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header.c
2803 lines (2345 loc) · 80 KB
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header.c
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/*
Copyright (c) 2018-2020, 2023 Genome Research Ltd.
Authors: James Bonfield <jkb@sanger.ac.uk>, Valeriu Ohan <vo2@sanger.ac.uk>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>
#include <string.h>
#include <assert.h>
#include <errno.h>
#include "textutils_internal.h"
#include "header.h"
// Hash table for removing multiple lines from the header
KHASH_SET_INIT_STR(rm)
// Used for long refs in SAM files
KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
typedef khash_t(rm) rmhash_t;
static int sam_hdr_link_pg(sam_hdr_t *bh);
static int sam_hrecs_vupdate(sam_hrecs_t *hrecs, sam_hrec_type_t *type, va_list ap);
static int sam_hrecs_update(sam_hrecs_t *hrecs, sam_hrec_type_t *type, ...);
#define MAX_ERROR_QUOTE 320 // Prevent over-long error messages
static void sam_hrecs_error(const char *msg, const char *line, size_t len, size_t lno) {
int j;
if (len > MAX_ERROR_QUOTE)
len = MAX_ERROR_QUOTE;
for (j = 0; j < len && line[j] != '\n'; j++)
;
hts_log_error("%s at line %zd: \"%.*s\"", msg, lno, j, line);
}
/* ==== Static methods ==== */
static int sam_hrecs_init_type_order(sam_hrecs_t *hrecs, char *type_list) {
if (!hrecs)
return -1;
if (!type_list) {
hrecs->type_count = 5;
hrecs->type_order = calloc(hrecs->type_count, 3);
if (!hrecs->type_order)
return -1;
memcpy(hrecs->type_order[0], "HD", 2);
memcpy(hrecs->type_order[1], "SQ", 2);
memcpy(hrecs->type_order[2], "RG", 2);
memcpy(hrecs->type_order[3], "PG", 2);
memcpy(hrecs->type_order[4], "CO", 2);
}
return 0;
}
static int sam_hrecs_add_ref_altnames(sam_hrecs_t *hrecs, int nref, const char *list) {
const char *token;
ks_tokaux_t aux;
if (!list)
return 0;
for (token = kstrtok(list, ",", &aux); token; token = kstrtok(NULL, NULL, &aux)) {
if (aux.p == token)
continue;
char *name = string_ndup(hrecs->str_pool, token, aux.p - token);
if (!name)
return -1;
int r;
khint_t k = kh_put(m_s2i, hrecs->ref_hash, name, &r);
if (r < 0) return -1;
if (r > 0)
kh_val(hrecs->ref_hash, k) = nref;
else if (kh_val(hrecs->ref_hash, k) != nref)
hts_log_warning("Duplicate entry AN:\"%s\" in sam header", name);
}
return 0;
}
static void sam_hrecs_remove_ref_altnames(sam_hrecs_t *hrecs, int expected, const char *list) {
const char *token, *sn;
ks_tokaux_t aux;
kstring_t str = KS_INITIALIZE;
if (expected < 0 || expected >= hrecs->nref)
return;
sn = hrecs->ref[expected].name;
for (token = kstrtok(list, ",", &aux); token; token = kstrtok(NULL, NULL, &aux)) {
kputsn(token, aux.p - token, ks_clear(&str));
khint_t k = kh_get(m_s2i, hrecs->ref_hash, str.s);
if (k != kh_end(hrecs->ref_hash)
&& kh_val(hrecs->ref_hash, k) == expected
&& strcmp(sn, str.s) != 0)
kh_del(m_s2i, hrecs->ref_hash, k);
}
free(str.s);
}
/* Updates the hash tables in the sam_hrecs_t structure.
