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bam_sort.c
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bam_sort.c
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/* bam_sort.c -- sorting and merging.
Copyright (C) 2008-2021 Genome Research Ltd.
Portions copyright (C) 2009-2012 Broad Institute.
Author: Heng Li <[email protected]>
Author: Martin Pollard <[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. */
#include <config.h>
#include <stdbool.h>
#include <stdlib.h>
#include <ctype.h>
#include <errno.h>
#include <stdio.h>
#include <string.h>
#include <time.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include <getopt.h>
#include <assert.h>
#include <pthread.h>
#include <inttypes.h>
#include "htslib/ksort.h"
#include "htslib/hts_os.h"
#include "htslib/khash.h"
#include "htslib/klist.h"
#include "htslib/kstring.h"
#include "htslib/sam.h"
#include "htslib/hts_endian.h"
#include "htslib/cram.h"
#include "sam_opts.h"
#include "samtools.h"
#include "bedidx.h"
// Struct which contains the a record, and the pointer to the sort tag (if any) or
// a combined ref / position / strand.
// Used to speed up tag and position sorts.
typedef struct bam1_tag {
bam1_t *bam_record;
union {
const uint8_t *tag;
uint8_t pos_tid[12];
} u;
} bam1_tag;
/* Minimum memory required in megabytes before sort will attempt to run. This
is to prevent accidents where failing to use the -m option correctly results
in the creation of a temporary file for each read in the input file.
Don't forget to update the man page if you change this. */
const size_t SORT_MIN_MEGS_PER_THREAD = 1;
/* Default per-thread memory for sort. Must be >= SORT_MIN_MEGS_PER_THREAD.
Don't forget to update the man page if you change this. */
const size_t SORT_DEFAULT_MEGS_PER_THREAD = 768;
#if !defined(__DARWIN_C_LEVEL) || __DARWIN_C_LEVEL < 900000L
#define NEED_MEMSET_PATTERN4
#endif
#ifdef NEED_MEMSET_PATTERN4
void memset_pattern4(void *target, const void *pattern, size_t size) {
uint32_t* target_iter = target;
size_t loops = size/4;
size_t i;
for (i = 0; i < loops; ++i) {
memcpy(target_iter, pattern, 4);
++target_iter;
}
if (size%4 != 0)
memcpy(target_iter, pattern, size%4);
}
#endif
KHASH_INIT(c2c, char*, char*, 1, kh_str_hash_func, kh_str_hash_equal)
KHASH_INIT(cset, char*, char, 0, kh_str_hash_func, kh_str_hash_equal)
KHASH_MAP_INIT_STR(c2i, int)
#define hdrln_free_char(p)
KLIST_INIT(hdrln, char*, hdrln_free_char)
static int g_is_by_qname = 0;
static int g_is_by_tag = 0;
static int g_is_by_minhash = 0;
static char g_sort_tag[2] = {0,0};
static int strnum_cmp(const char *_a, const char *_b)
{
const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
const unsigned char *pa = a, *pb = b;
while (*pa && *pb) {
if (isdigit(*pa) && isdigit(*pb)) {
while (*pa == '0') ++pa;
while (*pb == '0') ++pb;
while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
if (isdigit(*pa) && isdigit(*pb)) {
int i = 0;
while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
} else if (isdigit(*pa)) return 1;
else if (isdigit(*pb)) return -1;
else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
} else {
if (*pa != *pb) return (int)*pa - (int)*pb;
++pa; ++pb;
}
}
return *pa? 1 : *pb? -1 : 0;
}
#define HEAP_EMPTY (UINT64_MAX >> 1)
typedef struct {
int i;
uint32_t tid;
uint64_t pos:63, rev:1, idx;
bam1_tag entry;
} heap1_t;
static inline int bam1_cmp_by_tag(const bam1_tag a, const bam1_tag b);
static inline int bam1_cmp_by_minhash(const bam1_tag a, const bam1_tag b);
// Function to compare reads in the heap and determine which one is < the other
// Note, unlike the bam1_cmp_by_X functions which return <0, 0, >0 this
// is strictly 0 or 1 only.
