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sam.c
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/* sam.c -- SAM and BAM file I/O and manipulation.
Copyright (C) 2008-2010, 2012-2023 Genome Research Ltd.
Copyright (C) 2010, 2012, 2013 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>
#include <strings.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <zlib.h>
#include <assert.h>
#include <signal.h>
#include <inttypes.h>
#include <unistd.h>
#ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION
#include "fuzz_settings.h"
#endif
// Suppress deprecation message for cigar_tab, which we initialise
#include "htslib/hts_defs.h"
#undef HTS_DEPRECATED
#define HTS_DEPRECATED(message)
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include "cram/cram.h"
#include "hts_internal.h"
#include "sam_internal.h"
#include "htslib/hfile.h"
#include "htslib/hts_endian.h"
#include "htslib/hts_expr.h"
#include "header.h"
#include "htslib/khash.h"
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
KHASH_SET_INIT_INT(tag)
#ifndef EFTYPE
#define EFTYPE ENOEXEC
#endif
#ifndef EOVERFLOW
#define EOVERFLOW ERANGE
#endif
/**********************
*** BAM header I/O ***
**********************/
HTSLIB_EXPORT
const int8_t bam_cigar_table[256] = {
// 0 .. 47
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
// 48 .. 63 (including =)
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, BAM_CEQUAL, -1, -1,
// 64 .. 79 (including MIDNHB)
-1, -1, BAM_CBACK, -1, BAM_CDEL, -1, -1, -1,
BAM_CHARD_CLIP, BAM_CINS, -1, -1, -1, BAM_CMATCH, BAM_CREF_SKIP, -1,
// 80 .. 95 (including SPX)
BAM_CPAD, -1, -1, BAM_CSOFT_CLIP, -1, -1, -1, -1,
BAM_CDIFF, -1, -1, -1, -1, -1, -1, -1,
// 96 .. 127
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
// 128 .. 255
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1
};
sam_hdr_t *sam_hdr_init()
{
sam_hdr_t *bh = (sam_hdr_t*)calloc(1, sizeof(sam_hdr_t));
if (bh == NULL) return NULL;
bh->cigar_tab = bam_cigar_table;
return bh;
}
void sam_hdr_destroy(sam_hdr_t *bh)
{
int32_t i;
if (bh == NULL) return;
if (bh->ref_count > 0) {
--bh->ref_count;
return;
}
if (bh->target_name) {
for (i = 0; i < bh->n_targets; ++i)
free(bh->target_name[i]);
free(bh->target_name);
free(bh->target_len);
}
free(bh->text);
if (bh->hrecs)
sam_hrecs_free(bh->hrecs);
if (bh->sdict)
kh_destroy(s2i, (khash_t(s2i) *) bh->sdict);
free(bh);
}
// Copy the sam_hdr_t::sdict hash, used to store the real lengths of long
// references before sam_hdr_t::hrecs is populated
int sam_hdr_dup_sdict(const sam_hdr_t *h0, sam_hdr_t *h)
{
const khash_t(s2i) *src_long_refs = (khash_t(s2i) *) h0->sdict;
khash_t(s2i) *dest_long_refs = kh_init(s2i);
int i;
if (!dest_long_refs) return -1;
for (i = 0; i < h->n_targets; i++) {
int ret;
khiter_t ksrc, kdest;
if (h->target_len[i] < UINT32_MAX) continue;
ksrc = kh_get(s2i, src_long_refs, h->target_name[i]);
if (ksrc == kh_end(src_long_refs)) continue;
kdest = kh_put(s2i, dest_long_refs, h->target_name[i], &ret);
if (ret < 0) {
kh_destroy(s2i, dest_long_refs);
return -1;
}
kh_val(dest_long_refs, kdest) = kh_val(src_long_refs, ksrc);
}
h->sdict = dest_long_refs;
return 0;
}
sam_hdr_t *sam_hdr_dup(const sam_hdr_t *h0)
{
if (h0 == NULL) return NULL;
sam_hdr_t *h;
if ((h = sam_hdr_init()) == NULL) return NULL;
