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sam.c
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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <ctype.h>
#include <zlib.h>
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include "cram/cram.h"
#include "htslib/hfile.h"
#include "htslib/khash.h"
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
typedef khash_t(s2i) sdict_t;
/**********************
*** BAM header I/O ***
**********************/
bam_hdr_t *bam_hdr_init()
{
return (bam_hdr_t*)calloc(1, sizeof(bam_hdr_t));
}
void bam_hdr_destroy(bam_hdr_t *h)
{
int32_t i;
if (h == NULL) return;
if (h->target_name) {
for (i = 0; i < h->n_targets; ++i)
free(h->target_name[i]);
free(h->target_name);
free(h->target_len);
}
free(h->text); free(h->cigar_tab);
if (h->sdict) kh_destroy(s2i, (sdict_t*)h->sdict);
free(h);
}
bam_hdr_t *bam_hdr_dup(const bam_hdr_t *h0)
{
if (h0 == NULL) return NULL;
bam_hdr_t *h;
if ((h = bam_hdr_init()) == NULL) return NULL;
// copy the simple data
h->n_targets = h0->n_targets;
h->ignore_sam_err = h0->ignore_sam_err;
h->l_text = h0->l_text;
// Then the pointery stuff
h->cigar_tab = NULL; // TODO: check what this actually does and why it exists and document it
h->sdict = NULL;
h->text = (char*)calloc(h->l_text + 1, 1);
memcpy(h->text, h0->text, h->l_text);
h->target_len = (uint32_t*)calloc(h->n_targets, 4);
h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
int i;
for (i = 0; i < h->n_targets; ++i) {
h->target_len[i] = h0->target_len[i];
h->target_name[i] = strdup(h0->target_name[i]);
}
return h;
}
static bam_hdr_t *hdr_from_dict(sdict_t *d)
{
bam_hdr_t *h;
khint_t k;
h = bam_hdr_init();
h->sdict = d;
h->n_targets = kh_size(d);
h->target_len = (uint32_t*)malloc(4 * h->n_targets);
h->target_name = (char**)malloc(sizeof(char*) * h->n_targets);
for (k = kh_begin(d); k != kh_end(d); ++k) {
if (!kh_exist(d, k)) continue;
h->target_name[kh_val(d, k)>>32] = (char*)kh_key(d, k);
h->target_len[kh_val(d, k)>>32] = kh_val(d, k)<<32>>32;
kh_val(d, k) >>= 32;
}
return h;
}
bam_hdr_t *bam_hdr_read(BGZF *fp)
{
bam_hdr_t *h;
char buf[4];
int magic_len, has_EOF;
int32_t i = 1, name_len;
// check EOF
has_EOF = bgzf_check_EOF(fp);
if (has_EOF < 0) {
perror("[W::sam_hdr_read] bgzf_check_EOF");
} else if (has_EOF == 0 && hts_verbose >= 2)
fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__);
// read "BAM1"
magic_len = bgzf_read(fp, buf, 4);
if (magic_len != 4 || strncmp(buf, "BAM\1", 4)) {
if (hts_verbose >= 1) fprintf(stderr, "[E::%s] invalid BAM binary header\n", __func__);
return 0;
}
h = bam_hdr_init();
// read plain text and the number of reference sequences
bgzf_read(fp, &h->l_text, 4);
if (fp->is_be) ed_swap_4p(&h->l_text);
h->text = (char*)malloc(h->l_text + 1);
h->text[h->l_text] = 0; // make sure it is NULL terminated
bgzf_read(fp, h->text, h->l_text);
bgzf_read(fp, &h->n_targets, 4);
if (fp->is_be) ed_swap_4p(&h->n_targets);
// read reference sequence names and lengths
h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
h->target_len = (uint32_t*)calloc(h->n_targets, 4);
for (i = 0; i != h->n_targets; ++i) {
bgzf_read(fp, &name_len, 4);
if (fp->is_be) ed_swap_4p(&name_len);
h->target_name[i] = (char*)calloc(name_len, 1);
bgzf_read(fp, h->target_name[i], name_len);
bgzf_read(fp, &h->target_len[i], 4);
if (fp->is_be) ed_swap_4p(&h->target_len[i]);
}
return h;
}
int bam_hdr_write(BGZF *fp, const bam_hdr_t *h)
{
char buf[4];