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (!a.entry.bam_record)
return 1;
if (!b.entry.bam_record)
return 0;
if (g_is_by_tag) {
int t;
t = bam1_cmp_by_tag(a.entry, b.entry);
if (t != 0) return t > 0;
} else if (g_is_by_minhash) {
int t = bam1_cmp_by_minhash(a.entry, b.entry);
if (t != 0) return t > 0;
} else if (g_is_by_qname) {
int t, fa, fb;
t = strnum_cmp(bam_get_qname(a.entry.bam_record), bam_get_qname(b.entry.bam_record));
if (t != 0) return t > 0;
fa = a.entry.bam_record->core.flag & 0xc0;
fb = b.entry.bam_record->core.flag & 0xc0;
if (fa != fb) return fa > fb;
} else {
if (a.tid != b.tid) return a.tid > b.tid;
if (a.pos != b.pos) return a.pos > b.pos;
if (a.rev != b.rev) return a.rev > b.rev;
}
// This compares by position in the input file(s)
if (a.i != b.i) return a.i > b.i;
return a.idx > b.idx;
}
KSORT_INIT(heap, heap1_t, heap_lt)
typedef struct merged_header {
sam_hdr_t *hdr;
kstring_t out_rg;
kstring_t out_pg;
kstring_t out_co;
char **target_name;
uint32_t *target_len;
size_t n_targets;
size_t targets_sz;
khash_t(c2i) *sq_tids;
khash_t(cset) *rg_ids;
khash_t(cset) *pg_ids;
bool have_hd;
} merged_header_t;
typedef struct trans_tbl {
int32_t n_targets;
int* tid_trans;
kh_c2c_t* rg_trans;
kh_c2c_t* pg_trans;
bool lost_coord_sort;
} trans_tbl_t;
static void trans_tbl_destroy(trans_tbl_t *tbl) {
khiter_t iter;
free(tbl->tid_trans);
/*
* The values for the tbl->rg_trans and tbl->pg_trans hashes are pointers
* to keys in the rg_ids and pg_ids sets of the merged_header_t, so
* they should not be freed here.
*
* The keys are unique to each hash entry, so they do have to go.
*/
for (iter = kh_begin(tbl->rg_trans); iter != kh_end(tbl->rg_trans); ++iter) {
if (kh_exist(tbl->rg_trans, iter)) {
free(kh_key(tbl->rg_trans, iter));
}
}
for (iter = kh_begin(tbl->pg_trans); iter != kh_end(tbl->pg_trans); ++iter) {
if (kh_exist(tbl->pg_trans, iter)) {
free(kh_key(tbl->pg_trans, iter));
}
}
kh_destroy(c2c,tbl->rg_trans);
kh_destroy(c2c,tbl->pg_trans);
}
/*
* Create a merged_header_t struct.
