new file mode 100644

@@ -0,0 +1,491 @@

+#define _POSIX_C_SOURCE 200112L /* Rsamtools: c99 fileno */

+#define _SVID_SOURCE            /* Rsamtools: c99 strdup */

+#include <zlib.h>

+#include <stdio.h>

+#include <ctype.h>

+#include <string.h>

+#include <stdlib.h>

+#include <unistd.h>

+#include <assert.h>

+#ifdef _WIN32

+#include <fcntl.h>

+#endif

+#include "kstring.h"

+#include "bam.h"

+#include "sam_header.h"

+#include "kseq.h"

+#include "khash.h"

+

+KSTREAM_INIT(gzFile, gzread, 16384)

+KHASH_MAP_INIT_STR(ref, uint64_t)

+

+void bam_init_header_hash(bam_header_t *header);

+void bam_destroy_header_hash(bam_header_t *header);

+int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);

+

+unsigned char bam_nt16_table[256] = {

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,

+	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,

+	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,

+	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,

+	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

+	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15

+};

+

+unsigned short bam_char2flag_table[256] = {

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,

+	BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,

+	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0

+};

+

+char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";

+

+struct __tamFile_t {

+	gzFile fp;

+	kstream_t *ks;

+	kstring_t *str;

+	uint64_t n_lines;

+	int is_first;

+};

+

+char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only

+{

+	char **list = 0, *s;

+	int n = 0, dret, m = 0;

+	gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");

+	kstream_t *ks;

+	kstring_t *str;

+	str = (kstring_t*)calloc(1, sizeof(kstring_t));

+	ks = ks_init(fp);

+	while (ks_getuntil(ks, '\n', str, &dret) > 0) {

+		if (n == m) {

+			m = m? m << 1 : 16;

+			list = (char**)realloc(list, m * sizeof(char*));

+		}

+		if (str->s[str->l-1] == '\r')

+			str->s[--str->l] = '\0';

+		s = list[n++] = (char*)calloc(str->l + 1, 1);

+		strcpy(s, str->s);

+	}

+	ks_destroy(ks);

+	gzclose(fp);

+	free(str->s); free(str);

+	*_n = n;

+	return list;

+}

+

+static bam_header_t *hash2header(const kh_ref_t *hash)

+{

+	bam_header_t *header;

+	khiter_t k;

+	header = bam_header_init();

+	header->n_targets = kh_size(hash);

+	header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));

+	header->target_len = (uint32_t*)calloc(kh_size(hash), 4);

+	for (k = kh_begin(hash); k != kh_end(hash); ++k) {

+		if (kh_exist(hash, k)) {

+			int i = (int)kh_value(hash, k);

+			header->target_name[i] = (char*)kh_key(hash, k);

+			header->target_len[i] = kh_value(hash, k)>>32;

+		}

+	}

+	bam_init_header_hash(header);

+	return header;

+}

+bam_header_t *sam_header_read2(const char *fn)

+{

+	bam_header_t *header;

+	int c, dret, ret, error = 0;

+	gzFile fp;

+	kstream_t *ks;

+	kstring_t *str;

+	kh_ref_t *hash;

+	khiter_t k;

+	if (fn == 0) return 0;

+	fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");

+	if (fp == 0) return 0;

+	hash = kh_init(ref);

+	ks = ks_init(fp);

+	str = (kstring_t*)calloc(1, sizeof(kstring_t));

+	while (ks_getuntil(ks, 0, str, &dret) > 0) {

+		char *s = strdup(str->s);

+		int len, i;

+		i = kh_size(hash);

+		ks_getuntil(ks, 0, str, &dret);

+		len = atoi(str->s);

+		k = kh_put(ref, hash, s, &ret);

+		if (ret == 0) {

+			fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);

+			error = 1;

+		}

+		kh_value(hash, k) = (uint64_t)len<<32 | i;

+		if (dret != '\n')

+			while ((c = ks_getc(ks)) != '\n' && c != -1);