*
* Returns 0 on success;
* -1 on failure
*/
static int sam_hrecs_update_hashes(sam_hrecs_t *hrecs,
khint32_t type,
sam_hrec_type_t *h_type) {
/* Add to reference hash? */
if (type == TYPEKEY("SQ")) {
sam_hrec_tag_t *tag = h_type->tag;
int nref = hrecs->nref;
const char *name = NULL;
const char *altnames = NULL;
hts_pos_t len = -1;
int r;
khint_t k;
while (tag) {
if (tag->str[0] == 'S' && tag->str[1] == 'N') {
assert(tag->len >= 3);
name = tag->str+3;
} else if (tag->str[0] == 'L' && tag->str[1] == 'N') {
assert(tag->len >= 3);
len = strtoll(tag->str+3, NULL, 10);
} else if (tag->str[0] == 'A' && tag->str[1] == 'N') {
assert(tag->len >= 3);
altnames = tag->str+3;
}
tag = tag->next;
}
if (!name) {
hts_log_error("Header includes @SQ line with no SN: tag");
return -1; // SN should be present, according to spec.
}
if (len == -1) {
hts_log_error("Header includes @SQ line \"%s\" with no LN: tag",
name);
return -1; // LN should be present, according to spec.
}
// Seen already?
k = kh_get(m_s2i, hrecs->ref_hash, name);
if (k < kh_end(hrecs->ref_hash)) {
nref = kh_val(hrecs->ref_hash, k);
int ref_changed_flag = 0;
// Check for hash entry added by sam_hrecs_refs_from_targets_array()
if (hrecs->ref[nref].ty == NULL) {
// Attach header line to existing stub entry.
hrecs->ref[nref].ty = h_type;
// Check lengths match; correct if not.
if (len != hrecs->ref[nref].len) {
char tmp[32];
snprintf(tmp, sizeof(tmp), "%" PRIhts_pos,
hrecs->ref[nref].len);
if (sam_hrecs_update(hrecs, h_type, "LN", tmp, NULL) < 0)
return -1;
ref_changed_flag = 1;
}
if (sam_hrecs_add_ref_altnames(hrecs, nref, altnames) < 0)
return -1;
if (ref_changed_flag && (hrecs->refs_changed < 0 || hrecs->refs_changed > nref))
hrecs->refs_changed = nref;
return 0;
}
// Check to see if an existing entry is being updated
if (hrecs->ref[nref].ty == h_type) {
if (hrecs->ref[nref].len != len) {
hrecs->ref[nref].len = len;
ref_changed_flag = 1;
}
if (!hrecs->ref[nref].name || strcmp(hrecs->ref[nref].name, name)) {
hrecs->ref[nref].name = name;
ref_changed_flag = 1;
}
if (sam_hrecs_add_ref_altnames(hrecs, nref, altnames) < 0)
return -1;
if (ref_changed_flag && (hrecs->refs_changed < 0 || hrecs->refs_changed > nref))
hrecs->refs_changed = nref;
return 0;
}
// If here, the name is a duplicate.
// Check to see if it matches the SN: tag from the earlier record.
if (strcmp(hrecs->ref[nref].name, name) == 0) {
hts_log_error("Duplicate entry \"%s\" in sam header",
name);
return -1;
}
// Clash with an already-seen altname
// As SN: should be preferred to AN: add this as a new
// record and update the hash entry to point to it.
hts_log_warning("Ref name SN:\"%s\" is a duplicate of an existing AN key", name);
nref = hrecs->nref;
}
if (nref == hrecs->ref_sz) {
size_t new_sz = hrecs->ref_sz >= 4 ? hrecs->ref_sz + (hrecs->ref_sz / 4) : 32;
sam_hrec_sq_t *new_ref = realloc(hrecs->ref, sizeof(*hrecs->ref) * new_sz);
if (!new_ref)
return -1;
hrecs->ref = new_ref;
hrecs->ref_sz = new_sz;
}
hrecs->ref[nref].name = name;
hrecs->ref[nref].len = len;
hrecs->ref[nref].ty = h_type;
k = kh_put(m_s2i, hrecs->ref_hash, hrecs->ref[nref].name, &r);
if (-1 == r) return -1;
kh_val(hrecs->ref_hash, k) = nref;
if (sam_hrecs_add_ref_altnames(hrecs, nref, altnames) < 0)
return -1;
if (hrecs->refs_changed < 0 || hrecs->refs_changed > hrecs->nref)
hrecs->refs_changed = hrecs->nref;
hrecs->nref++;
}
/* Add to read-group hash? */
if (type == TYPEKEY("RG")) {
sam_hrec_tag_t *tag = sam_hrecs_find_key(h_type, "ID", NULL);
int nrg = hrecs->nrg, r;
khint_t k;
if (!tag) {
hts_log_error("Header includes @RG line with no ID: tag");
return -1; // ID should be present, according to spec.
