| 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);
}
}
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