*/
static merged_header_t * init_merged_header() {
merged_header_t *merged_hdr;
merged_hdr = calloc(1, sizeof(*merged_hdr));
if (merged_hdr == NULL) return NULL;
merged_hdr->hdr = sam_hdr_init();
if (!merged_hdr->hdr) goto fail;
merged_hdr->targets_sz = 16;
merged_hdr->target_name = malloc(merged_hdr->targets_sz
* sizeof(*merged_hdr->target_name));
if (NULL == merged_hdr->target_name) goto fail;
merged_hdr->target_len = malloc(merged_hdr->targets_sz
* sizeof(*merged_hdr->target_len));
if (NULL == merged_hdr->target_len) goto fail;
merged_hdr->sq_tids = kh_init(c2i);
if (merged_hdr->sq_tids == NULL) goto fail;
merged_hdr->rg_ids = kh_init(cset);
if (merged_hdr->rg_ids == NULL) goto fail;
merged_hdr->pg_ids = kh_init(cset);
if (merged_hdr->pg_ids == NULL) goto fail;
return merged_hdr;
fail:
perror("[init_merged_header]");
kh_destroy(cset, merged_hdr->pg_ids);
kh_destroy(cset, merged_hdr->rg_ids);
kh_destroy(c2i, merged_hdr->sq_tids);
free(merged_hdr->target_name);
free(merged_hdr->target_len);
sam_hdr_destroy(merged_hdr->hdr);
free(merged_hdr);
return NULL;
}
/* Some handy kstring manipulating functions */
// Append char range to kstring
static inline int range_to_ks(const char *src, int from, int to,
kstring_t *dest) {
return kputsn(src + from, to - from, dest) != to - from;
}
// Append a kstring to a kstring
static inline int ks_to_ks(kstring_t *src, kstring_t *dest) {
return kputsn(ks_str(src), ks_len(src), dest) != ks_len(src);
}
/*
* Generate a unique ID by appending a random suffix to a given prefix.
* existing_ids is the set of IDs that are already in use.
* If always_add_suffix is true, the suffix will always be included.
* If false, prefix will be returned unchanged if it isn't in existing_ids.
*/
static int gen_unique_id(char *prefix, khash_t(cset) *existing_ids,
bool always_add_suffix, kstring_t *dest) {
khiter_t iter;
if (!always_add_suffix) {
// Try prefix on its own first
iter = kh_get(cset, existing_ids, prefix);
if (iter == kh_end(existing_ids)) { // prefix isn't used yet
dest->l = 0;
if (kputs(prefix, dest) == EOF) return -1;
return 0;
}
}
do {
dest->l = 0;
ksprintf(dest, "%s-%0lX", prefix, lrand48());
iter = kh_get(cset, existing_ids, ks_str(dest));
} while (iter != kh_end(existing_ids));
return 0;
}
/*
* Add the @HD line to the new header
* In practice the @HD line will come from the first input header.
*/
static int trans_tbl_add_hd(merged_header_t* merged_hdr,
sam_hdr_t *translate) {
kstring_t hd_line = { 0, 0, NULL };
int res;
// TODO: handle case when @HD needs merging.
if (merged_hdr->have_hd) return 0;
res = sam_hdr_find_hd(translate, &hd_line);
if (res < -1) {
print_error("merge", "failed to get @HD line from header");
return -1;
}
if (res < 0) // Not found
return 0;
if (sam_hdr_add_lines(merged_hdr->hdr, hd_line.s, hd_line.l) < 0) {
print_error("merge", "failed to add @HD line to new header");
free(hd_line.s);
return -1;
}
free(hd_line.s);
merged_hdr->have_hd = true;
return 0;
}
/*
* Add @SQ records to the translation table.
*
* Go through the target list for the input header. Any new targets found
* are added to the output header target list. At the same time, a mapping
* from the input to output target ids is stored in tbl.
*
* If any new targets are found, the header text is scanned to find the
* corresponding @SQ records. They are then copied into the
* merged_hdr->out_text kstring (which will eventually become the
* output header text).
*
* Returns 0 on success, -1 on failure.
*/
static int trans_tbl_add_sq(merged_header_t* merged_hdr, sam_hdr_t *translate,
trans_tbl_t* tbl) {
int32_t i;
int min_tid = -1, res;
kstring_t sq_line = { 0, 0, NULL }, sq_sn = { 0, 0, NULL };
// Fill in the tid part of the translation table, adding new targets
// to the merged header as we go.
