bwaseqio.c

#include <zlib.h>
#include <ctype.h>
#include "bwtaln.h"
#include "utils.h"
#include "bamlite.h"

#include "kseq.h"
KSEQ_DECLARE(gzFile)

#ifdef USE_MALLOC_WRAPPERS
#  include "malloc_wrap.h"
#endif

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");
	if (0 == bs->fp) err_fatal_simple("Couldn't open bam file");
	h = bam_header_read(bs->fp);
	bam_header_destroy(h);
	return bs;
}

bwa_seqio_t *bwa_seq_open(const char *fn)
{
	return bwa_seq_open2(fn, -1);
}

bwa_seqio_t *bwa_seq_open2(const char *fn, int bufsize)
{
	gzFile fp;
	bwa_seqio_t *bs;
	bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
	if (0 < bufsize) {
		fp = xzopen2(fn, "r", bufsize);
		bs->ks = kseq_init2(fp, bufsize);
	}
	else {
		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) {
		if (0 != bam_close(bs->fp)) err_fatal_simple("Error closing bam file");
	} else {
		err_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;
	if (trim_qual < 1 || p->qual == 0) return 0;
	for (l = p->len - 1; l >= BWA_MIN_RDLEN; --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;
	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;
	int res;

	b = bam_init1();
	n_seqs = 0;
	seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
	while ((res = 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;
	}
	if (res < 0 && res != -1) err_fatal_simple("Error reading bam file");
	*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)
{
	return bwa_read_seq2(bs, n_needed, n, mode, trim_qual, 0);
}

bwa_seq_t *bwa_read_seq2(bwa_seqio_t *bs, int n_needed, int *n, int mode, int trim_qual, int interactive_mode)
{
	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));
	for (;;) {
		// Reading in one-sequence at a time.
		// - in interactive mode, keep reading until we have read at least one sequence and then stop after the first blank line.
		// - in non-interactive mode, read up to the number of sequences needed or the end-of-file.
		l = kseq_read2(seq, !interactive_mode); // read it in
		if (interactive_mode && l == -3) { // -3 is an empty line
			if (n_seqs == 0) continue; // need more, skip the empty line
			else break; // we have at least one read, so return the reads before the first emtpy line.
		}
		else if (l < 0) break; // did we get a read?

		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->full_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);
}