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#include <zlib.h>
#include <ctype.h>
#include "bwtaln.h"
#include "utils.h"
#include "bamlite.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
extern unsigned char nst_nt4_table[256];
static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
struct __bwa_seqio_t {
// for BAM input
int is_bam, which; // 1st bit: read1, 2nd bit: read2, 3rd: SE
bamFile fp;
// for fastq input
kseq_t *ks;
};
bwa_seqio_t *bwa_bam_open(const char *fn, int which)
{
bwa_seqio_t *bs;
bam_header_t *h;
bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
bs->is_bam = 1;
bs->which = which;
bs->fp = bam_open(fn, "r");
h = bam_header_read(bs->fp);
bam_header_destroy(h);
return bs;
}
bwa_seqio_t *bwa_seq_open(const char *fn)
{
gzFile fp;
bwa_seqio_t *bs;
bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
fp = xzopen(fn, "r");
bs->ks = kseq_init(fp);
return bs;
}
void bwa_seq_close(bwa_seqio_t *bs)
{
if (bs == 0) return;
if (bs->is_bam) bam_close(bs->fp);
else {
gzclose(bs->ks->f->f);
kseq_destroy(bs->ks);
}
free(bs);
}
void seq_reverse(int len, ubyte_t *seq, int is_comp)
{
int i;
if (is_comp) {
for (i = 0; i < len>>1; ++i) {
char tmp = seq[len-1-i];
if (tmp < 4) tmp = 3 - tmp;
seq[len-1-i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
seq[i] = tmp;
}
if (len&1) seq[i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
} else {
for (i = 0; i < len>>1; ++i) {
char tmp = seq[len-1-i];
seq[len-1-i] = seq[i]; seq[i] = tmp;
}
}
}
int bwa_trim_read(int trim_qual, bwa_seq_t *p)
{
int s = 0, l, max = 0, max_l = p->len - 1;
if (trim_qual < 1 || p->qual == 0) return 0;
for (l = p->len - 1; l >= BWA_MIN_RDLEN - 1; --l) {
s += trim_qual - (p->qual[l] - 33);
if (s < 0) break;
if (s > max) {
max = s; max_l = l;
}
}
p->clip_len = p->len = max_l + 1;
return p->full_len - p->len;
}
static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_comp, int trim_qual)
{
bwa_seq_t *seqs, *p;
int n_seqs, l, i;
long n_trimmed = 0, n_tot = 0;
bam1_t *b;
b = bam_init1();
n_seqs = 0;
seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
while (bam_read1(bs->fp, b) >= 0) {
uint8_t *s, *q;
int go = 0;
if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
if ((bs->which & 2) && (b->core.flag & BAM_FREAD2)) go = 1;
if ((bs->which & 4) && !(b->core.flag& BAM_FREAD1) && !(b->core.flag& BAM_FREAD2))go = 1;
if (go == 0) continue;
l = b->core.l_qseq;
p = &seqs[n_seqs++];
p->tid = -1; // no assigned to a thread
p->qual = 0;
p->full_len = p->clip_len = p->len = l;
n_tot += p->full_len;
s = bam1_seq(b); q = bam1_qual(b);
p->seq = (ubyte_t*)calloc(p->len + 1, 1);
p->qual = (ubyte_t*)calloc(p->len + 1, 1);
for (i = 0; i != p->full_len; ++i) {
p->seq[i] = bam_nt16_nt4_table[(int)bam1_seqi(s, i)];
p->qual[i] = q[i] + 33 < 126? q[i] + 33 : 126;
}
if (bam1_strand(b)) { // then reverse
seq_reverse(p->len, p->seq, 1);
seq_reverse(p->len, p->qual, 0);
}
if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
p->rseq = (ubyte_t*)calloc(p->full_len, 1);
memcpy(p->rseq, p->seq, p->len);
seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
seq_reverse(p->len, p->rseq, is_comp);
p->name = strdup((const char*)bam1_qname(b));
if (n_seqs == n_needed) break;
}
*n = n_seqs;
if (n_seqs && trim_qual >= 1)
fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
if (n_seqs == 0) {
free(seqs);
bam_destroy1(b);
return 0;
}
bam_destroy1(b);
return seqs;
}
#define BARCODE_LOW_QUAL 13
bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int trim_qual)
{
bwa_seq_t *seqs, *p;
kseq_t *seq = bs->ks;
int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
long n_trimmed = 0, n_tot = 0;
if (l_bc > BWA_MAX_BCLEN) {
fprintf(stderr, "[%s] the maximum barcode length is %d.\n", __func__, BWA_MAX_BCLEN);
return 0;
}
if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input
n_seqs = 0;
seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
while ((l = kseq_read(seq)) >= 0) {
if ((mode & BWA_MODE_CFY) && (seq->comment.l != 0)) {
// skip reads that are marked to be filtered by Casava
char *s = index(seq->comment.s, ':');
if (s && *(++s) == 'Y') {
continue;
}
}
if (is_64 && seq->qual.l)
for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
if (seq->seq.l <= l_bc) continue; // sequence length equals or smaller than the barcode length
p = &seqs[n_seqs++];
if (l_bc) { // then trim barcode
for (i = 0; i < l_bc; ++i)
p->bc[i] = (seq->qual.l && seq->qual.s[i]-33 < BARCODE_LOW_QUAL)? tolower(seq->seq.s[i]) : toupper(seq->seq.s[i]);
p->bc[i] = 0;
for (; i < seq->seq.l; ++i)
seq->seq.s[i - l_bc] = seq->seq.s[i];
seq->seq.l -= l_bc; seq->seq.s[seq->seq.l] = 0;
if (seq->qual.l) {
for (i = l_bc; i < seq->qual.l; ++i)
seq->qual.s[i - l_bc] = seq->qual.s[i];
seq->qual.l -= l_bc; seq->qual.s[seq->qual.l] = 0;
}
l = seq->seq.l;
} else p->bc[0] = 0;
p->tid = -1; // no assigned to a thread
p->qual = 0;
p->full_len = p->clip_len = p->len = l;
n_tot += p->full_len;
p->seq = (ubyte_t*)calloc(p->len, 1);
for (i = 0; i != p->full_len; ++i)
p->seq[i] = nst_nt4_table[(int)seq->seq.s[i]];
if (seq->qual.l) { // copy quality
p->qual = (ubyte_t*)strdup((char*)seq->qual.s);
if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
}
p->rseq = (ubyte_t*)calloc(p->full_len, 1);
memcpy(p->rseq, p->seq, p->len);
seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
seq_reverse(p->len, p->rseq, is_comp);
p->name = strdup((const char*)seq->name.s);
{ // trim /[12]$
int t = strlen(p->name);
if (t > 2 && p->name[t-2] == '/' && (p->name[t-1] == '1' || p->name[t-1] == '2')) p->name[t-2] = '\0';
}
if (n_seqs == n_needed) break;
}
*n = n_seqs;
if (n_seqs && trim_qual >= 1)
fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
if (n_seqs == 0) {
free(seqs);
return 0;
}
return seqs;
}
void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs)
{
int i, j;
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *p = seqs + i;
for (j = 0; j < p->n_multi; ++j)
if (p->multi[j].cigar) free(p->multi[j].cigar);
free(p->name);
free(p->seq); free(p->rseq); free(p->qual); free(p->aln); free(p->md); free(p->multi);
free(p->cigar);
}
free(seqs);
}
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