int32_t i, name_len, x;
// write "BAM1"
strncpy(buf, "BAM\1", 4);
bgzf_write(fp, buf, 4);
// write plain text and the number of reference sequences
if (fp->is_be) {
x = ed_swap_4(h->l_text);
bgzf_write(fp, &x, 4);
if (h->l_text) bgzf_write(fp, h->text, h->l_text);
x = ed_swap_4(h->n_targets);
bgzf_write(fp, &x, 4);
} else {
bgzf_write(fp, &h->l_text, 4);
if (h->l_text) bgzf_write(fp, h->text, h->l_text);
bgzf_write(fp, &h->n_targets, 4);
}
// write sequence names and lengths
for (i = 0; i != h->n_targets; ++i) {
char *p = h->target_name[i];
name_len = strlen(p) + 1;
if (fp->is_be) {
x = ed_swap_4(name_len);
bgzf_write(fp, &x, 4);
} else bgzf_write(fp, &name_len, 4);
bgzf_write(fp, p, name_len);
if (fp->is_be) {
x = ed_swap_4(h->target_len[i]);
bgzf_write(fp, &x, 4);
} else bgzf_write(fp, &h->target_len[i], 4);
}
bgzf_flush(fp);
return 0;
}
int bam_name2id(bam_hdr_t *h, const char *ref)
{
sdict_t *d = (sdict_t*)h->sdict;
khint_t k;
if (h->sdict == 0) {
int i, absent;
d = kh_init(s2i);
for (i = 0; i < h->n_targets; ++i) {
k = kh_put(s2i, d, h->target_name[i], &absent);
kh_val(d, k) = i;
}
h->sdict = d;
}
k = kh_get(s2i, d, ref);
return k == kh_end(d)? -1 : kh_val(d, k);
}
/*************************
*** BAM alignment I/O ***
*************************/
bam1_t *bam_init1()
{
return (bam1_t*)calloc(1, sizeof(bam1_t));
}
void bam_destroy1(bam1_t *b)
{
if (b == 0) return;
free(b->data); free(b);
}
bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
{
uint8_t *data = bdst->data;
int m_data = bdst->m_data; // backup data and m_data
if (m_data < bsrc->l_data) { // double the capacity
m_data = bsrc->l_data; kroundup32(m_data);
data = (uint8_t*)realloc(data, m_data);
}
memcpy(data, bsrc->data, bsrc->l_data); // copy var-len data
*bdst = *bsrc; // copy the rest
// restore the backup
bdst->m_data = m_data;
bdst->data = data;
return bdst;
}
bam1_t *bam_dup1(const bam1_t *bsrc)
{
if (bsrc == NULL) return NULL;
bam1_t *bdst = bam_init1();
if (bdst == NULL) return NULL;
return bam_copy1(bdst, bsrc);
}
int bam_cigar2qlen(int n_cigar, const uint32_t *cigar)
{
int k, l;
for (k = l = 0; k < n_cigar; ++k)
if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
l += bam_cigar_oplen(cigar[k]);
return l;
}
int bam_cigar2rlen(int n_cigar, const uint32_t *cigar)
{
int k, l;
for (k = l = 0; k < n_cigar; ++k)
if (bam_cigar_type(bam_cigar_op(cigar[k]))&2)
l += bam_cigar_oplen(cigar[k]);
return l;
}
int32_t bam_endpos(const bam1_t *b)
{
if (!(b->core.flag & BAM_FUNMAP) && b->core.n_cigar > 0)
return b->core.pos + bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b));
else
return b->core.pos + 1;
}
static inline int aux_type2size(uint8_t type)
{
switch (type) {
case 'A': case 'c': case 'C':
return 1;
case 's': case 'S':
return 2;
case 'i': case 'I': case 'f':
return 4;
case 'd':
return 8;
case 'Z': case 'H': case 'B':
return type;
default:
return 0;
}
}
static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data)
{
uint8_t *s;
uint32_t *cigar = (uint32_t*)(data + c->l_qname);
uint32_t i, n;
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) ed_swap_4p(&cigar[i]);
while (s < data + l_data) {
int size;
s += 2; // skip key
size = aux_type2size(*s); ++s; // skip type
switch (size) {
case 1: ++s; break;
case 2: ed_swap_2p(s); s += 2; break;
case 4: ed_swap_4p(s); s += 4; break;
case 8: ed_swap_8p(s); s += 8; break;
case 'Z':
case 'H':
while (*s) ++s;
++s;
break;
case 'B':
size = aux_type2size(*s); ++s;
