src/samtools/bam_import.c
5bb21ad5
 #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);
 	}
 }