}
assert(tag->str && tag->len >= 3);
// Seen already?
k = kh_get(m_s2i, hrecs->rg_hash, tag->str + 3);
if (k < kh_end(hrecs->rg_hash)) {
nrg = kh_val(hrecs->rg_hash, k);
assert(hrecs->rg[nrg].ty != NULL);
if (hrecs->rg[nrg].ty != h_type) {
hts_log_warning("Duplicate entry \"%s\" in sam header",
tag->str + 3);
} else {
hrecs->rg[nrg].name = tag->str + 3;
hrecs->rg[nrg].name_len = tag->len - 3;
}
return 0;
}
if (nrg == hrecs->rg_sz) {
size_t new_sz = hrecs->rg_sz >= 4 ? hrecs->rg_sz + hrecs->rg_sz / 4 : 4;
sam_hrec_rg_t *new_rg = realloc(hrecs->rg, sizeof(*hrecs->rg) * new_sz);
if (!new_rg)
return -1;
hrecs->rg = new_rg;
hrecs->rg_sz = new_sz;
}
hrecs->rg[nrg].name = tag->str + 3;
hrecs->rg[nrg].name_len = tag->len - 3;
hrecs->rg[nrg].ty = h_type;
hrecs->rg[nrg].id = nrg;
k = kh_put(m_s2i, hrecs->rg_hash, hrecs->rg[nrg].name, &r);
if (-1 == r) return -1;
kh_val(hrecs->rg_hash, k) = nrg;
hrecs->nrg++;
}
/* Add to program hash? */
if (type == TYPEKEY("PG")) {
sam_hrec_tag_t *tag;
sam_hrec_pg_t *new_pg;
int npg = hrecs->npg;
if (npg == hrecs->pg_sz) {
size_t new_sz = hrecs->pg_sz >= 4 ? hrecs->pg_sz + hrecs->pg_sz / 4 : 4;
new_pg = realloc(hrecs->pg, sizeof(*hrecs->pg) * new_sz);
if (!new_pg)
return -1;
hrecs->pg = new_pg;
hrecs->pg_sz = new_sz;
}
tag = h_type->tag;
hrecs->pg[npg].name = NULL;
hrecs->pg[npg].name_len = 0;
hrecs->pg[npg].ty = h_type;
hrecs->pg[npg].id = npg;
hrecs->pg[npg].prev_id = -1;
while (tag) {
if (tag->str[0] == 'I' && tag->str[1] == 'D') {
/* Avoid duplicate ID tags coming from other applications */
if (!hrecs->pg[npg].name) {
assert(tag->len >= 3);
hrecs->pg[npg].name = tag->str + 3;
hrecs->pg[npg].name_len = tag->len - 3;
} else {
hts_log_warning("PG line with multiple ID tags. The first encountered was preferred - ID:%s", hrecs->pg[npg].name);
}
} else if (tag->str[0] == 'P' && tag->str[1] == 'P') {
// Resolve later if needed
khint_t k;
k = kh_get(m_s2i, hrecs->pg_hash, tag->str+3);
if (k != kh_end(hrecs->pg_hash)) {
int p_id = kh_val(hrecs->pg_hash, k);
hrecs->pg[npg].prev_id = hrecs->pg[p_id].id;
/* Unmark previous entry as a PG termination */
if (hrecs->npg_end > 0 &&
hrecs->pg_end[hrecs->npg_end-1] == p_id) {
hrecs->npg_end--;
} else {
int i;
for (i = 0; i < hrecs->npg_end; i++) {
if (hrecs->pg_end[i] == p_id) {
memmove(&hrecs->pg_end[i], &hrecs->pg_end[i+1],
(hrecs->npg_end-i-1)*sizeof(*hrecs->pg_end));
hrecs->npg_end--;
}
}
}
} else {
hrecs->pg[npg].prev_id = -1;
}
}
tag = tag->next;
}
if (hrecs->pg[npg].name) {
khint_t k;
int r;
k = kh_put(m_s2i, hrecs->pg_hash, hrecs->pg[npg].name, &r);
if (-1 == r) return -1;
kh_val(hrecs->pg_hash, k) = npg;
} else {
return -1; // ID should be present, according to spec.