+	}

+	ks_destroy(ks);

+	gzclose(fp);

+	free(str->s); free(str);

+	fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));

+	if (error) return 0;

+	header = hash2header(hash);

+	kh_destroy(ref, hash);

+	return header;

+}

+static inline uint8_t *alloc_data(bam1_t *b, int size)

+{

+	if (b->m_data < size) {

+		b->m_data = size;

+		kroundup32(b->m_data);

+		b->data = (uint8_t*)realloc(b->data, b->m_data);

+	}

+	return b->data;

+}

+static inline void parse_error(int64_t n_lines, const char * __restrict msg)

+{

+	fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);

+	abort();

+}

+static inline void append_text(bam_header_t *header, kstring_t *str)

+{

+	size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null

+	kroundup32(x); kroundup32(y);

+	if (x < y) 

+    {

+        header->n_text = y;

+        header->text = (char*)realloc(header->text, y);

+        if ( !header->text ) 

+        {

+            fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);

+            abort();

+        }

+    }

+    // Sanity check

+    if ( header->l_text+str->l+1 >= header->n_text )

+    {

+        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);

+        abort();

+    }

+	strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.

+	header->l_text += str->l + 1;

+	header->text[header->l_text] = 0;

+}

+

+int sam_header_parse(bam_header_t *h)

+{

+	char **tmp;

+	int i;

+	free(h->target_len); free(h->target_name);

+	h->n_targets = 0; h->target_len = 0; h->target_name = 0;

+	if (h->l_text < 3) return 0;

+	if (h->dict == 0) h->dict = sam_header_parse2(h->text);

+	tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);

+	if (h->n_targets == 0) return 0;

+	h->target_name = calloc(h->n_targets, sizeof(void*));

+	for (i = 0; i < h->n_targets; ++i)

+		h->target_name[i] = strdup(tmp[i]);

+	free(tmp);

+	tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);

+	h->target_len = calloc(h->n_targets, 4);

+	for (i = 0; i < h->n_targets; ++i)

+		h->target_len[i] = atoi(tmp[i]);

+	free(tmp);

+	return h->n_targets;

+}

+

+bam_header_t *sam_header_read(tamFile fp)

+{

+	int ret, dret;

+	bam_header_t *header = bam_header_init();

+	kstring_t *str = fp->str;

+	while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header

+		str->s[str->l] = dret; // note that str->s is NOT null terminated!!

+		append_text(header, str);

+		if (dret != '\n') {

+			ret = ks_getuntil(fp->ks, '\n', str, &dret);

+			str->s[str->l] = '\n'; // NOT null terminated!!

+			append_text(header, str);

+		}

+		++fp->n_lines;

+	}

+	sam_header_parse(header);

+	bam_init_header_hash(header);

+	fp->is_first = ret >= 0; /* MTM: not header-only SAM */

+	return header;

+}

+

+int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)

+{

+	int ret, doff, doff0, dret, z = 0;

+	bam1_core_t *c = &b->core;

+	kstring_t *str = fp->str;

+	kstream_t *ks = fp->ks;

+

+	if (fp->is_first) {

+		fp->is_first = 0;

+		ret = str->l;

+	} else {

+		do { // special consideration for empty lines

+			ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);

+			if (ret >= 0) z += str->l + 1;

+		} while (ret == 0);

+	}

+	if (ret < 0) return -1;

+	++fp->n_lines;

+	doff = 0;

+

+	{ // name

+		c->l_qname = strlen(str->s) + 1;

+		memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);

+		doff += c->l_qname;

+	}

+	{ // flag

+		long flag;

+		char *s;

+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;

+		flag = strtol((char*)str->s, &s, 0);

+		if (*s) { // not the end of the string

+			flag = 0;

+			for (s = str->s; *s; ++s)

+				flag |= bam_char2flag_table[(int)*s];

+		}

+		c->flag = flag;

+	}

+	{ // tid, pos, qual

+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);