for (i = 0; i < sam_hdr_nref(translate); ++i) {
int trans_tid;
sq_sn.l = 0;
res = sam_hdr_find_tag_pos(translate, "SQ", i, "SN", &sq_sn);
if (res < 0) {
print_error("merge", "failed to get @SQ SN #%d from header", i + 1);
goto fail;
}
trans_tid = sam_hdr_name2tid(merged_hdr->hdr, sq_sn.s);
if (trans_tid < -1) {
print_error("merge", "failed to lookup ref");
goto fail;
}
if (trans_tid < 0) {
// Append missing entries to out_hdr
sq_line.l = 0;
res = sam_hdr_find_line_id(translate, "SQ", "SN", sq_sn.s, &sq_line);
if (res < 0) {
print_error("merge", "failed to get @SQ SN:%s from header", sq_sn.s);
goto fail;
}
trans_tid = sam_hdr_nref(merged_hdr->hdr);
res = sam_hdr_add_lines(merged_hdr->hdr, sq_line.s, sq_line.l);
if (res < 0) {
print_error("merge", "failed to add @SQ SN:%s to new header", sq_sn.s);
goto fail;
}
}
tbl->tid_trans[i] = trans_tid;
if (tbl->tid_trans[i] > min_tid) {
min_tid = tbl->tid_trans[i];
} else {
tbl->lost_coord_sort = true;
}
}
free(sq_line.s);
free(sq_sn.s);
return 0;
fail:
free(sq_line.s);
free(sq_sn.s);
return -1;
}
/*
* Common code for setting up RG and PG record ID tag translation.
*
* is_rg is true for RG translation, false for PG.
* translate is the input bam header
* merge is true if tags with the same ID are to be merged.
* known_ids is the set of IDs already in the output header.
* id_map is the translation map from input header IDs to output header IDs
* If override is set, it will be used to replace the existing ID (RG only)
*
* known_ids and id_map have entries for the new IDs added to them.
*
* Return value is a linked list of header lines with the translated IDs,
* or NULL if something went wrong (probably out of memory).
*
*/
static klist_t(hdrln) * trans_rg_pg(bool is_rg, sam_hdr_t *translate,
bool merge, khash_t(cset)* known_ids,
khash_t(c2c)* id_map, char *override) {
khiter_t iter;
int num_ids, i;
const char *rec_type = is_rg ? "RG" : "PG";
klist_t(hdrln) *hdr_lines;
hdr_lines = kl_init(hdrln);
// Search through translate's header
num_ids = sam_hdr_count_lines(translate, rec_type);
if (num_ids < 0)
goto fail;
for (i = 0; i < num_ids; i++) {
kstring_t orig_id = { 0, 0, NULL }; // ID in original header
kstring_t transformed_id = { 0, 0, NULL }; // ID in output header
char *map_value; // Value to store in id_map
bool id_changed; // Have we changed the ID?
bool not_found_in_output; // ID isn't in the output header (yet)
if (sam_hdr_find_tag_pos(translate, rec_type, i, "ID", &orig_id) < 0)
goto fail;
// is our matched ID in our output ID set already?
iter = kh_get(cset, known_ids, ks_str(&orig_id));
not_found_in_output = (iter == kh_end(known_ids));
if (override) {
// Override original ID (RG only)
#ifdef OVERRIDE_DOES_NOT_MERGE
if (gen_unique_id(override, known_ids, false, &transformed_id))
goto memfail;
not_found_in_output = true; // As ID now unique
#else
if (kputs(override, &transformed_id) == EOF) goto memfail;
// Know about override already?
iter = kh_get(cset, known_ids, ks_str(&transformed_id));
not_found_in_output = (iter == kh_end(known_ids));
#endif
id_changed = true;
} else {
if ( not_found_in_output || merge) {
// Not in there or merging so can add it as 1-1 mapping
if (ks_to_ks(&orig_id, &transformed_id)) goto memfail;
id_changed = false;
} else {
// It's in there so we need to transform it by appending
// a random number to the id
if (gen_unique_id(ks_str(&orig_id), known_ids,
true, &transformed_id))
goto memfail;
id_changed = true;
not_found_in_output = true; // As ID now unique
}
}
// Does this line need to go into our output header?