}
/* Add to npg_end[] array. Remove later if we find a PP line */
if (hrecs->npg_end >= hrecs->npg_end_alloc) {
int *new_pg_end;
int new_alloc = hrecs->npg_end_alloc ? hrecs->npg_end_alloc*2 : 4;
new_pg_end = realloc(hrecs->pg_end, new_alloc * sizeof(int));
if (!new_pg_end)
return -1;
hrecs->npg_end_alloc = new_alloc;
hrecs->pg_end = new_pg_end;
}
hrecs->pg_end[hrecs->npg_end++] = npg;
hrecs->npg++;
}
return 0;
}
static int sam_hrecs_remove_hash_entry(sam_hrecs_t *hrecs, khint32_t type, sam_hrec_type_t *h_type) {
if (!hrecs || !h_type)
return -1;
sam_hrec_tag_t *tag;
const char *key = NULL;
khint_t k;
/* Remove name and any alternative names from reference hash */
if (type == TYPEKEY("SQ")) {
const char *altnames = NULL;
tag = h_type->tag;
while (tag) {
if (tag->str[0] == 'S' && tag->str[1] == 'N') {
assert(tag->len >= 3);
key = tag->str + 3;
} else if (tag->str[0] == 'A' && tag->str[1] == 'N') {
assert(tag->len >= 3);
altnames = tag->str + 3;
}
tag = tag->next;
}
if (key) {
k = kh_get(m_s2i, hrecs->ref_hash, key);
if (k != kh_end(hrecs->ref_hash)) {
int idx = kh_val(hrecs->ref_hash, k);
if (idx + 1 < hrecs->nref)
memmove(&hrecs->ref[idx], &hrecs->ref[idx+1],
sizeof(sam_hrec_sq_t)*(hrecs->nref - idx - 1));
if (altnames)
sam_hrecs_remove_ref_altnames(hrecs, idx, altnames);
kh_del(m_s2i, hrecs->ref_hash, k);
hrecs->nref--;
if (hrecs->refs_changed < 0 || hrecs->refs_changed > idx)
hrecs->refs_changed = idx;
for (k = 0; k < kh_end(hrecs->ref_hash); k++) {
if (kh_exist(hrecs->ref_hash, k)
&& kh_value(hrecs->ref_hash, k) > idx) {
kh_value(hrecs->ref_hash, k)--;
}
}
}
}
}
/* Remove from read-group hash */
if (type == TYPEKEY("RG")) {
tag = h_type->tag;
while (tag) {
if (tag->str[0] == 'I' && tag->str[1] == 'D') {
assert(tag->len >= 3);
key = tag->str + 3;
k = kh_get(m_s2i, hrecs->rg_hash, key);
if (k != kh_end(hrecs->rg_hash)) {
int idx = kh_val(hrecs->rg_hash, k);
if (idx + 1 < hrecs->nrg)
memmove(&hrecs->rg[idx], &hrecs->rg[idx+1], sizeof(sam_hrec_rg_t)*(hrecs->nrg - idx - 1));
kh_del(m_s2i, hrecs->rg_hash, k);
hrecs->nrg--;
for (k = 0; k < kh_end(hrecs->rg_hash); k++) {
if (kh_exist(hrecs->rg_hash, k)
&& kh_value(hrecs->rg_hash, k) > idx) {
kh_value(hrecs->rg_hash, k)--;
}
}
}
break;
}
tag = tag->next;
}
}
return 0;
}
/** Add a header record to the global line ordering
*
* If @p after is not NULL, the new record will be inserted after this one,
* otherwise it will go at the end.
