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sam.c
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/* sam.c -- SAM and BAM file I/O and manipulation.
Copyright (C) 2008-2010, 2012-2018 Genome Research Ltd.
Copyright (C) 2010, 2012, 2013 Broad Institute.
Author: Heng Li <lh3@sanger.ac.uk>
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. */
#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 "htslib/sam.h"
#include "htslib/bgzf.h"
#include "cram/cram.h"
#include "hts_internal.h"
#include "htslib/hfile.h"
#include "htslib/hts_endian.h"
#include "htslib/khash.h"
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
typedef khash_t(s2i) sdict_t;
#ifndef EOVERFLOW
#define EOVERFLOW ERANGE
#endif
/**********************
*** 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;
h->sdict = NULL;
// TODO Check for memory allocation failures
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, sizeof(uint32_t));
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);
// TODO Check for memory allocation failures
h->target_len = (uint32_t*)malloc(sizeof(uint32_t) * 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) & 0xffffffffUL;
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, 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 || strncmp(buf, "BAM\1", 4)) {
hts_log_error("Invalid BAM binary header");
return 0;
}
h = bam_hdr_init();
if (!h) goto nomem;
// read plain text and the number of reference sequences
bytes = bgzf_read(fp, &h->l_text, 4);
if (bytes != 4) goto read_err;
if (fp->is_be) ed_swap_4p(&h->l_text);
bufsize = ((size_t) h->l_text) + 1;
if (bufsize < h->l_text) goto nomem; // so large that adding 1 overflowed
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
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
bam_hdr_destroy(h);
}
return NULL;
}
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);
if (bgzf_write(fp, buf, 4) < 0) return -1;
// write plain text and the number of reference sequences
if (fp->is_be) {
x = ed_swap_4(h->l_text);
if (bgzf_write(fp, &x, 4) < 0) return -1;
if (h->l_text) {
if (bgzf_write(fp, h->text, h->l_text) < 0) return -1;
}
x = ed_swap_4(h->n_targets);
if (bgzf_write(fp, &x, 4) < 0) return -1;
} else {
if (bgzf_write(fp, &h->l_text, 4) < 0) return -1;
if (h->l_text) {
if (bgzf_write(fp, h->text, h->l_text) < 0) return -1;
}
if (bgzf_write(fp, &h->n_targets, 4) < 0) return -1;
}
// 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;
}
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);
}
void bam_cigar2rqlens(int n_cigar, const uint32_t *cigar, int *rlen, int *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;
}
}
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 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;
if ((CG = bam_aux_get(b, "CG")) == 0) return 0; // no CG tag
if (CG[0] != 'B' || 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;
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
if (b->m_data < b->l_data) {
uint8_t *new_data;
uint32_t new_max = b->l_data;
kroundup32(new_max);
new_data = (uint8_t*)realloc(b->data, new_max);
if (new_data == 0) return -1;
b->m_data = new_max, b->data = new_data;
}
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, b->core.pos + bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(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]);
}
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 (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 = 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;
if ((uint32_t) c->l_qname + c->l_extranul > 255) // l_qname would overflow
return -4;
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 + c->l_extranul;
if (b->l_data < 0 || 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) b->l_data)
return -4;
if (b->m_data < b->l_data) {
uint8_t *new_data;
uint32_t new_m = b->l_data;
kroundup32(new_m);
new_data = (uint8_t*)realloc(b->data, new_m);
if (!new_data)
return -4;
b->data = new_data;
b->m_data = new_m;
}
if (bgzf_read(fp, b->data, c->l_qname) != c->l_qname) 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
int rlen, qlen;
bam_cigar2rqlens(c->n_cigar, bam_get_cigar(b), &rlen, &qlen);
if ((b->core.flag & BAM_FUNMAP)) 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->n_cigar > 0xffff) block_len += 16; // "16" for "CGBI", 4-byte tag length and 8-byte fake CIGAR
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];
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)bam_cigar2rlen(c->n_cigar, bam_get_cigar(b)) << 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;
