new file mode 100644

@@ -0,0 +1,474 @@

+#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;

+}