// copy the simple data
h->n_targets = 0;
h->ignore_sam_err = h0->ignore_sam_err;
h->l_text = 0;
// Then the pointery stuff
if (!h0->hrecs) {
h->target_len = (uint32_t*)calloc(h0->n_targets, sizeof(uint32_t));
if (!h->target_len) goto fail;
h->target_name = (char**)calloc(h0->n_targets, sizeof(char*));
if (!h->target_name) goto fail;
int i;
for (i = 0; i < h0->n_targets; ++i) {
h->target_len[i] = h0->target_len[i];
h->target_name[i] = strdup(h0->target_name[i]);
if (!h->target_name[i]) break;
}
h->n_targets = i;
if (i < h0->n_targets) goto fail;
if (h0->sdict) {
if (sam_hdr_dup_sdict(h0, h) < 0) goto fail;
}
}
if (h0->hrecs) {
kstring_t tmp = { 0, 0, NULL };
if (sam_hrecs_rebuild_text(h0->hrecs, &tmp) != 0) {
free(ks_release(&tmp));
goto fail;
}
h->l_text = tmp.l;
h->text = ks_release(&tmp);
if (sam_hdr_update_target_arrays(h, h0->hrecs, 0) != 0)
goto fail;
} else {
h->l_text = h0->l_text;
h->text = malloc(h->l_text + 1);
if (!h->text) goto fail;
memcpy(h->text, h0->text, h->l_text);
h->text[h->l_text] = '\0';
}
return h;
fail:
sam_hdr_destroy(h);
return NULL;
}
sam_hdr_t *bam_hdr_read(BGZF *fp)
{
sam_hdr_t *h;
uint8_t buf[4];
int magic_len, has_EOF;
int32_t i, name_len, num_names = 0;
size_t bufsize;
ssize_t bytes;
// check EOF
has_EOF = bgzf_check_EOF(fp);
if (has_EOF < 0) {
perror("[W::bam_hdr_read] bgzf_check_EOF");
} else if (has_EOF == 0) {
hts_log_warning("EOF marker is absent. The input is probably truncated");
}
// read "BAM1"
magic_len = bgzf_read(fp, buf, 4);
if (magic_len != 4 || memcmp(buf, "BAM\1", 4)) {
hts_log_error("Invalid BAM binary header");
return 0;
}
h = sam_hdr_init();
if (!h) goto nomem;
// read plain text and the number of reference sequences
bytes = bgzf_read(fp, buf, 4);
if (bytes != 4) goto read_err;
h->l_text = le_to_u32(buf);
bufsize = h->l_text + 1;
if (bufsize < h->l_text) goto nomem; // so large that adding 1 overflowed
#ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION
if (bufsize > FUZZ_ALLOC_LIMIT) goto nomem;
#endif
h->text = (char*)malloc(bufsize);
if (!h->text) goto nomem;
h->text[h->l_text] = 0; // make sure it is NULL terminated
bytes = bgzf_read(fp, h->text, h->l_text);
if (bytes != h->l_text) goto read_err;
bytes = bgzf_read(fp, &h->n_targets, 4);
if (bytes != 4) goto read_err;
if (fp->is_be) ed_swap_4p(&h->n_targets);
if (h->n_targets < 0) goto invalid;
// read reference sequence names and lengths
#ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION
if (h->n_targets > (FUZZ_ALLOC_LIMIT - bufsize)/(sizeof(char*)+sizeof(uint32_t)))
goto nomem;
#endif
if (h->n_targets > 0) {
h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
if (!h->target_name) goto nomem;
h->target_len = (uint32_t*)calloc(h->n_targets, sizeof(uint32_t));
if (!h->target_len) goto nomem;
}
else {
h->target_name = NULL;
h->target_len = NULL;
}
for (i = 0; i != h->n_targets; ++i) {
bytes = bgzf_read(fp, &name_len, 4);
if (bytes != 4) goto read_err;
if (fp->is_be) ed_swap_4p(&name_len);
if (name_len <= 0) goto invalid;
h->target_name[i] = (char*)malloc(name_len);
if (!h->target_name[i]) goto nomem;
num_names++;
bytes = bgzf_read(fp, h->target_name[i], name_len);
if (bytes != name_len) goto read_err;
if (h->target_name[i][name_len - 1] != '\0') {
/* Fix missing NUL-termination. Is this being too nice?