if (not_found_in_output) {
// Take matched line and replace ID with transformed_id
kstring_t new_hdr_line = { 0, 0, NULL };
if (sam_hdr_find_line_id(translate, rec_type,
"ID", ks_str(&orig_id), &new_hdr_line) < 0){
goto fail;
}
if (id_changed) {
char *idp = strstr(ks_str(&new_hdr_line), "\tID:"), *id_end;
ptrdiff_t id_offset, id_len;
if (!idp) {
print_error("merge", "failed to find ID in \"%s\"\n",
ks_str(&new_hdr_line));
goto fail;
}
idp += 4;
for (id_end = idp; *id_end >= '\n'; id_end++) {}
id_offset = idp - new_hdr_line.s;
id_len = id_end - idp;
if (id_len < transformed_id.l) {
if (ks_resize(&new_hdr_line, new_hdr_line.l
+ transformed_id.l - id_len + 1/*nul*/))
goto fail;
}
if (id_len != transformed_id.l) {
memmove(new_hdr_line.s + id_offset + transformed_id.l,
new_hdr_line.s + id_offset + id_len,
new_hdr_line.l - id_offset - id_len + 1);
}
memcpy(new_hdr_line.s + id_offset, transformed_id.s,
transformed_id.l);
}
// append line to output linked list
char** ln = kl_pushp(hdrln, hdr_lines);
*ln = ks_release(&new_hdr_line); // Give away to linked list
// Need to add it to known_ids set
int in_there = 0;
iter = kh_put(cset, known_ids, ks_str(&transformed_id), &in_there);
if (in_there < 0) goto memfail;
assert(in_there > 0); // Should not already be in the map
map_value = ks_release(&transformed_id);
} else {
// Use existing string in id_map
assert(kh_exist(known_ids, iter));
map_value = kh_key(known_ids, iter);
free(ks_release(&transformed_id));
}
// Insert it into our translation map
int in_there = 0;
iter = kh_put(c2c, id_map, ks_release(&orig_id), &in_there);
kh_value(id_map, iter) = map_value;
}
// If there are no RG lines in the file and we are overriding add one
if (is_rg && override && kl_begin(hdr_lines) == NULL) {
kstring_t new_id = {0, 0, NULL};
kstring_t line = {0, 0, NULL};
kstring_t empty = {0, 0, NULL};
int in_there = 0;
char** ln;
// Get the new ID
if (gen_unique_id(override, known_ids, false, &new_id))
goto memfail;
// Make into a header line and add to linked list
ksprintf(&line, "@RG\tID:%s", ks_str(&new_id));
ln = kl_pushp(hdrln, hdr_lines);
*ln = ks_release(&line);
// Put into known_ids set
iter = kh_put(cset, known_ids, ks_str(&new_id), &in_there);
if (in_there < 0) goto memfail;
assert(in_there > 0); // Should be a new entry
// Put into translation map (key is empty string)
if (kputs("", &empty) == EOF) goto memfail;
iter = kh_put(c2c, id_map, ks_release(&empty), &in_there);
if (in_there < 0) goto memfail;
assert(in_there > 0); // Should be a new entry
kh_value(id_map, iter) = ks_release(&new_id);
}
return hdr_lines;
memfail:
perror(__func__);
fail:
if (hdr_lines) kl_destroy(hdrln, hdr_lines);
return NULL;
}
/*
* Common code for completing RG and PG record translation.
*
* Input is a list of header lines, and the mapping from input to
* output @PG record IDs.
*
* RG and PG records can contain tags that cross-reference to other @PG
* records. This fixes the tags to contain the new IDs before adding
* them to the output header text.