}
/********************
*** BAM indexing ***
********************/
static hts_idx_t *bam_index(BGZF *fp, int min_shift)
{
int n_lvls, i, fmt, ret;
bam1_t *b;
hts_idx_t *idx;
bam_hdr_t *h;
h = bam_hdr_read(fp);
if (h == NULL) return NULL;
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 ((ret = bam_read1(fp, b)) >= 0) {
ret = hts_idx_push(idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp), !(b->core.flag&BAM_FUNMAP));
if (ret < 0) goto err; // unsorted
}
if (ret < -1) goto err; // corrupted BAM file
hts_idx_finish(idx, bgzf_tell(fp));
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;
int ret = 0;
if ((fp = hts_open(fn, "r")) == 0) return -2;
if (nthreads)
hts_set_threads(fp, nthreads);
switch (fp->format.format) {
case cram:
ret = cram_index_build(fp->fp.cram, fn, fnidx);
break;
case bam:
idx = bam_index(fp->fp.bgzf, min_shift);
if (idx) {
ret = hts_idx_save_as(idx, fn, fnidx, (min_shift > 0)? HTS_FMT_CSI : HTS_FMT_BAI);
if (ret < 0) ret = -4;
hts_idx_destroy(idx);
}
else ret = -1;
break;
default:
ret = -3;
break;
}
hts_close(fp);
return ret;
}
int sam_index_build2(const char *fn, const char *fnidx, int min_shift)
{
return sam_index_build3(fn, fnidx, min_shift, 0);
}
int sam_index_build(const char *fn, int min_shift)
{
return sam_index_build3(fn, NULL, min_shift, 0);
}
// Provide bam_index_build() symbol for binary compability with earlier HTSlib
#undef bam_index_build
int bam_index_build(const char *fn, int min_shift)
{
return sam_index_build2(fn, NULL, min_shift);
}
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 = bam_endpos(b);
}
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;
int ret = cram_get_bam_seq(fp->fp.cram, &b);
if (ret < 0)
return cram_eof(fp->fp.cram) ? -1 : -2;
if (bam_tag2cigar(b, 1, 1) < 0)
return -2;
*tid = b->core.tid;
*beg = b->core.pos;
*end = bam_endpos(b);
return ret;
}
static int cram_pseek(void *fp, int64_t offset, int whence)
{
cram_fd *fd = (cram_fd *)fp;
if ((0 != cram_seek(fd, offset, SEEK_SET))
&& (0 != cram_seek(fd, offset - fd->first_container, SEEK_CUR)))
return -1;
if (fd->ctr) {
cram_free_container(fd->ctr);
if (fd->ctr_mt && fd->ctr_mt != fd->ctr)
cram_free_container(fd->ctr_mt);
fd->ctr = NULL;
fd->ctr_mt = NULL;
fd->ooc = 0;
}
return 0;
}
/*
* cram_ptell is a pseudo-tell function, because it matches the position of the disk cursor only
* after a fresh seek call. Otherwise it indicates that the read takes place inside the buffered
* container previously fetched. It was designed like this to integrate with the functionality
* of the iterator stepping logic.
*/
static int64_t cram_ptell(void *fp)
{
cram_fd *fd = (cram_fd *)fp;
cram_container *c;
int64_t ret = -1L;
if (fd && fd->fp) {
ret = htell(fd->fp);
if ((c = fd->ctr) != NULL) {
ret -= ((c->curr_slice < c->max_slice || c->curr_rec < c->num_records) ? c->offset + 1 : 0);
}
}
return ret;
}
static int bam_pseek(void *fp, int64_t offset, int whence)
{
BGZF *fd = (BGZF *)fp;
return bgzf_seek(fd, offset, whence);
}
static int64_t bam_ptell(void *fp)
{
BGZF *fd = (BGZF *)fp;
if (!fd)
return -1L;
return bgzf_tell(fd);
}
// 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;
switch (fp->format.format) {
case bam: return bam_read1(bgzfp, b);
case cram: {
int ret = cram_get_bam_seq(fp->fp.cram, &b);
if (ret < 0)
return cram_eof(fp->fp.cram) ? -1 : -2;
if (bam_tag2cigar(b, 1, 1) < 0)
return -2;
return ret;
}
default:
// TODO Need headers available to implement this for SAM files
hts_log_error("Not implemented for SAM files");
abort();
}
}
hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx)
{
switch (fp->format.format) {
case bam:
return fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_BAI);
case cram: {
if (cram_index_load(fp->fp.cram, fn, fnidx) < 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;
}
default:
return NULL; // TODO Would use tbx_index_load if it returned hts_idx_t
}
}
hts_idx_t *sam_index_load(htsFile *fp, const char *fn)
{
return sam_index_load2(fp, fn, NULL);
}
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->is_cram = 1;
iter->read_rest = 1;
iter->off = NULL;
iter->bins.a = NULL;
iter->readrec = readrec;
if (tid >= 0 || tid == HTS_IDX_NOCOOR || tid == HTS_IDX_START) {
cram_range r = { tid, beg+1, end };
int ret = cram_set_option(cidx->cram, CRAM_OPT_RANGE, &r);
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;
switch (ret) {
case 0:
break;
case -2:
// No data vs this ref, so mark iterator as completed.