ed_swap_4p(s); memcpy(&n, s, 4); s += 4;
switch (size) {
case 1: s += n; break;
case 2: for (i = 0; i < n; ++i, s += 2) ed_swap_2p(s); break;
case 4: for (i = 0; i < n; ++i, s += 4) ed_swap_4p(s); break;
case 8: for (i = 0; i < n; ++i, s += 8) ed_swap_8p(s); break;
}
break;
}
}
}
int bam_read1(BGZF *fp, bam1_t *b)
{
bam1_core_t *c = &b->core;
int32_t block_len, ret, i;
uint32_t x[8];
if ((ret = bgzf_read(fp, &block_len, 4)) != 4) {
if (ret == 0) return -1; // normal end-of-file
else return -2; // truncated
}
if (bgzf_read(fp, x, 32) != 32) return -3;
if (fp->is_be) {
ed_swap_4p(&block_len);
for (i = 0; i < 8; ++i) ed_swap_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->l_data = block_len - 32;
if (b->l_data < 0 || c->l_qseq < 0) return -4;
if ((char *)bam_get_aux(b) - (char *)b->data > b->l_data)
return -4;
if (b->m_data < b->l_data) {
b->m_data = b->l_data;
kroundup32(b->m_data);
b->data = (uint8_t*)realloc(b->data, b->m_data);
if (!b->data)
return -4;
}
if (bgzf_read(fp, b->data, b->l_data) != b->l_data) return -4;
//b->l_aux = b->l_data - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
if (fp->is_be) swap_data(c, b->l_data, b->data);
return 4 + block_len;
}
int bam_write1(BGZF *fp, const bam1_t *b)
{
const bam1_core_t *c = &b->core;
uint32_t x[8], block_len = b->l_data + 32, y;
int i;
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 (fp->is_be) {
for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
y = block_len;
bgzf_write(fp, ed_swap_4p(&y), 4);
swap_data(c, b->l_data, b->data);
} else bgzf_write(fp, &block_len, 4);
bgzf_write(fp, x, 32);
bgzf_write(fp, b->data, b->l_data);
if (fp->is_be) swap_data(c, b->l_data, b->data);
return 4 + block_len;
}
/********************
*** BAM indexing ***
********************/
static hts_idx_t *bam_index(BGZF *fp, int min_shift)
{
int n_lvls, i, fmt;
bam1_t *b;
hts_idx_t *idx;
bam_hdr_t *h;
h = bam_hdr_read(fp);
if (min_shift > 0) {
int64_t max_len = 0, s;
for (i = 0; i < h->n_targets; ++i)
if (max_len < h->target_len[i]) max_len = h->target_len[i];
max_len += 256;
for (n_lvls = 0, s = 1<<min_shift; max_len > s; ++n_lvls, s <<= 3);
fmt = HTS_FMT_CSI;
} else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_BAI;
idx = hts_idx_init(h->n_targets, fmt, bgzf_tell(fp), min_shift, n_lvls);
bam_hdr_destroy(h);
b = bam_init1();
while (bam_read1(fp, b) >= 0) {
int l, ret;
l = bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b));
if (l == 0) l = 1; // no zero-length records
ret = hts_idx_push(idx, b->core.tid, b->core.pos, b->core.pos + l, bgzf_tell(fp), !(b->core.flag&BAM_FUNMAP));
if (ret < 0) break; // unsorted
}
hts_idx_finish(idx, bgzf_tell(fp));
bam_destroy1(b);
return idx;
}
int bam_index_build(const char *fn, int min_shift)
{
hts_idx_t *idx;
htsFile *fp;
int ret = 0;
if ((fp = hts_open(fn, "r")) == 0) return -1;
if (fp->is_cram) {
ret = cram_index_build(fp->fp.cram, fn);
} else {
idx = bam_index(fp->fp.bgzf, min_shift);
hts_idx_save(idx, fn, min_shift > 0
? HTS_FMT_CSI : HTS_FMT_BAI);
hts_idx_destroy(idx);
}
hts_close(fp);
return ret;
}
static int bam_readrec(BGZF *fp, void *ignored, void *bv, int *tid, int *beg, int *end)
{
bam1_t *b = bv;
int ret;
if ((ret = bam_read1(fp, b)) >= 0) {
*tid = b->core.tid; *beg = b->core.pos;
*end = b->core.pos + (b->core.n_cigar? bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b)) : 1);
}
return ret;
}
// This is used only with read_rest=1 iterators, so need not set tid/beg/end.