+		if (c->tid < 0 && strcmp(str->s, "*")) {

+			if (header->n_targets == 0) {

+				fprintf(stderr, "[sam_read1] missing header? Abort!\n");

+				exit(1);

+			} else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);

+		}

+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;

+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;

+		if (ret < 0) return -2;

+	}

+	{ // cigar

+		char *s, *t;

+		int i, op;

+		long x;

+		c->n_cigar = 0;

+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;

+		z += str->l + 1;

+		if (str->s[0] != '*') {

+			uint32_t *cigar;

+			for (s = str->s; *s; ++s) {

+				if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;

+				else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");

+			}

+			b->data = alloc_data(b, doff + c->n_cigar * 4);

+			cigar = bam1_cigar(b);

+			for (i = 0, s = str->s; i != c->n_cigar; ++i) {

+				x = strtol(s, &t, 10);

+				op = toupper(*t);

+				if (op == 'M') op = BAM_CMATCH;

+				else if (op == 'I') op = BAM_CINS;

+				else if (op == 'D') op = BAM_CDEL;

+				else if (op == 'N') op = BAM_CREF_SKIP;

+				else if (op == 'S') op = BAM_CSOFT_CLIP;

+				else if (op == 'H') op = BAM_CHARD_CLIP;

+				else if (op == 'P') op = BAM_CPAD;

+				else if (op == '=') op = BAM_CEQUAL;

+				else if (op == 'X') op = BAM_CDIFF;

+				else if (op == 'B') op = BAM_CBACK;

+				else parse_error(fp->n_lines, "invalid CIGAR operation");

+				s = t + 1;

+				cigar[i] = bam_cigar_gen(x, op);

+			}

+			if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");

+			c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar));

+			doff += c->n_cigar * 4;

+		} else {

+			if (!(c->flag&BAM_FUNMAP)) {

+				fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);

+				c->flag |= BAM_FUNMAP;

+			}

+			c->bin = bam_reg2bin(c->pos, c->pos + 1);

+		}

+	}

+	{ // mtid, mpos, isize

+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;

+		c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;

+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;

+		c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;

+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;

+		c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;

+		if (ret < 0) return -4;

+	}

+	{ // seq and qual

+		int i;

+		uint8_t *p = 0;

+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq

+		z += str->l + 1;

+		if (strcmp(str->s, "*")) {

+			c->l_qseq = strlen(str->s);

+			if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {

+				fprintf(stderr, "Line %ld, sequence length %i vs %i from CIGAR\n",

+						(long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));

+				parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");

+			}

+			p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;

+			memset(p, 0, (c->l_qseq+1)/2);

+			for (i = 0; i < c->l_qseq; ++i)

+				p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);

+		} else c->l_qseq = 0;

+		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual

+		z += str->l + 1;

+		if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))

+			parse_error(fp->n_lines, "sequence and quality are inconsistent");

+		p += (c->l_qseq+1)/2;

+		if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;

+		else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;

+		doff += c->l_qseq + (c->l_qseq+1)/2;

+	}

+	doff0 = doff;

+	if (dret != '\n' && dret != '\r') { // aux

+		while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {

+			uint8_t *s, type, key[2];

+			z += str->l + 1;

+			if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')

+				parse_error(fp->n_lines, "missing colon in auxiliary data");

+			key[0] = str->s[0]; key[1] = str->s[1];

+			type = str->s[3];

+			s = alloc_data(b, doff + 3) + doff;

+			s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;

+			if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility

+				s = alloc_data(b, doff + 2) + doff;

+				*s++ = 'A'; *s = str->s[5];

+				doff += 2;

+			} else if (type == 'I' || type == 'i') {

+				long long x;

+				s = alloc_data(b, doff + 5) + doff;

+				x = (long long)atoll(str->s + 5);

+				if (x < 0) {

+					if (x >= -127) {

+						*s++ = 'c'; *(int8_t*)s = (int8_t)x;