*
* An exception is an HD record, which will always be put first unless
* one is already present.
*/
static void sam_hrecs_global_list_add(sam_hrecs_t *hrecs,
sam_hrec_type_t *h_type,
sam_hrec_type_t *after) {
const khint32_t hd_type = TYPEKEY("HD");
int update_first_line = 0;
// First line seen
if (!hrecs->first_line) {
hrecs->first_line = h_type->global_next = h_type->global_prev = h_type;
return;
}
// @HD goes at the top (unless there's one already)
if (h_type->type == hd_type && hrecs->first_line->type != hd_type) {
after = hrecs->first_line->global_prev;
update_first_line = 1;
}
// If no instructions given, put it at the end
if (!after)
after = hrecs->first_line->global_prev;
h_type->global_prev = after;
h_type->global_next = after->global_next;
h_type->global_prev->global_next = h_type;
h_type->global_next->global_prev = h_type;
if (update_first_line)
hrecs->first_line = h_type;
}
/*! Add header record with a va_list interface.
*
* Adds a single record to a SAM header.
*
* This takes a header record type, a va_list argument and one or more
* key,value pairs, ending with the NULL key.
*
* Eg. sam_hrecs_vadd(h, "SQ", args, "ID", "foo", "LN", "100", NULL).
*
* The purpose of the additional va_list parameter is to permit other
* varargs functions to call this while including their own additional
* parameters; an example is in sam_hdr_add_pg().
*
* Note: this function invokes va_arg at least once, making the value
* of ap indeterminate after the return. The caller should call
* va_start/va_end before/after calling this function or use va_copy.
*
* @return
* Returns >= 0 on success;
* -1 on failure
*/
static int sam_hrecs_vadd(sam_hrecs_t *hrecs, const char *type, va_list ap, ...) {
va_list args;
sam_hrec_type_t *h_type;
sam_hrec_tag_t *h_tag, *last=NULL;
int new;
khint32_t type_i = TYPEKEY(type), k;
if (!strncmp(type, "HD", 2) && (h_type = sam_hrecs_find_type_id(hrecs, "HD", NULL, NULL)))
return sam_hrecs_vupdate(hrecs, h_type, ap);
if (!(h_type = pool_alloc(hrecs->type_pool)))
return -1;
k = kh_put(sam_hrecs_t, hrecs->h, type_i, &new);
if (new < 0)
return -1;
h_type->type = type_i;
// Form the ring, either with self or other lines of this type
if (!new) {
sam_hrec_type_t *t = kh_val(hrecs->h, k), *p;
p = t->prev;
assert(p->next == t);
p->next = h_type;
h_type->prev = p;
t->prev = h_type;
h_type->next = t;
} else {
kh_val(hrecs->h, k) = h_type;
h_type->prev = h_type->next = h_type;
}
h_type->tag = NULL;
// Add to global line ordering after any existing line of the same type,
// or at the end if no line of this type exists yet.