static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, int *beg, int *end)
{
htsFile *fp = fpv;
bam1_t *b = bv;
return cram_get_bam_seq(fp->fp.cram, &b);
}
// This is used only with read_rest=1 iterators, so need not set tid/beg/end.
static int sam_bam_cram_readrec(BGZF *bgzfp, void *fpv, void *bv, int *tid, int *beg, int *end)
{
htsFile *fp = fpv;
bam1_t *b = bv;
if (fp->is_bin) return bam_read1(bgzfp, b);
else if (fp->is_cram) return cram_get_bam_seq(fp->fp.cram, &b);
else {
// TODO Need headers available to implement this for SAM files
fprintf(stderr, "[sam_bam_cram_readrec] Not implemented for SAM files -- Exiting\n");
abort();
}
}
// The CRAM implementation stores the loaded index within the cram_fd rather
// than separately as is done elsewhere in htslib. So if p is a pointer to
// an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an
// hts_cram_idx_t and should be cast accordingly.
typedef struct hts_cram_idx_t {
int fmt;
cram_fd *cram;
} hts_cram_idx_t;
hts_idx_t *sam_index_load(samFile *fp, const char *fn)
{
if (fp->is_bin) return bam_index_load(fn);
else if (fp->is_cram) {
if (cram_index_load(fp->fp.cram, fn) < 0) return NULL;
// Cons up a fake "index" just pointing at the associated cram_fd:
hts_cram_idx_t *idx = malloc(sizeof (hts_cram_idx_t));
if (idx == NULL) return NULL;
idx->fmt = HTS_FMT_CRAI;
idx->cram = fp->fp.cram;
return (hts_idx_t *) idx;
}
else return NULL; // TODO Would use tbx_index_load if it returned hts_idx_t
}
static hts_itr_t *cram_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec)
{
const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
hts_itr_t *iter = (hts_itr_t *) calloc(1, sizeof(hts_itr_t));
if (iter == NULL) return NULL;
// Cons up a dummy iterator for which hts_itr_next() will simply invoke
// the readrec function:
iter->read_rest = 1;
iter->off = NULL;
iter->bins.a = NULL;
iter->readrec = readrec;
if (tid >= 0) {
cram_range r = { tid, beg+1, end };
if (cram_set_option(cidx->cram, CRAM_OPT_RANGE, &r) != 0) { free(iter); return NULL; }
iter->curr_off = 0;
// The following fields are not required by hts_itr_next(), but are
// filled in in case user code wants to look at them.
iter->tid = tid;
iter->beg = beg;
iter->end = end;
}
else switch (tid) {
case HTS_IDX_REST:
iter->curr_off = 0;
break;
case HTS_IDX_NONE:
iter->curr_off = 0;
iter->finished = 1;
break;
default:
fprintf(stderr, "[cram_itr_query] tid=%d not implemented for CRAM files -- Exiting\n", tid);
abort();
break;
}
return iter;
}
hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
{
const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
if (idx == NULL)
return hts_itr_query(NULL, tid, beg, end, sam_bam_cram_readrec);
else if (cidx->fmt == HTS_FMT_CRAI)
return cram_itr_query(idx, tid, beg, end, cram_readrec);
else