+						s += 1; doff += 2;

+					} else if (x >= -32767) {

+						*s++ = 's'; *(int16_t*)s = (int16_t)x;

+						s += 2; doff += 3;

+					} else {

+						*s++ = 'i'; *(int32_t*)s = (int32_t)x;

+						s += 4; doff += 5;

+						if (x < -2147483648ll)

+							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",

+									(long long)fp->n_lines, x);

+					}

+				} else {

+					if (x <= 255) {

+						*s++ = 'C'; *s++ = (uint8_t)x;

+						doff += 2;

+					} else if (x <= 65535) {

+						*s++ = 'S'; *(uint16_t*)s = (uint16_t)x;

+						s += 2; doff += 3;

+					} else {

+						*s++ = 'I'; *(uint32_t*)s = (uint32_t)x;

+						s += 4; doff += 5;

+						if (x > 4294967295ll)

+							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",

+									(long long)fp->n_lines, x);

+					}

+				}

+			} else if (type == 'f') {

+				s = alloc_data(b, doff + 5) + doff;

+				*s++ = 'f';

+				*(float*)s = (float)atof(str->s + 5);

+				s += 4; doff += 5;

+			} else if (type == 'd') {

+				s = alloc_data(b, doff + 9) + doff;

+				*s++ = 'd';

+				*(float*)s = (float)atof(str->s + 9);

+				s += 8; doff += 9;

+			} else if (type == 'Z' || type == 'H') {

+				int size = 1 + (str->l - 5) + 1;

+				if (type == 'H') { // check whether the hex string is valid

+					int i;

+					if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");

+					for (i = 0; i < str->l - 5; ++i) {

+						int c = toupper(str->s[5 + i]);

+						if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))

+							parse_error(fp->n_lines, "invalid hex character");

+					}

+				}

+				s = alloc_data(b, doff + size) + doff;

+				*s++ = type;

+				memcpy(s, str->s + 5, str->l - 5);

+				s[str->l - 5] = 0;

+				doff += size;

+			} else if (type == 'B') {

+				int32_t n = 0, Bsize, k = 0, size;

+				char *p;

+				if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");

+				Bsize = bam_aux_type2size(str->s[5]); // the size of each element

+				for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array

+					if (*p == ',') ++n;

+				p = str->s + 7; // now p points to the first number in the array

+				size = 6 + Bsize * n; // total number of bytes allocated to this tag

+				s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory

+				*s++ = 'B'; *s++ = str->s[5];

+				memcpy(s, &n, 4); s += 4; // write the number of elements

+				if (str->s[5] == 'c')      while (p < str->s + str->l) ((int8_t*)s)[k++]   = (int8_t)strtol(p, &p, 0),   ++p;

+				else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++]  = (uint8_t)strtol(p, &p, 0),  ++p;

+				else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++]  = (int16_t)strtol(p, &p, 0),  ++p; // FIXME: avoid unaligned memory

+				else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;

+				else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;

+				else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;

+				else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++]    = (float)strtod(p, &p),       ++p;

+				else parse_error(fp->n_lines, "unrecognized array type");

+				s += Bsize * n; doff += size;

+			} else parse_error(fp->n_lines, "unrecognized type");

+			if (dret == '\n' || dret == '\r') break;

+		}

+	}

+	b->l_aux = doff - doff0;

+	b->data_len = doff;

+	if (bam_no_B) bam_remove_B(b);

+	return z;

+}

+

+tamFile sam_open(const char *fn)

+{

+	tamFile fp;

+	gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");

+	if (gzfp == 0) return 0;

+	fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));

+	fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));

+	fp->fp = gzfp;

+	fp->ks = ks_init(fp->fp);

+	return fp;

+}

+

+void sam_close(tamFile fp)

+{

+	if (fp) {

+		ks_destroy(fp->ks);

+		gzclose(fp->fp);

+		free(fp->str->s); free(fp->str);

+		free(fp);

+	}

+}