sam_hrecs_global_list_add(hrecs, h_type, !new ? h_type->prev : NULL);
// Check linked-list invariants
assert(h_type->prev->next == h_type);
assert(h_type->next->prev == h_type);
assert(h_type->global_prev->global_next == h_type);
assert(h_type->global_next->global_prev == h_type);
// Any ... varargs
va_start(args, ap);
for (;;) {
char *key, *val = NULL, *str;
if (!(key = (char *)va_arg(args, char *)))
break;
if (strncmp(type, "CO", 2) && !(val = (char *)va_arg(args, char *)))
break;
if (*val == '\0')
continue;
if (!(h_tag = pool_alloc(hrecs->tag_pool)))
return -1;
if (strncmp(type, "CO", 2)) {
h_tag->len = 3 + strlen(val);
str = string_alloc(hrecs->str_pool, h_tag->len+1);
if (!str || snprintf(str, h_tag->len+1, "%2.2s:%s", key, val) < 0)
return -1;
h_tag->str = str;
} else {
h_tag->len = strlen(key);
h_tag->str = string_ndup(hrecs->str_pool, key, h_tag->len);
if (!h_tag->str)
return -1;
}
h_tag->next = NULL;
if (last)
last->next = h_tag;
else
h_type->tag = h_tag;
last = h_tag;
}
va_end(args);
// Plus the specified va_list params
for (;;) {
char *key, *val = NULL, *str;
if (!(key = (char *)va_arg(ap, char *)))
break;
if (strncmp(type, "CO", 2) && !(val = (char *)va_arg(ap, char *)))
break;
if (!(h_tag = pool_alloc(hrecs->tag_pool)))
return -1;
if (strncmp(type, "CO", 2)) {
h_tag->len = 3 + strlen(val);
str = string_alloc(hrecs->str_pool, h_tag->len+1);
if (!str || snprintf(str, h_tag->len+1, "%2.2s:%s", key, val) < 0)
return -1;
h_tag->str = str;
} else {
h_tag->len = strlen(key);
h_tag->str = string_ndup(hrecs->str_pool, key, h_tag->len);
if (!h_tag->str)
return -1;
}
h_tag->next = NULL;
if (last)
last->next = h_tag;
else
h_type->tag = h_tag;
last = h_tag;
}
if (-1 == sam_hrecs_update_hashes(hrecs, TYPEKEY(type), h_type))
return -1;
if (!strncmp(type, "PG", 2))
hrecs->pgs_changed = 1;
hrecs->dirty = 1;
return 0;
}
// As sam_hrecs_vadd(), but without the extra va_list parameter
static int sam_hrecs_add(sam_hrecs_t *hrecs, const char *type, ...) {
va_list args;
int res;
va_start(args, type);
res = sam_hrecs_vadd(hrecs, type, args, NULL);
va_end(args);
return res;
}
/*
* Function for deallocating a list of tags
*/
static void sam_hrecs_free_tags(sam_hrecs_t *hrecs, sam_hrec_tag_t *tag) {
if (!hrecs || !tag)
return;
if (tag->next)
sam_hrecs_free_tags(hrecs, tag->next);
pool_free(hrecs->tag_pool, tag);
}
static int sam_hrecs_remove_line(sam_hrecs_t *hrecs, const char *type_name, sam_hrec_type_t *type_found, int remove_hash) {
if (!hrecs || !type_name || !type_found)
return -1;
khint32_t itype = TYPEKEY(type_name);
khint_t k = kh_get(sam_hrecs_t, hrecs->h, itype);
if (k == kh_end(hrecs->h))
return -1;
// Remove from global list (remembering it could be the only line)
if (hrecs->first_line == type_found) {
hrecs->first_line = (type_found->global_next != type_found
? type_found->global_next : NULL);
}
type_found->global_next->global_prev = type_found->global_prev;
type_found->global_prev->global_next = type_found->global_next;
/* single element in the list */
if (type_found->prev == type_found || type_found->next == type_found) {