We could alternatively bail out with an error. */
char *new_name;
if (name_len == INT32_MAX) goto invalid;
new_name = realloc(h->target_name[i], name_len + 1);
if (new_name == NULL) goto nomem;
h->target_name[i] = new_name;
h->target_name[i][name_len] = '\0';
}
bytes = bgzf_read(fp, &h->target_len[i], 4);
if (bytes != 4) goto read_err;
if (fp->is_be) ed_swap_4p(&h->target_len[i]);
}
return h;
nomem:
hts_log_error("Out of memory");
goto clean;
read_err:
if (bytes < 0) {
hts_log_error("Error reading BGZF stream");
} else {
hts_log_error("Truncated BAM header");
}
goto clean;
invalid:
hts_log_error("Invalid BAM binary header");
clean:
if (h != NULL) {
h->n_targets = num_names; // ensure we free only allocated target_names
sam_hdr_destroy(h);
}
return NULL;
}
int bam_hdr_write(BGZF *fp, const sam_hdr_t *h)
{
int32_t i, name_len, x;
kstring_t hdr_ks = { 0, 0, NULL };
char *text;
uint32_t l_text;
if (!h) return -1;
if (h->hrecs) {
if (sam_hrecs_rebuild_text(h->hrecs, &hdr_ks) != 0) return -1;
if (hdr_ks.l > UINT32_MAX) {
hts_log_error("Header too long for BAM format");
free(hdr_ks.s);
return -1;
} else if (hdr_ks.l > INT32_MAX) {
hts_log_warning("Header too long for BAM specification (>2GB)");
hts_log_warning("Output file may not be portable");
}
text = hdr_ks.s;
l_text = hdr_ks.l;
} else {
if (h->l_text > UINT32_MAX) {
hts_log_error("Header too long for BAM format");
return -1;
} else if (h->l_text > INT32_MAX) {
hts_log_warning("Header too long for BAM specification (>2GB)");
hts_log_warning("Output file may not be portable");
}
text = h->text;
l_text = h->l_text;
}
// write "BAM1"
if (bgzf_write(fp, "BAM\1", 4) < 0) { free(hdr_ks.s); return -1; }
// write plain text and the number of reference sequences
if (fp->is_be) {
x = ed_swap_4(l_text);
if (bgzf_write(fp, &x, 4) < 0) { free(hdr_ks.s); return -1; }
if (l_text) {
if (bgzf_write(fp, text, l_text) < 0) { free(hdr_ks.s); return -1; }
}
x = ed_swap_4(h->n_targets);
if (bgzf_write(fp, &x, 4) < 0) { free(hdr_ks.s); return -1; }
} else {
if (bgzf_write(fp, &l_text, 4) < 0) { free(hdr_ks.s); return -1; }
if (l_text) {
if (bgzf_write(fp, text, l_text) < 0) { free(hdr_ks.s); return -1; }
}
if (bgzf_write(fp, &h->n_targets, 4) < 0) { free(hdr_ks.s); return -1; }
}
free(hdr_ks.s);
// 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);
if (bgzf_write(fp, &x, 4) < 0) return -1;
} else {
if (bgzf_write(fp, &name_len, 4) < 0) return -1;
}
if (bgzf_write(fp, p, name_len) < 0) return -1;
if (fp->is_be) {
x = ed_swap_4(h->target_len[i]);
if (bgzf_write(fp, &x, 4) < 0) return -1;
} else {
if (bgzf_write(fp, &h->target_len[i], 4) < 0) return -1;
}
}
if (bgzf_flush(fp) < 0) return -1;
return 0;
}
const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid,
hts_pos_t *beg, hts_pos_t *end, int flags) {
return hts_parse_region(s, tid, beg, end, (hts_name2id_f)bam_name2id, h, flags);
}
/*************************
*** BAM alignment I/O ***
*************************/
bam1_t *bam_init1()
{
return (bam1_t*)calloc(1, sizeof(bam1_t));
}
int sam_realloc_bam_data(bam1_t *b, size_t desired)
{
uint32_t new_m_data;
uint8_t *new_data;
new_m_data = desired;
kroundup32(new_m_data);
if (new_m_data < desired) {
errno = ENOMEM; // Not strictly true but we can't store the size
return -1;
}
#ifdef FUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION
if (new_m_data > FUZZ_ALLOC_LIMIT) {