*/
static int finish_rg_pg(bool is_rg, klist_t(hdrln) *hdr_lines,
khash_t(c2c)* pg_map, kstring_t *out_text) {
const char *search = is_rg ? "\tPG:" : "\tPP:";
khiter_t idx;
char *line = NULL;
while ((kl_shift(hdrln, hdr_lines, &line)) == 0) {
char *id = strstr(line, search); // Look for tag to fix
int pos1 = 0, pos2 = 0;
char *new_id = NULL;
if (id) {
// Found a tag. Look up the value in the translation map
// to see what it should be changed to in the output file.
char *end, tmp;
id += 4; // Point to value
end = strchr(id, '\t'); // Find end of tag
if (!end) end = id + strlen(id);
tmp = *end;
*end = '\0'; // Temporarily get the value on its own.
// Look-up in translation table
idx = kh_get(c2c, pg_map, id);
if (idx == kh_end(pg_map)) {
// Not found, warn.
fprintf(stderr, "[W::%s] Tag %s%s not found in @PG records\n",
__func__, search + 1, id);
} else {
// Remember new id and splice points on original string
new_id = kh_value(pg_map, idx);
pos1 = id - line;
pos2 = end - line;
}
*end = tmp; // Restore string
}
// Copy line to output:
// line[0..pos1), new_id (if not NULL), line[pos2..end), '\n'
if (pos1 && range_to_ks(line, 0, pos1, out_text)) goto memfail;
if (new_id && kputs(new_id, out_text) == EOF) goto memfail;
if (kputs(line + pos2, out_text) == EOF) goto memfail;
if (kputc('\n', out_text) == EOF) goto memfail;
free(line); // No longer needed
line = NULL;
}
return 0;
memfail:
perror(__func__);
free(line); // Prevent leakage as no longer on list
return -1;
}
/*
* Build the translation table for an input *am file. This stores mappings
* which allow IDs to be converted from those used in the input file
* to the ones which will be used in the output. The mappings are for:
* Reference sequence IDs (for @SQ records)
* @RG record ID tags
* @PG record ID tags
*
* At the same time, new header text is built up by copying records
* from the input bam file. This will eventually become the header for
* the output file. When copied, the ID tags for @RG and @PG records
* are replaced with their values. The @PG PP: and @RG PG: tags
* are also modified if necessary.
*
* merged_hdr holds state on the output header (which IDs are present, etc.)
* translate is the input header
* tbl is the translation table that gets filled in.
* merge_rg controls merging of @RG records
* merge_pg controls merging of @PG records
* If rg_override is not NULL, it will be used to replace the existing @RG ID
*
* Returns 0 on success, -1 on failure.
*/
static int trans_tbl_init(merged_header_t* merged_hdr, sam_hdr_t* translate,
trans_tbl_t* tbl, bool merge_rg, bool merge_pg,
bool copy_co, char* rg_override)
{
kstring_t lines = { 0, 0, NULL };
klist_t(hdrln) *rg_list = NULL;
klist_t(hdrln) *pg_list = NULL;
tbl->n_targets = sam_hdr_nref(translate);
tbl->rg_trans = tbl->pg_trans = NULL;
tbl->tid_trans = (int*)calloc(tbl->n_targets ? tbl->n_targets : 1,
sizeof(int));
if (tbl->tid_trans == NULL) goto memfail;
tbl->rg_trans = kh_init(c2c);
if (tbl->rg_trans == NULL) goto memfail;
tbl->pg_trans = kh_init(c2c);
if (tbl->pg_trans == NULL) goto memfail;
tbl->lost_coord_sort = false;
// Get the @HD record (if not there already).