kh_del(sam_hrecs_t, hrecs->h, k);
} else {
type_found->prev->next = type_found->next;
type_found->next->prev = type_found->prev;
if (kh_val(hrecs->h, k) == type_found) { //first element
kh_val(hrecs->h, k) = type_found->next;
}
}
if (remove_hash && (!strncmp(type_name, "SQ", 2) || !strncmp(type_name, "RG", 2)))
sam_hrecs_remove_hash_entry(hrecs, itype, type_found);
sam_hrecs_free_tags(hrecs, type_found->tag);
pool_free(hrecs->type_pool, type_found);
hrecs->dirty = 1;
return 0;
}
// Paste together a line from the parsed data structures
static int build_header_line(const sam_hrec_type_t *ty, kstring_t *ks) {
sam_hrec_tag_t *tag;
int r = 0;
char c[2]= { ty->type >> 8, ty->type & 0xff };
r |= (kputc_('@', ks) == EOF);
r |= (kputsn(c, 2, ks) == EOF);
for (tag = ty->tag; tag; tag = tag->next) {
r |= (kputc_('\t', ks) == EOF);
r |= (kputsn(tag->str, tag->len, ks) == EOF);
}
return r;
}
static int sam_hrecs_rebuild_lines(const sam_hrecs_t *hrecs, kstring_t *ks) {
const sam_hrec_type_t *t1, *t2;
if (!hrecs->first_line)
return kputsn("", 0, ks) >= 0 ? 0 : -1;
t1 = t2 = hrecs->first_line;
do {
if (build_header_line(t1, ks) != 0)
return -1;
if (kputc('\n', ks) < 0)
return -1;
t1 = t1->global_next;
} while (t1 != t2);
return 0;
}
static int sam_hrecs_parse_lines(sam_hrecs_t *hrecs, const char *hdr, size_t len) {
size_t i, lno;
if (!hrecs || len > SSIZE_MAX)
return -1;
if (!len)
len = strlen(hdr);
if (len < 3) {
if (len == 0 || *hdr == '\0') return 0;
sam_hrecs_error("Header line too short", hdr, len, 1);
return -1;
}
for (i = 0, lno = 1; i < len - 3 && hdr[i] != '\0'; i++, lno++) {
khint32_t type;
khint_t k;
int l_start = i, new;
sam_hrec_type_t *h_type;
sam_hrec_tag_t *h_tag, *last;
if (hdr[i] != '@') {
sam_hrecs_error("Header line does not start with '@'",
&hdr[l_start], len - l_start, lno);
return -1;
}
if (!isalpha_c(hdr[i+1]) || !isalpha_c(hdr[i+2])) {
sam_hrecs_error("Header line does not have a two character key",
&hdr[l_start], len - l_start, lno);
return -1;
}
type = TYPEKEY(&hdr[i+1]);
i += 3;
if (i == len || hdr[i] == '\n')
continue;
// Add the header line type
if (!(h_type = pool_alloc(hrecs->type_pool)))
return -1;
k = kh_put(sam_hrecs_t, hrecs->h, type, &new);
if (new < 0)
return -1;
h_type->type = type;
// Add to end of global list
sam_hrecs_global_list_add(hrecs, h_type, NULL);
// Form the ring, either with self or other lines of this type
if (!new) {
sam_hrec_type_t *t = kh_val(hrecs->h, k), *p;
p = t->prev;
assert(p->next == t);
p->next = h_type;
h_type->prev = p;
t->prev = h_type;
h_type->next = t;
} else {
kh_val(hrecs->h, k) = h_type;
h_type->prev = h_type->next = h_type;
}
// Parse the tags on this line
last = NULL;
if (type == TYPEKEY("CO")) {
size_t j;
if (i == len || hdr[i] != '\t') {
sam_hrecs_error("Missing tab",
&hdr[l_start], len - l_start, lno);
return -1;
}
for (j = ++i; j < len && hdr[j] != '\0' && hdr[j] != '\n'; j++)
;
if (!(h_type->tag = h_tag = pool_alloc(hrecs->tag_pool)))
return -1;
h_tag->str = string_ndup(hrecs->str_pool, &hdr[i], j-i);
h_tag->len = j-i;
h_tag->next = NULL;
if (!h_tag->str)
return -1;