return hts_itr_query(idx, tid, beg, end, bam_readrec);
}
static int cram_name2id(void *fdv, const char *ref)
{
cram_fd *fd = (cram_fd *) fdv;
return sam_hdr_name2ref(fd->header, ref);
}
hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region)
{
const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
if (cidx->fmt == HTS_FMT_CRAI)
return hts_itr_querys(idx, region, cram_name2id, cidx->cram, cram_itr_query, cram_readrec);
else
return hts_itr_querys(idx, region, (hts_name2id_f)(bam_name2id), hdr, hts_itr_query, bam_readrec);
}
/**********************
*** SAM header I/O ***
**********************/
#include "htslib/kseq.h"
#include "htslib/kstring.h"
bam_hdr_t *sam_hdr_parse(int l_text, const char *text)
{
const char *q, *r, *p;
khash_t(s2i) *d;
d = kh_init(s2i);
for (p = text; *p; ++p) {
if (strncmp(p, "@SQ", 3) == 0) {
char *sn = 0;
int ln = -1;
for (q = p + 4;; ++q) {
if (strncmp(q, "SN:", 3) == 0) {
q += 3;
for (r = q; *r != '\t' && *r != '\n'; ++r);
sn = (char*)calloc(r - q + 1, 1);
strncpy(sn, q, r - q);
q = r;
} else if (strncmp(q, "LN:", 3) == 0)
ln = strtol(q + 3, (char**)&q, 10);
while (*q != '\t' && *q != '\n') ++q;
if (*q == '\n') break;
}
p = q;
if (sn && ln >= 0) {
khint_t k;
int absent;
k = kh_put(s2i, d, sn, &absent);
if (!absent) {
if (hts_verbose >= 2)
fprintf(stderr, "[W::%s] duplicated sequence '%s'\n", __func__, sn);
free(sn);
} else kh_val(d, k) = (int64_t)(kh_size(d) - 1)<<32 | ln;
}
}
while (*p != '\n') ++p;
}
return hdr_from_dict(d);
}
bam_hdr_t *sam_hdr_read(htsFile *fp)
{
if (fp->is_bin) {
return bam_hdr_read(fp->fp.bgzf);
} else if (fp->is_cram) {
return cram_header_to_bam(fp->fp.cram->header);
} else {
kstring_t str;
bam_hdr_t *h;
int has_SQ = 0;
str.l = str.m = 0; str.s = 0;
while (hts_getline(fp, KS_SEP_LINE, &fp->line) >= 0) {
if (fp->line.s[0] != '@') break;
if (fp->line.l > 3 && strncmp(fp->line.s,"@SQ",3) == 0) has_SQ = 1;
kputsn(fp->line.s, fp->line.l, &str);
kputc('\n', &str);
}
if (! has_SQ && fp->fn_aux) {
char line[2048];
FILE *f = fopen(fp->fn_aux, "r");
if (f == NULL) return NULL;
while (fgets(line, sizeof line, f)) {
const char *name = strtok(line, "\t");
const char *length = strtok(NULL, "\t");
ksprintf(&str, "@SQ\tSN:%s\tLN:%s\n", name, length);
}
fclose(f);
}
if (str.l == 0) kputsn("", 0, &str);
h = sam_hdr_parse(str.l, str.s);
h->l_text = str.l; h->text = str.s;
return h;
}
}
int sam_hdr_write(htsFile *fp, const bam_hdr_t *h)
{
if (fp->is_bin) {
bam_hdr_write(fp->fp.bgzf, h);
} else if (fp->is_cram) {
cram_fd *fd = fp->fp.cram;
if (cram_set_header(fd, bam_header_to_cram((bam_hdr_t *)h)) < 0) return -1;
if (cram_write_SAM_hdr(fd, fd->header) < 0) return -1;
} else {
char *p;
hputs(h->text, fp->fp.hfile);
p = strstr(h->text, "@SQ\t"); // FIXME: we need a loop to make sure "@SQ\t" does not match something unwanted!!!