errno = ENOMEM;
return -1;
}
#endif
if ((bam_get_mempolicy(b) & BAM_USER_OWNS_DATA) == 0) {
new_data = realloc(b->data, new_m_data);
} else {
if ((new_data = malloc(new_m_data)) != NULL) {
if (b->l_data > 0)
memcpy(new_data, b->data,
b->l_data < b->m_data ? b->l_data : b->m_data);
bam_set_mempolicy(b, bam_get_mempolicy(b) & (~BAM_USER_OWNS_DATA));
}
}
if (!new_data) return -1;
b->data = new_data;
b->m_data = new_m_data;
return 0;
}
void bam_destroy1(bam1_t *b)
{
if (b == 0) return;
if ((bam_get_mempolicy(b) & BAM_USER_OWNS_DATA) == 0) {
free(b->data);
if ((bam_get_mempolicy(b) & BAM_USER_OWNS_STRUCT) != 0) {
// In case of reuse
b->data = NULL;
b->m_data = 0;
b->l_data = 0;
}
}
if ((bam_get_mempolicy(b) & BAM_USER_OWNS_STRUCT) == 0)
free(b);
}
bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
{
if (realloc_bam_data(bdst, bsrc->l_data) < 0) return NULL;
memcpy(bdst->data, bsrc->data, bsrc->l_data); // copy var-len data
memcpy(&bdst->core, &bsrc->core, sizeof(bsrc->core)); // copy the rest
bdst->l_data = bsrc->l_data;
bdst->id = bsrc->id;
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;
if (bam_copy1(bdst, bsrc) == NULL) {
bam_destroy1(bdst);
return NULL;
}
return bdst;
}
static void bam_cigar2rqlens(int n_cigar, const uint32_t *cigar,
hts_pos_t *rlen, hts_pos_t *qlen)
{
int k;
*rlen = *qlen = 0;
for (k = 0; k < n_cigar; ++k) {
int type = bam_cigar_type(bam_cigar_op(cigar[k]));
int len = bam_cigar_oplen(cigar[k]);
if (type & 1) *qlen += len;
if (type & 2) *rlen += len;
}
}
static int subtract_check_underflow(size_t length, size_t *limit)
{
if (length <= *limit) {
*limit -= length;
return 0;
}
return -1;
}
int bam_set1(bam1_t *bam,
size_t l_qname, const char *qname,
uint16_t flag, int32_t tid, hts_pos_t pos, uint8_t mapq,
size_t n_cigar, const uint32_t *cigar,
int32_t mtid, hts_pos_t mpos, hts_pos_t isize,
size_t l_seq, const char *seq, const char *qual,
size_t l_aux)
{
// use a default qname "*" if none is provided
if (l_qname == 0) {
l_qname = 1;
qname = "*";
}
// note: the qname is stored nul terminated and padded as described in the
// documentation for the bam1_t struct.
size_t qname_nuls = 4 - l_qname % 4;
// the aligment length, needed for bam_reg2bin(), is calculated as in bam_endpos().
// can't use bam_endpos() directly as some fields not yet set up.
hts_pos_t rlen = 0, qlen = 0;
if (!(flag & BAM_FUNMAP)) {
bam_cigar2rqlens((int)n_cigar, cigar, &rlen, &qlen);
}
if (rlen == 0) {
rlen = 1;
}
// validate parameters
if (l_qname > 254) {
hts_log_error("Query name too long");
errno = EINVAL;
return -1;
}
if (HTS_POS_MAX - rlen <= pos) {
hts_log_error("Read ends beyond highest supported position");
errno = EINVAL;
return -1;
}
if (!(flag & BAM_FUNMAP) && l_seq > 0 && n_cigar == 0) {
hts_log_error("Mapped query must have a CIGAR");
errno = EINVAL;
return -1;
}
if (!(flag & BAM_FUNMAP) && l_seq > 0 && l_seq != qlen) {
hts_log_error("CIGAR and query sequence are of different length");
errno = EINVAL;
return -1;
}
size_t limit = INT32_MAX;
int u = subtract_check_underflow(l_qname + qname_nuls, &limit);
u += subtract_check_underflow(n_cigar * 4, &limit);
u += subtract_check_underflow((l_seq + 1) / 2, &limit);
u += subtract_check_underflow(l_seq, &limit);
u += subtract_check_underflow(l_aux, &limit);
if (u != 0) {
hts_log_error("Size overflow");
errno = EINVAL;
return -1;
}
// re-allocate the data buffer as needed.