i = j;
} else {
do {
size_t j;
if (i == len || hdr[i] != '\t') {
sam_hrecs_error("Missing tab",
&hdr[l_start], len - l_start, lno);
return -1;
}
for (j = ++i; j < len && hdr[j] != '\0' && hdr[j] != '\n' && hdr[j] != '\t'; j++)
;
if (j - i < 3 || hdr[i + 2] != ':') {
sam_hrecs_error("Malformed key:value pair",
&hdr[l_start], len - l_start, lno);
return -1;
}
if (!(h_tag = pool_alloc(hrecs->tag_pool)))
return -1;
h_tag->str = string_ndup(hrecs->str_pool, &hdr[i], j-i);
h_tag->len = j-i;
h_tag->next = NULL;
if (!h_tag->str)
return -1;
if (last)
last->next = h_tag;
else
h_type->tag = h_tag;
last = h_tag;
i = j;
} while (i < len && hdr[i] != '\0' && hdr[i] != '\n');
}
/* Update RG/SQ hashes */
if (-1 == sam_hrecs_update_hashes(hrecs, type, h_type))
return -1;
}
return 0;
}
/*! Update sam_hdr_t target_name and target_len arrays
*
* @return 0 on success; -1 on failure
*/
int sam_hdr_update_target_arrays(sam_hdr_t *bh, const sam_hrecs_t *hrecs,
int refs_changed) {
if (!bh || !hrecs)
return -1;
if (refs_changed < 0)
return 0;
// Grow arrays if necessary
if (bh->n_targets < hrecs->nref) {
char **new_names = realloc(bh->target_name,
hrecs->nref * sizeof(*new_names));
if (!new_names)
return -1;
bh->target_name = new_names;
uint32_t *new_lens = realloc(bh->target_len,
hrecs->nref * sizeof(*new_lens));
if (!new_lens)
return -1;
bh->target_len = new_lens;
}
// Update names and lengths where changed
// hrecs->refs_changed is the first ref that has been updated, so ones
// before that can be skipped.
int i;
khint_t k;
khash_t(s2i) *long_refs = (khash_t(s2i) *) bh->sdict;
for (i = refs_changed; i < hrecs->nref; i++) {
if (i >= bh->n_targets
|| strcmp(bh->target_name[i], hrecs->ref[i].name) != 0) {
if (i < bh->n_targets)
free(bh->target_name[i]);
bh->target_name[i] = strdup(hrecs->ref[i].name);
if (!bh->target_name[i])
return -1;
}
if (hrecs->ref[i].len < UINT32_MAX) {
bh->target_len[i] = hrecs->ref[i].len;
if (!long_refs)
continue;
// Check if we have an old length, if so remove it.
k = kh_get(s2i, long_refs, bh->target_name[i]);
if (k < kh_end(long_refs))
kh_del(s2i, long_refs, k);
} else {
bh->target_len[i] = UINT32_MAX;
if (bh->hrecs != hrecs) {
// Called from sam_hdr_dup; need to add sdict entries
if (!long_refs) {
if (!(bh->sdict = long_refs = kh_init(s2i)))
return -1;
}
// Add / update length
int absent;
k = kh_put(s2i, long_refs, bh->target_name[i], &absent);
if (absent < 0)
return -1;
kh_val(long_refs, k) = hrecs->ref[i].len;
}
}
}
// Free up any names that have been removed
for (; i < bh->n_targets; i++) {
if (long_refs) {
k = kh_get(s2i, long_refs, bh->target_name[i]);
if (k < kh_end(long_refs))
kh_del(s2i, long_refs, k);
}
free(bh->target_name[i]);
}
bh->n_targets = hrecs->nref;
return 0;
}
static int rebuild_target_arrays(sam_hdr_t *bh) {
if (!bh || !bh->hrecs)
return -1;
sam_hrecs_t *hrecs = bh->hrecs;
if (hrecs->refs_changed < 0)
return 0;
if (sam_hdr_update_target_arrays(bh, hrecs, hrecs->refs_changed) != 0)
return -1;
hrecs->refs_changed = -1;
return 0;
}
/// Populate hrecs refs array from header target_name, target_len arrays