = (bntamb1_t*)calloc(bns->n_holes, sizeof(bntamb1_t));
for (i = 0; i < bns->n_holes; ++i) {
bntamb1_t *p = bns->ambs + i;
fscanf(fp, "%lld%d%s", &xx, &p->len, str);
p->offset = xx;
p->amb = str[0];
}
fclose(fp);
}
{ // open .pac
bns->fp_pac = xopen(pac_filename, "rb");
}
return bns;
}
bntseq_t *bns_restore(const char *prefix)
{
char ann_filename[1024], amb_filename[1024], pac_filename[1024];
strcat(strcpy(ann_filename, prefix), ".ann");
strcat(strcpy(amb_filename, prefix), ".amb");
strcat(strcpy(pac_filename, prefix), ".pac");
return bns_restore_core(ann_filename, amb_filename, pac_filename);
}
void bns_destroy(bntseq_t *bns)
{
if (bns == 0) return;
else {
int i;
if (bns->fp_pac) fclose(bns->fp_pac);
free(bns->ambs);
for (i = 0; i < bns->n_seqs; ++i) {
free(bns->anns[i].name);
free(bns->anns[i].anno);
}
free(bns->anns);
free(bns);
}
}
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;
int64_t ret = -1;
FILE *fp;
// 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;
bns->anns = (bntann1_t*)calloc(m_seqs, sizeof(bntann1_t));
bns->ambs = (bntamb1_t*)calloc(m_holes, sizeof(bntamb1_t));
q = bns->ambs;
l_buf = 0;
strcpy(name, prefix); strcat(name, ".pac");
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;
}
xassert(bns->l_pac, "zero length sequence.");
ret = bns->l_pac;
{ // finalize .pac file
ubyte_t ct;
fwrite(buf, 1, (l_buf>>2) + ((l_buf&3) == 0? 0 : 1), fp);
// the following codes make the pac file size always (l_pac/4+1+1)
if (bns->l_pac % 4 == 0) {
ct = 0;
fwrite(&ct, 1, 1, fp);
}
ct = bns->l_pac % 4;
fwrite(&ct, 1, 1, fp);
// close .pac file
fclose(fp);
}
bns_dump(bns, prefix);
bns_destroy(bns);
kseq_destroy(seq);
return ret;
}
int bwa_fa2pac(int argc, char *argv[])
{
gzFile fp;
if (argc < 2) {
fprintf(stderr, "Usage: bwa fa2pac <in.fasta> [<out.prefix>]\n");
return 1;
}
fp = xzopen(argv[1], "r");
bns_fasta2bntseq(fp, (argc < 3)? argv[1] : argv[2]);
gzclose(fp);
return 0;
}
int bns_coor_pac2real(const bntseq_t *bns, int64_t pac_coor, int len, int32_t *real_seq)
{
int left, mid, right, nn;
if (pac_coor >= bns->l_pac)
err_fatal("bns_coor_pac2real", "bug! Coordinate is longer than sequence (%lld>=%lld).", pac_coor, bns->l_pac);
// binary search for the sequence ID. Note that this is a bit different from the following one...
left = 0; mid = 0; right = bns->n_seqs;
while (left < right) {
mid = (left + right) >> 1;
if (pac_coor >= bns->anns[mid].offset) {
if (mid == bns->n_seqs - 1) break;
if (pac_coor < bns->anns[mid+1].offset) break;
left = mid + 1;
} else right = mid;
}
*real_seq = mid;
// binary search for holes
left = 0; right = bns->n_holes; nn = 0;
while (left < right) {
int64_t mid = (left + right) >> 1;
if (pac_coor >= bns->ambs[mid].offset + bns->ambs[mid].len) left = mid + 1;
else if (pac_coor + len <= bns->ambs[mid].offset) right = mid;
else { // overlap
if (pac_coor >= bns->ambs[mid].offset) {
nn += bns->ambs[mid].offset + bns->ambs[mid].len < pac_coor + len?
bns->ambs[mid].offset + bns->ambs[mid].len - pac_coor : len;
} else {
nn += bns->ambs[mid].offset + bns->ambs[mid].len < pac_coor + len?
bns->ambs[mid].len : len - (bns->ambs[mid].offset - pac_coor);
}
break;
}
}
return nn;
}
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