size_t data_len = l_qname + qname_nuls + n_cigar * 4 + (l_seq + 1) / 2 + l_seq;
if (realloc_bam_data(bam, data_len + l_aux) < 0) {
return -1;
}
bam->l_data = (int)data_len;
bam->core.pos = pos;
bam->core.tid = tid;
bam->core.bin = bam_reg2bin(pos, pos + rlen);
bam->core.qual = mapq;
bam->core.l_extranul = (uint8_t)(qname_nuls - 1);
bam->core.flag = flag;
bam->core.l_qname = (uint16_t)(l_qname + qname_nuls);
bam->core.n_cigar = (uint32_t)n_cigar;
bam->core.l_qseq = (int32_t)l_seq;
bam->core.mtid = mtid;
bam->core.mpos = mpos;
bam->core.isize = isize;
uint8_t *cp = bam->data;
strncpy((char *)cp, qname, l_qname);
int i;
for (i = 0; i < qname_nuls; i++) {
cp[l_qname + i] = '\0';
}
cp += l_qname + qname_nuls;
if (n_cigar > 0) {
memcpy(cp, cigar, n_cigar * 4);
}
cp += n_cigar * 4;
#define NN 16
const uint8_t *useq = (uint8_t *)seq;
for (i = 0; i + NN < l_seq; i += NN) {
int j;
const uint8_t *u2 = useq+i;
for (j = 0; j < NN/2; j++)
cp[j] = (seq_nt16_table[u2[j*2]]<<4) | seq_nt16_table[u2[j*2+1]];
cp += NN/2;
}
for (; i + 1 < l_seq; i += 2) {
*cp++ = (seq_nt16_table[useq[i]] << 4) | seq_nt16_table[useq[i + 1]];
}
for (; i < l_seq; i++) {
*cp++ = seq_nt16_table[(unsigned char)seq[i]] << 4;
}
if (qual) {
memcpy(cp, qual, l_seq);
}
else {
memset(cp, '\xff', l_seq);
}
return (int)data_len;
}
hts_pos_t bam_cigar2qlen(int n_cigar, const uint32_t *cigar)
{
int k;
hts_pos_t 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;
}
hts_pos_t bam_cigar2rlen(int n_cigar, const uint32_t *cigar)
{
int k;
hts_pos_t 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;
}
hts_pos_t bam_endpos(const bam1_t *b)
{
hts_pos_t rlen = (b->core.flag & BAM_FUNMAP)? 0 : bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b));
if (rlen == 0) rlen = 1;
return b->core.pos + rlen;
}
static int bam_tag2cigar(bam1_t *b, int recal_bin, int give_warning) // return 0 if CIGAR is untouched; 1 if CIGAR is updated with CG
{
bam1_core_t *c = &b->core;
uint32_t cigar_st, n_cigar4, CG_st, CG_en, ori_len = b->l_data, *cigar0, CG_len, fake_bytes;
uint8_t *CG;
// test where there is a real CIGAR in the CG tag to move
if (c->n_cigar == 0 || c->tid < 0 || c->pos < 0) return 0;
cigar0 = bam_get_cigar(b);
if (bam_cigar_op(cigar0[0]) != BAM_CSOFT_CLIP || bam_cigar_oplen(cigar0[0]) != c->l_qseq) return 0;
fake_bytes = c->n_cigar * 4;
int saved_errno = errno;
CG = bam_aux_get(b, "CG");
if (!CG) {
if (errno != ENOENT) return -1; // Bad aux data
errno = saved_errno; // restore errno on expected no-CG-tag case
return 0;
}
if (CG[0] != 'B' || !(CG[1] == 'I' || CG[1] == 'i'))
return 0; // not of type B,I
CG_len = le_to_u32(CG + 2);
if (CG_len < c->n_cigar || CG_len >= 1U<<29) return 0; // don't move if the real CIGAR length is shorter than the fake cigar length
// move from the CG tag to the right position
cigar_st = (uint8_t*)cigar0 - b->data;