if (p == 0) {
int i;
for (i = 0; i < h->n_targets; ++i) {
fp->line.l = 0;
kputsn("@SQ\tSN:", 7, &fp->line); kputs(h->target_name[i], &fp->line);
kputsn("\tLN:", 4, &fp->line); kputw(h->target_len[i], &fp->line); kputc('\n', &fp->line);
if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
}
}
if ( hflush(fp->fp.hfile) != 0 ) return -1;
}
return 0;
}
/**********************
*** SAM record I/O ***
**********************/
int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b)
{
#define _read_token(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); if (*(_p) != '\t') goto err_ret; *(_p)++ = 0
#define _read_token_aux(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); *(_p)++ = 0 // this is different in that it does not test *(_p)=='\t'
#define _get_mem(type_t, _x, _s, _l) ks_resize((_s), (_s)->l + (_l)); *(_x) = (type_t*)((_s)->s + (_s)->l); (_s)->l += (_l)
#define _parse_err(cond, msg) do { if ((cond) && hts_verbose >= 1) { fprintf(stderr, "[E::%s] " msg "\n", __func__); goto err_ret; } } while (0)
#define _parse_warn(cond, msg) if ((cond) && hts_verbose >= 2) fprintf(stderr, "[W::%s] " msg "\n", __func__)
uint8_t *t;
char *p = s->s, *q;
int i;
kstring_t str;
bam1_core_t *c = &b->core;
str.l = b->l_data = 0;
str.s = (char*)b->data; str.m = b->m_data;
memset(c, 0, 32);
if (h->cigar_tab == 0) {
h->cigar_tab = (uint8_t*)calloc(128, sizeof(uint8_t));
for (i = 0; BAM_CIGAR_STR[i]; ++i)
h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;
}
// qname
q = _read_token(p);
kputsn_(q, p - q, &str);
c->l_qname = p - q;
// flag
c->flag = strtol(p, &p, 0);
if (*p++ != '\t') goto err_ret; // malformated flag
// chr
q = _read_token(p);
if (strcmp(q, "*")) {
_parse_err(h->n_targets == 0, "missing SAM header");
c->tid = bam_name2id(h, q);
_parse_warn(c->tid < 0, "urecognized reference name; treated as unmapped");
} else c->tid = -1;
// pos
c->pos = strtol(p, &p, 10) - 1;
if (*p++ != '\t') goto err_ret;
if (c->pos < 0 && c->tid >= 0) {
_parse_warn(1, "mapped query cannot have zero coordinate; treated as unmapped");
c->tid = -1;
}
if (c->tid < 0) c->flag |= BAM_FUNMAP;
// mapq
c->qual = strtol(p, &p, 10);
if (*p++ != '\t') goto err_ret;
// cigar
if (*p != '*') {
uint32_t *cigar;
for (q = p, c->n_cigar = 0; *q && *q != '\t'; ++q)
if (!isdigit(*q)) ++c->n_cigar;
_get_mem(uint32_t, &cigar, &str, c->n_cigar<<2);
for (i = 0, q = p; i < c->n_cigar; ++i, ++q) {
int op;
cigar[i] = strtol(q, &q, 10)<<BAM_CIGAR_SHIFT;
op = (uint8_t)*q >= 128? -1 : h->cigar_tab[(int)*q];
_parse_err(op < 0, "urecognized CIGAR operator");
cigar[i] |= op;
}
p = q + 1;
i = bam_cigar2rlen(c->n_cigar, cigar);
} else {
_parse_warn(!(c->flag&BAM_FUNMAP), "mapped query must have a CIGAR; treated as unmapped");
c->flag |= BAM_FUNMAP;
q = _read_token(p);
i = 1;
}
c->bin = hts_reg2bin(c->pos, c->pos + i, 14, 5);
// mate chr
q = _read_token(p);
if (strcmp(q, "=") == 0) c->mtid = c->tid;
else if (strcmp(q, "*") == 0) c->mtid = -1;
else c->mtid = bam_name2id(h, q);
// mpos
c->mpos = strtol(p, &p, 10) - 1;
if (*p++ != '\t') goto err_ret;
if (c->mpos < 0 && c->mtid >= 0) {
_parse_warn(1, "mapped mate cannot have zero coordinate; treated as unmapped");
c->mtid = -1;
}
// tlen
c->isize = strtol(p, &p, 10);
if (*p++ != '\t') goto err_ret;
// seq
q = _read_token(p);
if (strcmp(q, "*")) {
c->l_qseq = p - q - 1;
i = bam_cigar2qlen(c->n_cigar, (uint32_t*)(str.s + c->l_qname));
_parse_err(c->n_cigar && i != c->l_qseq, "CIGAR and query sequence are of different length");
i = (c->l_qseq + 1) >> 1;
_get_mem(uint8_t, &t, &str, i);
memset(t, 0, i);
for (i = 0; i < c->l_qseq; ++i)
t[i>>1] |= seq_nt16_table[(int)q[i]] << ((~i&1)<<2);
} else c->l_qseq = 0;
// qual
q = _read_token_aux(p);
_get_mem(uint8_t, &t, &str, c->l_qseq);
if (strcmp(q, "*")) {
_parse_err(p - q - 1 != c->l_qseq, "SEQ and QUAL are of different length");
for (i = 0; i < c->l_qseq; ++i) t[i] = q[i] - 33;
} else memset(t, 0xff, c->l_qseq);
// aux
// Note that (like the bam1_core_t fields) this aux data in b->data is
// stored in host endianness; so there is no byte swapping needed here.
