File: bam.c

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#include <stdio.h>
#include <ctype.h>
#include <errno.h>
#include <assert.h>
#include "bam.h"
#include "bam_endian.h"
#include "kstring.h"
#include "sam_header.h"

int bam_is_be = 0, bam_verbose = 2, bam_no_B = 0;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";

/**************************
 * CIGAR related routines *
 **************************/

uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
{
	int k, end = c->pos;
	for (k = 0; k < c->n_cigar; ++k) {
		int op  = bam_cigar_op(cigar[k]);
		int len = bam_cigar_oplen(cigar[k]);
		if (op == BAM_CBACK) { // move backward
			int l, u, v;
			if (k == c->n_cigar - 1) break; // skip trailing 'B'
			for (l = k - 1, u = v = 0; l >= 0; --l) {
				int op1  = bam_cigar_op(cigar[l]);
				int len1 = bam_cigar_oplen(cigar[l]);
				if (bam_cigar_type(op1)&1) { // consume query
					if (u + len1 >= len) { // stop
						if (bam_cigar_type(op1)&2) v += len - u;
						break;
					} else u += len1;
				}
				if (bam_cigar_type(op1)&2) v += len1;
			}
			end = l < 0? c->pos : end - v;
		} else if (bam_cigar_type(op)&2) end += bam_cigar_oplen(cigar[k]);
	}
	return end;
}

int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
{
	uint32_t k;
	int32_t l = 0;
	for (k = 0; k < c->n_cigar; ++k)
		if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
			l += bam_cigar_oplen(cigar[k]);
	return l;
}

/********************
 * BAM I/O routines *
 ********************/

bam_header_t *bam_header_init()
{
	bam_is_be = bam_is_big_endian();
	return (bam_header_t*)calloc(1, sizeof(bam_header_t));
}

void bam_header_destroy(bam_header_t *header)
{
	int32_t i;
	extern void bam_destroy_header_hash(bam_header_t *header);
	if (header == 0) return;
	if (header->target_name) {
		for (i = 0; i < header->n_targets; ++i)
			free(header->target_name[i]);
		free(header->target_name);
		free(header->target_len);
	}
	free(header->text);
	if (header->dict) sam_header_free(header->dict);
	if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
	bam_destroy_header_hash(header);
	free(header);
}

bam_header_t *bam_header_read(bamFile fp)
{
	bam_header_t *header;
	char buf[4];
	int magic_len;
	int32_t i = 1, name_len;
	// check EOF
	i = bgzf_check_EOF(fp);
	if (i < 0) {
		// If the file is a pipe, checking the EOF marker will *always* fail
		// with ESPIPE.  Suppress the error message in this case.
		if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
	}
	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
	// read "BAM1"
	magic_len = bam_read(fp, buf, 4);
	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
		fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
		return 0;
	}
	header = bam_header_init();
	// read plain text and the number of reference sequences
	bam_read(fp, &header->l_text, 4);
	if (bam_is_be) bam_swap_endian_4p(&header->l_text);
	header->text = (char*)calloc(header->l_text + 1, 1);
	bam_read(fp, header->text, header->l_text);
	bam_read(fp, &header->n_targets, 4);
	if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
	// read reference sequence names and lengths
	header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
	header->target_len = (uint32_t*)calloc(header->n_targets, 4);
	for (i = 0; i != header->n_targets; ++i) {
		bam_read(fp, &name_len, 4);
		if (bam_is_be) bam_swap_endian_4p(&name_len);
		header->target_name[i] = (char*)calloc(name_len, 1);
		bam_read(fp, header->target_name[i], name_len);
		bam_read(fp, &header->target_len[i], 4);
		if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
	}
	return header;
}

int bam_header_write(bamFile fp, const bam_header_t *header)
{
	char buf[4];
	int32_t i, name_len, x;
	// write "BAM1"
	strncpy(buf, "BAM\001", 4);
	bam_write(fp, buf, 4);
	// write plain text and the number of reference sequences
	if (bam_is_be) {
		x = bam_swap_endian_4(header->l_text);
		bam_write(fp, &x, 4);
		if (header->l_text) bam_write(fp, header->text, header->l_text);
		x = bam_swap_endian_4(header->n_targets);
		bam_write(fp, &x, 4);
	} else {
		bam_write(fp, &header->l_text, 4);
		if (header->l_text) bam_write(fp, header->text, header->l_text);
		bam_write(fp, &header->n_targets, 4);
	}
	// write sequence names and lengths
	for (i = 0; i != header->n_targets; ++i) {
		char *p = header->target_name[i];
		name_len = strlen(p) + 1;
		if (bam_is_be) {
			x = bam_swap_endian_4(name_len);
			bam_write(fp, &x, 4);
		} else bam_write(fp, &name_len, 4);
		bam_write(fp, p, name_len);
		if (bam_is_be) {
			x = bam_swap_endian_4(header->target_len[i]);
			bam_write(fp, &x, 4);
		} else bam_write(fp, &header->target_len[i], 4);
	}
	bgzf_flush(fp);
	return 0;
}