c->n_cigar = CG_len;
n_cigar4 = c->n_cigar * 4;
CG_st = CG - b->data - 2;
CG_en = CG_st + 8 + n_cigar4;
if (possibly_expand_bam_data(b, n_cigar4 - fake_bytes) < 0) return -1;
b->l_data = b->l_data - fake_bytes + n_cigar4; // we need c->n_cigar-fake_bytes bytes to swap CIGAR to the right place
memmove(b->data + cigar_st + n_cigar4, b->data + cigar_st + fake_bytes, ori_len - (cigar_st + fake_bytes)); // insert c->n_cigar-fake_bytes empty space to make room
memcpy(b->data + cigar_st, b->data + (n_cigar4 - fake_bytes) + CG_st + 8, n_cigar4); // copy the real CIGAR to the right place; -fake_bytes for the fake CIGAR
if (ori_len > CG_en) // move data after the CG tag
memmove(b->data + CG_st + n_cigar4 - fake_bytes, b->data + CG_en + n_cigar4 - fake_bytes, ori_len - CG_en);
b->l_data -= n_cigar4 + 8; // 8: CGBI (4 bytes) and CGBI length (4)
if (recal_bin)
b->core.bin = hts_reg2bin(b->core.pos, bam_endpos(b), 14, 5);
if (give_warning)
hts_log_error("%s encodes a CIGAR with %d operators at the CG tag", bam_get_qname(b), c->n_cigar);
return 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, int is_host)
{
uint32_t *cigar = (uint32_t*)(data + c->l_qname);
uint32_t i;
for (i = 0; i < c->n_cigar; ++i) ed_swap_4p(&cigar[i]);
}
// Fix bad records where qname is not terminated correctly.
static int fixup_missing_qname_nul(bam1_t *b) {
bam1_core_t *c = &b->core;
// Note this is called before c->l_extranul is added to c->l_qname
if (c->l_extranul > 0) {
b->data[c->l_qname++] = '\0';
c->l_extranul--;
} else {
if (b->l_data > INT_MAX - 4) return -1;
if (realloc_bam_data(b, b->l_data + 4) < 0) return -1;
b->l_data += 4;
b->data[c->l_qname++] = '\0';
c->l_extranul = 3;
}
return 0;
}
/*
* Note a second interface that returns a bam pointer instead would avoid bam_copy1
* in multi-threaded handling. This may be worth considering for htslib2.
*/
int bam_read1(BGZF *fp, bam1_t *b)
{
bam1_core_t *c = &b->core;
int32_t block_len, ret, i;
uint32_t x[8], new_l_data;
b->l_data = 0;
if ((ret = bgzf_read(fp, &block_len, 4)) != 4) {
if (ret == 0) return -1; // normal end-of-file
else return -2; // truncated
}
if (fp->is_be)
ed_swap_4p(&block_len);
if (block_len < 32) return -4; // block_len includes core data
if (bgzf_read(fp, x, 32) != 32) return -3;
if (fp->is_be) {
for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
}
c->tid = x[0]; c->pos = (int32_t)x[1];
c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
c->l_extranul = (c->l_qname%4 != 0)? (4 - c->l_qname%4) : 0;
c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
c->l_qseq = x[4];
c->mtid = x[5]; c->mpos = (int32_t)x[6]; c->isize = (int32_t)x[7];
new_l_data = block_len - 32 + c->l_extranul;
if (new_l_data > INT_MAX || c->l_qseq < 0 || c->l_qname < 1) return -4;
if (((uint64_t) c->n_cigar << 2) + c->l_qname + c->l_extranul