while (p < s->s + s->l) {
uint8_t type;
q = _read_token_aux(p); // FIXME: can be accelerated for long 'B' arrays
_parse_err(p - q - 1 < 6, "incomplete aux field");
kputsn_(q, 2, &str);
q += 3; type = *q++; ++q; // q points to value
if (type == 'A' || type == 'a' || type == 'c' || type == 'C') {
kputc_('A', &str);
kputc_(*q, &str);
} else if (type == 'i' || type == 'I') {
long x;
x = strtol(q, &q, 10);
if (x < 0) {
if (x >= INT8_MIN) {
kputc_('c', &str); kputc_(x, &str);
} else if (x >= INT16_MIN) {
int16_t y = x;
kputc_('s', &str); kputsn_((char*)&y, 2, &str);
} else {
int32_t y = x;
kputc_('i', &str); kputsn_(&y, 4, &str);
}
} else {
if (x <= UINT8_MAX) {
kputc_('C', &str); kputc_(x, &str);
} else if (x <= UINT16_MAX) {
uint16_t y = x;
kputc_('S', &str); kputsn_(&y, 2, &str);
} else {
uint32_t y = x;
kputc_('I', &str); kputsn_(&y, 4, &str);
}
}
} else if (type == 'f') {
float x;
x = strtod(q, &q);
kputc_('f', &str); kputsn_(&x, 4, &str);
} else if (type == 'd') {
double x;
x = strtod(q, &q);
kputc_('d', &str); kputsn_(&x, 8, &str);
} else if (type == 'Z' || type == 'H') {
kputc_(type, &str);kputsn_(q, p - q, &str); // note that this include the trailing NULL
} else if (type == 'B') {
int32_t n;
char *r;
_parse_err(p - q - 1 < 3, "incomplete B-typed aux field");
type = *q++; // q points to the first ',' following the typing byte
for (r = q, n = 0; *r; ++r)
if (*r == ',') ++n;
kputc_('B', &str); kputc_(type, &str); kputsn_(&n, 4, &str);
// FIXME: to evaluate which is faster: a) aligned array and then memmove(); b) unaligned array; c) kputsn_()
if (type == 'c') while (q + 1 < p) { int8_t x = strtol(q + 1, &q, 0); kputc_(x, &str); }
else if (type == 'C') while (q + 1 < p) { uint8_t x = strtoul(q + 1, &q, 0); kputc_(x, &str); }
else if (type == 's') while (q + 1 < p) { int16_t x = strtol(q + 1, &q, 0); kputsn_(&x, 2, &str); }
else if (type == 'S') while (q + 1 < p) { uint16_t x = strtoul(q + 1, &q, 0); kputsn_(&x, 2, &str); }
else if (type == 'i') while (q + 1 < p) { int32_t x = strtol(q + 1, &q, 0); kputsn_(&x, 4, &str); }
else if (type == 'I') while (q + 1 < p) { uint32_t x = strtoul(q + 1, &q, 0); kputsn_(&x, 4, &str); }
else if (type == 'f') while (q + 1 < p) { float x = strtod(q + 1, &q); kputsn_(&x, 4, &str); }
else _parse_err(1, "unrecognized type");
} else _parse_err(1, "unrecognized type");
}
b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
return 0;
#undef _parse_warn
#undef _parse_err
#undef _get_mem
#undef _read_token_aux
#undef _read_token
err_ret:
b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
return -2;
}
int sam_read1(htsFile *fp, bam_hdr_t *h, bam1_t *b)
{
if (fp->is_bin) {
int r = bam_read1(fp->fp.bgzf, b);
if (r >= 0) {
if (b->core.tid >= h->n_targets || b->core.tid < -1 ||
b->core.mtid >= h->n_targets || b->core.mtid < -1)
return -3;
}
return r;
} else if (fp->is_cram) {
return cram_get_bam_seq(fp->fp.cram, &b);
} else {
int ret;
err_recover:
if (fp->line.l == 0) {
ret = hts_getline(fp, KS_SEP_LINE, &fp->line);
if (ret < 0) return -1;
}
ret = sam_parse1(&fp->line, h, b);
fp->line.l = 0;
if (ret < 0) {
if (hts_verbose >= 1)
fprintf(stderr, "[W::%s] parse error at line %lld\n", __func__, (long long)fp->lineno);
if (h->ignore_sam_err) goto err_recover;
}
return ret;
}
}