// Same as HTS_IDX_NONE.
iter->finished = 1;
break;
default:
free(iter);
return NULL;
}
}
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:
hts_log_error("Query with tid=%d not implemented for CRAM files", 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);
}
hts_itr_multi_t *sam_itr_regions(const hts_idx_t *idx, bam_hdr_t *hdr, hts_reglist_t *reglist, unsigned int regcount)
{
const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
if (cidx->fmt == HTS_FMT_CRAI)
return hts_itr_regions(idx, reglist, regcount, cram_name2id, cidx->cram,
hts_itr_multi_cram, cram_readrec, cram_pseek, cram_ptell);
else
return hts_itr_regions(idx, reglist, regcount, (hts_name2id_f)(bam_name2id), hdr,
hts_itr_multi_bam, bam_readrec, bam_pseek, bam_ptell);
}
/**********************
*** 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\t", 4) == 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 != '\0'; ++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 != '\0') ++q;
if (*q == '\0' || *q == '\n') break;
}
p = q;
if (sn && ln >= 0) {
khint_t k;
int absent;
k = kh_put(s2i, d, sn, &absent);
if (!absent) {
hts_log_warning("Duplicated sequence '%s'", sn);
free(sn);
} else kh_val(d, k) = (int64_t)(kh_size(d) - 1)<<32 | ln;
}
}
while (*p != '\0' && *p != '\n') ++p;
}
return hdr_from_dict(d);
}
// Minimal sanitisation of a header to ensure.
// - null terminated string.
// - all lines start with @ (also implies no blank lines).
//
// Much more could be done, but currently is not, including:
// - checking header types are known (HD, SQ, etc).
// - syntax (eg checking tab separated fields).
// - validating n_targets matches @SQ records.
// - validating target lengths against @SQ records.
static bam_hdr_t *sam_hdr_sanitise(bam_hdr_t *h) {
if (!h)
return NULL;
// Special case for empty headers.
if (h->l_text == 0)
return h;
uint32_t i, lnum = 0;
char *cp = h->text, last = '\n';
for (i = 0; i < h->l_text; i++) {
// NB: l_text excludes terminating nul. This finds early ones.
if (cp[i] == 0)
break;
// Error on \n[^@], including duplicate newlines
if (last == '\n') {
lnum++;
if (cp[i] != '@') {
hts_log_error("Malformed SAM header at line %u", lnum);
bam_hdr_destroy(h);
return NULL;
}
}
last = cp[i];
}
if (i < h->l_text) { // Early nul found. Complain if not just padding.
uint32_t j = i;
while (j < h->l_text && cp[j] == '\0') j++;
if (j < h->l_text)
hts_log_warning("Unexpected NUL character in header. Possibly truncated");
}
// Add trailing newline and/or trailing nul if required.
if (last != '\n') {
hts_log_warning("Missing trailing newline on SAM header. Possibly truncated");
if (h->l_text == UINT32_MAX) {
hts_log_error("No room for extra newline");
bam_hdr_destroy(h);
return NULL;
}
if (i >= h->l_text - 1) {
cp = realloc(h->text, (size_t) h->l_text+2);
if (!cp) {
bam_hdr_destroy(h);
return NULL;
}
h->text = cp;
}
cp[i++] = '\n';
// l_text may be larger already due to multiple nul padding
if (h->l_text < i)
h->l_text = i;
cp[h->l_text] = '\0';
}
return h;
}
bam_hdr_t *sam_hdr_read(htsFile *fp)
{
switch (fp->format.format) {
case bam:
return sam_hdr_sanitise(bam_hdr_read(fp->fp.bgzf));
case cram:
return sam_hdr_sanitise(cram_header_to_bam(fp->fp.cram->header));
case sam: {
kstring_t str = { 0, 0, NULL };
bam_hdr_t *h = NULL;