+ (((uint64_t) c->l_qseq + 1) >> 1) + c->l_qseq > (uint64_t) new_l_data)
return -4;
if (realloc_bam_data(b, new_l_data) < 0) return -4;
b->l_data = new_l_data;
if (bgzf_read(fp, b->data, c->l_qname) != c->l_qname) return -4;
if (b->data[c->l_qname - 1] != '\0') { // Try to fix missing NUL termination
if (fixup_missing_qname_nul(b) < 0) return -4;
}
for (i = 0; i < c->l_extranul; ++i) b->data[c->l_qname+i] = '\0';
c->l_qname += c->l_extranul;
if (b->l_data < c->l_qname ||
bgzf_read(fp, b->data + c->l_qname, b->l_data - c->l_qname) != b->l_data - c->l_qname)
return -4;
if (fp->is_be) swap_data(c, b->l_data, b->data, 0);
if (bam_tag2cigar(b, 0, 0) < 0)
return -4;
if (c->n_cigar > 0) { // recompute "bin" and check CIGAR-qlen consistency
hts_pos_t rlen, qlen;
bam_cigar2rqlens(c->n_cigar, bam_get_cigar(b), &rlen, &qlen);
if ((b->core.flag & BAM_FUNMAP) || rlen == 0) rlen = 1;
b->core.bin = hts_reg2bin(b->core.pos, b->core.pos + rlen, 14, 5);
// Sanity check for broken CIGAR alignments
if (c->l_qseq > 0 && !(c->flag & BAM_FUNMAP) && qlen != c->l_qseq) {
hts_log_error("CIGAR and query sequence lengths differ for %s",
bam_get_qname(b));
return -4;
}
}
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 - c->l_extranul + 32, y;
int i, ok;
if (c->l_qname - c->l_extranul > 255) {
hts_log_error("QNAME \"%s\" is longer than 254 characters", bam_get_qname(b));
errno = EOVERFLOW;
return -1;
}
if (c->n_cigar > 0xffff) block_len += 16; // "16" for "CGBI", 4-byte tag length and 8-byte fake CIGAR
if (c->pos > INT_MAX ||
c->mpos > INT_MAX ||
c->isize < INT_MIN || c->isize > INT_MAX) {
hts_log_error("Positional data is too large for BAM format");
return -1;
}
x[0] = c->tid;
x[1] = c->pos;
x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | (c->l_qname - c->l_extranul);
if (c->n_cigar > 0xffff) x[3] = (uint32_t)c->flag << 16 | 2;
else x[3] = (uint32_t)c->flag << 16 | (c->n_cigar & 0xffff);
x[4] = c->l_qseq;
x[5] = c->mtid;
x[6] = c->mpos;
x[7] = c->isize;
ok = (bgzf_flush_try(fp, 4 + block_len) >= 0);
if (fp->is_be) {
for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
y = block_len;
if (ok) ok = (bgzf_write(fp, ed_swap_4p(&y), 4) >= 0);
swap_data(c, b->l_data, b->data, 1);
} else {
if (ok) ok = (bgzf_write(fp, &block_len, 4) >= 0);
}
if (ok) ok = (bgzf_write(fp, x, 32) >= 0);
if (ok) ok = (bgzf_write(fp, b->data, c->l_qname - c->l_extranul) >= 0);
if (c->n_cigar <= 0xffff) { // no long CIGAR; write normally
if (ok) ok = (bgzf_write(fp, b->data + c->l_qname, b->l_data - c->l_qname) >= 0);
} else { // with long CIGAR, insert a fake CIGAR record and move the real CIGAR to the CG:B,I tag
uint8_t buf[8];
uint32_t cigar_st, cigar_en, cigar[2];
hts_pos_t cigreflen = bam_cigar2rlen(c->n_cigar, bam_get_cigar(b));
if (cigreflen >= (1<<28)) {
// Length of reference covered is greater than the biggest
// CIGAR operation currently allowed.