int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
{
int i;
uint8_t *s;
const bam1_core_t *c = &b->core;
str->l = 0;
kputsn(bam_get_qname(b), c->l_qname-1, str); kputc('\t', str); // query name
kputw(c->flag, str); kputc('\t', str); // flag
if (c->tid >= 0) { // chr
kputs(h->target_name[c->tid] , str);
kputc('\t', str);
} else kputsn("*\t", 2, str);
kputw(c->pos + 1, str); kputc('\t', str); // pos
kputw(c->qual, str); kputc('\t', str); // qual
if (c->n_cigar) { // cigar
uint32_t *cigar = bam_get_cigar(b);
for (i = 0; i < c->n_cigar; ++i) {
kputw(bam_cigar_oplen(cigar[i]), str);
kputc(bam_cigar_opchr(cigar[i]), str);
}
} else kputc('*', str);
kputc('\t', str);
if (c->mtid < 0) kputsn("*\t", 2, str); // mate chr
else if (c->mtid == c->tid) kputsn("=\t", 2, str);
else {
kputs(h->target_name[c->mtid], str);
kputc('\t', str);
}
kputw(c->mpos + 1, str); kputc('\t', str); // mate pos
kputw(c->isize, str); kputc('\t', str); // template len
if (c->l_qseq) { // seq and qual
uint8_t *s = bam_get_seq(b);
for (i = 0; i < c->l_qseq; ++i) kputc("=ACMGRSVTWYHKDBN"[bam_seqi(s, i)], str);
kputc('\t', str);
s = bam_get_qual(b);
if (s[0] == 0xff) kputc('*', str);
else for (i = 0; i < c->l_qseq; ++i) kputc(s[i] + 33, str);
} else kputsn("*\t*", 3, str);
s = bam_get_aux(b); // aux
while (s+4 <= b->data + b->l_data) {
uint8_t type, key[2];
key[0] = s[0]; key[1] = s[1];
s += 2; type = *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') {
if (s+2 <= b->data + b->l_data) {
kputsn("i:", 2, str);
kputw(*(uint16_t*)s, str);
s += 2;
} else return -1;
} else if (type == 's') {
if (s+2 <= b->data + b->l_data) {
kputsn("i:", 2, str);
kputw(*(int16_t*)s, str);
s += 2;
} else return -1;
} else if (type == 'I') {
if (s+4 <= b->data + b->l_data) {
kputsn("i:", 2, str);
kputuw(*(uint32_t*)s, str);
s += 4;
} else return -1;
} else if (type == 'i') {
if (s+4 <= b->data + b->l_data) {
kputsn("i:", 2, str);
kputw(*(int32_t*)s, str);
s += 4;
} else return -1;
} else if (type == 'f') {
if (s+4 <= b->data + b->l_data) {
ksprintf(str, "f:%g", *(float*)s);
s += 4;
} else return -1;
} else if (type == 'd') {
if (s+8 <= b->data + b->l_data) {
ksprintf(str, "d:%g", *(double*)s);
s += 8;
} else return -1;
} else if (type == 'Z' || type == 'H') {
kputc(type, str); kputc(':', str);
while (s < b->data + b->l_data && *s) kputc(*s++, str);
if (s >= b->data + b->l_data)
return -1;
++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
if (s + n >= b->data + b->l_data)
return -1;
kputsn("B:", 2, str); kputc(sub_type, str); // write the typing
for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if"
kputc(',', str);
if ('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->l;
}
int sam_write1(htsFile *fp, const bam_hdr_t *h, const bam1_t *b)
{
if (fp->is_bin) {
return bam_write1(fp->fp.bgzf, b);
} else if (fp->is_cram) {
return cram_put_bam_seq(fp->fp.cram, (bam1_t *)b);
} else {
if (sam_format1(h, b, &fp->line) < 0) return -1;
if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
hputc('\n', fp->fp.hfile);
return fp->line.l + 1;
}
}
/************************
*** Auxiliary fields ***
************************/
void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
{
int ori_len = b->l_data;
b->l_data += 3 + len;
if (b->m_data < b->l_data) {