static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
{
	uint8_t *s;
	uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
	s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
	for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
	while (s < data + data_len) {
		uint8_t type;
		s += 2; // skip key
		type = toupper(*s); ++s; // skip type
		if (type == 'C' || type == 'A') ++s;
		else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
		else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
		else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
		else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
		else if (type == 'B') {
			int32_t n, Bsize = bam_aux_type2size(*s);
			memcpy(&n, s + 1, 4);
			if (1 == Bsize) {
			} else if (2 == Bsize) {
				for (i = 0; i < n; i += 2)
					bam_swap_endian_2p(s + 5 + i);
			} else if (4 == Bsize) {
				for (i = 0; i < n; i += 4)
					bam_swap_endian_4p(s + 5 + i);
			}
			bam_swap_endian_4p(s+1); 
		}
	}
}

int bam_read1(bamFile fp, bam1_t *b)
{
	bam1_core_t *c = &b->core;
	int32_t block_len, ret, i;
	uint32_t x[8];

	assert(BAM_CORE_SIZE == 32);
	if ((ret = bam_read(fp, &block_len, 4)) != 4) {
		if (ret == 0) return -1; // normal end-of-file
		else return -2; // truncated
	}
	if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
	if (bam_is_be) {
		bam_swap_endian_4p(&block_len);
		for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
	}
	c->tid = x[0]; c->pos = x[1];
	c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
	c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
	c->l_qseq = x[4];
	c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
	b->data_len = block_len - BAM_CORE_SIZE;
	if (b->m_data < b->data_len) {
		b->m_data = b->data_len;
		kroundup32(b->m_data);
		b->data = (uint8_t*)realloc(b->data, b->m_data);
	}
	if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
	b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
	if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
	if (bam_no_B) bam_remove_B(b);
	return 4 + block_len;
}

inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
{
	uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
	int i;
	assert(BAM_CORE_SIZE == 32);
	x[0] = c->tid;
	x[1] = c->pos;
	x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
	x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
	x[4] = c->l_qseq;
	x[5] = c->mtid;
	x[6] = c->mpos;
	x[7] = c->isize;
	bgzf_flush_try(fp, 4 + block_len);
	if (bam_is_be) {
		for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
		y = block_len;
		bam_write(fp, bam_swap_endian_4p(&y), 4);
		swap_endian_data(c, data_len, data);
	} else bam_write(fp, &block_len, 4);
	bam_write(fp, x, BAM_CORE_SIZE);
	bam_write(fp, data, data_len);
	if (bam_is_be) swap_endian_data(c, data_len, data);
	return 4 + block_len;
}

int bam_write1(bamFile fp, const bam1_t *b)
{
	return bam_write1_core(fp, &b->core, b->data_len, b->data);
}

char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
{
	uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
	int i;
	const bam1_core_t *c = &b->core;
	kstring_t str;
	str.l = str.m = 0; str.s = 0;

	kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
	if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
	else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
	else { // BAM_OFSTR
		for (i = 0; i < 16; ++i)
			if ((c->flag & 1<<i) && bam_flag2char_table[i])
				kputc(bam_flag2char_table[i], &str);
		kputc('\t', &str);
	}
	if (c->tid < 0) kputsn("*\t", 2, &str);
	else {
		if (header) kputs(header->target_name[c->tid] , &str);
		else kputw(c->tid, &str);
		kputc('\t', &str);
	}
	kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
	if (c->n_cigar == 0) kputc('*', &str);
	else {
		uint32_t *cigar = bam1_cigar(b);
		for (i = 0; i < c->n_cigar; ++i) {
			kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
			kputc(bam_cigar_opchr(cigar[i]), &str);
		}
	}
	kputc('\t', &str);
	if (c->mtid < 0) kputsn("*\t", 2, &str);
	else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
	else {
		if (header) kputs(header->target_name[c->mtid], &str);
		else kputw(c->mtid, &str);
		kputc('\t', &str);
	}
	kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
	if (c->l_qseq) {
		for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
		kputc('\t', &str);
		if (t[0] == 0xff) kputc('*', &str);
		else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
	} else kputsn("*\t*", 3, &str);
	s = bam1_aux(b);
	while (s < b->data + b->data_len) {
		uint8_t type, key[2];
		key[0] = s[0]; key[1] = s[1];
		s += 2; type = *s; ++s;
		kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
		if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
		else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
		else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
		else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
		else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
		else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
		else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
		else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
		else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
		else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
		else if (type == 'B') {
			uint8_t sub_type = *(s++);
			int32_t n;
			memcpy(&n, s, 4);
			s += 4; // no point to the start of the array
			kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
			for (i = 0; i < n; ++i) {
				kputc(',', &str);
				if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
				else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
				else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
				else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
				else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
				else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
				else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
			}
		}
	}
	return str.s;
}