hts_log_error("Record %s with %d CIGAR ops and ref length %"PRIhts_pos
" cannot be written in BAM. Try writing SAM or CRAM instead.\n",
bam_get_qname(b), c->n_cigar, cigreflen);
return -1;
}
cigar_st = (uint8_t*)bam_get_cigar(b) - b->data;
cigar_en = cigar_st + c->n_cigar * 4;
cigar[0] = (uint32_t)c->l_qseq << 4 | BAM_CSOFT_CLIP;
cigar[1] = (uint32_t)cigreflen << 4 | BAM_CREF_SKIP;
u32_to_le(cigar[0], buf);
u32_to_le(cigar[1], buf + 4);
if (ok) ok = (bgzf_write(fp, buf, 8) >= 0); // write cigar: <read_length>S<ref_length>N
if (ok) ok = (bgzf_write(fp, &b->data[cigar_en], b->l_data - cigar_en) >= 0); // write data after CIGAR
if (ok) ok = (bgzf_write(fp, "CGBI", 4) >= 0); // write CG:B,I
u32_to_le(c->n_cigar, buf);
if (ok) ok = (bgzf_write(fp, buf, 4) >= 0); // write the true CIGAR length
if (ok) ok = (bgzf_write(fp, &b->data[cigar_st], c->n_cigar * 4) >= 0); // write the real CIGAR
}
if (fp->is_be) swap_data(c, b->l_data, b->data, 0);
return ok? 4 + block_len : -1;
}
/*
* Write a BAM file and append to the in-memory index simultaneously.
*/
static int bam_write_idx1(htsFile *fp, const sam_hdr_t *h, const bam1_t *b) {
BGZF *bfp = fp->fp.bgzf;
if (!fp->idx)
return bam_write1(bfp, b);
uint32_t block_len = b->l_data - b->core.l_extranul + 32;
if (bgzf_flush_try(bfp, 4 + block_len) < 0)
return -1;
if (!bfp->mt)
hts_idx_amend_last(fp->idx, bgzf_tell(bfp));
int ret = bam_write1(bfp, b);
if (ret < 0)
return -1;
if (bgzf_idx_push(bfp, fp->idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(bfp), !(b->core.flag&BAM_FUNMAP)) < 0) {
hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed",
bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), b->core.flag, b->core.pos+1);
ret = -1;
}
return ret;
}
/*
* Set the qname in a BAM record
*/
int bam_set_qname(bam1_t *rec, const char *qname)
{
if (!rec) return -1;
if (!qname || !*qname) return -1;
size_t old_len = rec->core.l_qname;
size_t new_len = strlen(qname) + 1;
if (new_len < 1 || new_len > 255) return -1;
int extranul = (new_len%4 != 0) ? (4 - new_len%4) : 0;
size_t new_data_len = rec->l_data - old_len + new_len + extranul;
if (realloc_bam_data(rec, new_data_len) < 0) return -1;
// Make room
if (new_len + extranul != rec->core.l_qname)
memmove(rec->data + new_len + extranul, rec->data + rec->core.l_qname, rec->l_data - rec->core.l_qname);
// Copy in new name and pad if needed
memcpy(rec->data, qname, new_len);
int n;
for (n = 0; n < extranul; n++) rec->data[new_len + n] = '\0';
rec->l_data = new_data_len;
rec->core.l_qname = new_len + extranul;
rec->core.l_extranul = extranul;
return 0;
}
/********************
*** BAM indexing ***
********************/
static hts_idx_t *sam_index(htsFile *fp, int min_shift)
{
int n_lvls, i, fmt, ret;
bam1_t *b;
hts_idx_t *idx;
sam_hdr_t *h;
h = sam_hdr_read(fp);
if (h == NULL) return NULL;
if (min_shift > 0) {
hts_pos_t max_len = 0, s;
for (i = 0; i < h->n_targets; ++i) {
hts_pos_t len = sam_hdr_tid2len(h, i);
if (max_len < len) max_len = len;
}
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->fp.bgzf), min_shift, n_lvls);
b = bam_init1();
while ((ret = sam_read1(fp, h, b)) >= 0) {
ret = hts_idx_push(idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp->fp.bgzf), !(b->core.flag&BAM_FUNMAP));
if (ret < 0) { // unsorted or doesn't fit
hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), b->core.flag, b->core.pos+1);
goto err;
}
}
if (ret < -1) goto err; // corrupted BAM file
hts_idx_finish(idx, bgzf_tell(fp->fp.bgzf));
sam_hdr_destroy(h);
bam_destroy1(b);
return idx;
err:
bam_destroy1(b);
hts_idx_destroy(idx);
return NULL;
}
int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthreads)
{
hts_idx_t *idx;
htsFile *fp;