char *bam_format1(const bam_header_t *header, const bam1_t *b)
{
	return bam_format1_core(header, b, BAM_OFDEC);
}

void bam_view1(const bam_header_t *header, const bam1_t *b)
{
	char *s = bam_format1(header, b);
	puts(s);
	free(s);
}

int bam_validate1(const bam_header_t *header, const bam1_t *b)
{
	char *s;

	if (b->core.tid < -1 || b->core.mtid < -1) return 0;
	if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;

	if (b->data_len < b->core.l_qname) return 0;
	s = memchr(bam1_qname(b), '\0', b->core.l_qname);
	if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;

	// FIXME: Other fields could also be checked, especially the auxiliary data

	return 1;
}

// FIXME: we should also check the LB tag associated with each alignment
const char *bam_get_library(bam_header_t *h, const bam1_t *b)
{
	const uint8_t *rg;
	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
	if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
	rg = bam_aux_get(b, "RG");
	return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
}

/************
 * Remove B *
 ************/

int bam_remove_B(bam1_t *b)
{
	int i, j, end_j, k, l, no_qual;
	uint32_t *cigar, *new_cigar;
	uint8_t *seq, *qual, *p;
	// test if removal is necessary
	if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
	cigar = bam1_cigar(b);
	for (k = 0; k < b->core.n_cigar; ++k)
		if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
	if (k == b->core.n_cigar) return 0; // no 'B'
	if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
	// allocate memory for the new CIGAR
	if (b->data_len + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
		b->m_data = b->data_len + b->core.n_cigar * 4;
		kroundup32(b->m_data);
		b->data = (uint8_t*)realloc(b->data, b->m_data);
		cigar = bam1_cigar(b); // after realloc, cigar may be changed
	}
	new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
	// the core loop
	seq = bam1_seq(b); qual = bam1_qual(b);
	no_qual = (qual[0] == 0xff); // test whether base quality is available
	i = j = 0; end_j = -1;
	for (k = l = 0; k < b->core.n_cigar; ++k) {
		int op  = bam_cigar_op(cigar[k]);
		int len = bam_cigar_oplen(cigar[k]);
		if (op == BAM_CBACK) { // the backward operation
			int t, u;
			if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
			if (len > j) goto rmB_err; // an excessively long backward
			for (t = l - 1, u = 0; t >= 0; --t) { // look back
				int op1  = bam_cigar_op(new_cigar[t]);
				int len1 = bam_cigar_oplen(new_cigar[t]);
				if (bam_cigar_type(op1)&1) { // consume the query
					if (u + len1 >= len) { // stop
						new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
						break;
					} else u += len1;
				}
			}
			if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
			l = t + 1;
			end_j = j; j -= len;
		} else { // other CIGAR operations
			new_cigar[l++] = cigar[k];
			if (bam_cigar_type(op)&1) { // consume the query
				if (i != j) { // no need to copy if i == j
					int u, c, c0;
					for (u = 0; u < len; ++u) { // construct the consensus
						c = bam1_seqi(seq, i+u);
						if (j + u < end_j) { // in an overlap
							c0 = bam1_seqi(seq, j+u);
							if (c != c0) { // a mismatch; choose the better base
								if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
									bam1_seq_seti(seq, j+u, c);
									qual[j+u] = qual[i+u] - qual[j+u];
								} else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
							} else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
						} else { // not in an overlap; copy over
							bam1_seq_seti(seq, j+u, c);
							qual[j+u] = qual[i+u];
						}
					}
				}
				i += len, j += len;
			}
		}
	}
	if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
	// merge adjacent operations if possible
	for (k = 1; k < l; ++k)
		if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
			new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
	// kill zero length operations
	for (k = i = 0; k < l; ++k)
		if (new_cigar[k] >> BAM_CIGAR_SHIFT)
			new_cigar[i++] = new_cigar[k];
	l = i;
	// update b
	memcpy(cigar, new_cigar, l * 4); // set CIGAR
	p = b->data + b->core.l_qname + l * 4;
	memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
	memmove(p, qual, j); p += j; // set QUAL
	memmove(p, bam1_aux(b), b->l_aux); p += b->l_aux; // set optional fields
	b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
	b->data_len = p - b->data; // update record length
	return 0;

rmB_err:
	b->core.flag |= BAM_FUNMAP;
	return -1;
}