if (trans_tbl_add_hd(merged_hdr, translate)) goto fail;
// Fill in map and add header lines for @SQ records
if (trans_tbl_add_sq(merged_hdr, translate, tbl)) goto fail;
// Get translated header lines and fill in map for @RG records
rg_list = trans_rg_pg(true, translate, merge_rg, merged_hdr->rg_ids,
tbl->rg_trans, rg_override);
if (!rg_list) goto fail;
// Get translated header lines and fill in map for @PG records
pg_list = trans_rg_pg(false, translate, merge_pg, merged_hdr->pg_ids,
tbl->pg_trans, NULL);
if (!pg_list) goto fail;
// Fix-up PG: tags in the new @RG records and add to output
if (finish_rg_pg(true, rg_list, tbl->pg_trans, &merged_hdr->out_rg))
goto fail;
// Fix-up PP: tags in the new @PG records and add to output
lines.l = 0;
if (finish_rg_pg(false, pg_list, tbl->pg_trans, &merged_hdr->out_pg))
goto fail;
kl_destroy(hdrln, rg_list); rg_list = NULL;
kl_destroy(hdrln, pg_list); pg_list = NULL;
if (copy_co) {
// Just append @CO headers without translation
int num_co = sam_hdr_count_lines(translate, "CO"), i;
if (num_co < 0)
goto fail;
for (i = 0; i < num_co; i++) {
if (sam_hdr_find_line_pos(translate, "CO", i, &lines) < 0)
goto fail;
if (ks_to_ks(&lines, &merged_hdr->out_co))
goto fail;
if (kputc('\n', &merged_hdr->out_co) < 0)
goto fail;
}
}
free(lines.s);
return 0;
memfail:
perror(__func__);
fail:
trans_tbl_destroy(tbl);
if (rg_list) kl_destroy(hdrln, rg_list);
if (pg_list) kl_destroy(hdrln, pg_list);
free(lines.s);
return -1;
}
static int finish_merged_header(merged_header_t *merged_hdr) {
if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_rg),
ks_len(&merged_hdr->out_rg)) < 0)
return -1;
if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_pg),
ks_len(&merged_hdr->out_pg)) < 0)
return -1;
if (sam_hdr_add_lines(merged_hdr->hdr, ks_c_str(&merged_hdr->out_co),
ks_len(&merged_hdr->out_co)) < 0)
return -1;
return 0;
}
/*
* Free a merged_header_t struct and all associated data.
*
* Note that the keys to the rg_ids and pg_ids sets are also used as
* values in the translation tables. This function should therefore not
* be called until the translation tables are no longer needed.
*/
static void free_merged_header(merged_header_t *merged_hdr) {
size_t i;
khiter_t iter;
if (!merged_hdr) return;
free(ks_release(&merged_hdr->out_rg));
free(ks_release(&merged_hdr->out_pg));
free(ks_release(&merged_hdr->out_co));
if (merged_hdr->target_name) {
for (i = 0; i < merged_hdr->n_targets; i++) {
free(merged_hdr->target_name[i]);
}
free(merged_hdr->target_name);
}
free(merged_hdr->target_len);
kh_destroy(c2i, merged_hdr->sq_tids);
if (merged_hdr->rg_ids) {
for (iter = kh_begin(merged_hdr->rg_ids);
iter != kh_end(merged_hdr->rg_ids); ++iter) {
if (kh_exist(merged_hdr->rg_ids, iter))
free(kh_key(merged_hdr->rg_ids, iter));
}
kh_destroy(cset, merged_hdr->rg_ids);
}
if (merged_hdr->pg_ids) {
for (iter = kh_begin(merged_hdr->pg_ids);
iter != kh_end(merged_hdr->pg_ids); ++iter) {
if (kh_exist(merged_hdr->pg_ids, iter))
free(kh_key(merged_hdr->pg_ids, iter));
}
kh_destroy(cset, merged_hdr->pg_ids);
}
free(merged_hdr);
}
static void bam_translate(bam1_t* b, trans_tbl_t* tbl)
{
// Update target id if not unmapped tid
if ( b->core.tid >= 0 ) { b->core.tid = tbl->tid_trans[b->core.tid]; }
if ( b->core.mtid >= 0 ) { b->core.mtid = tbl->tid_trans[b->core.mtid]; }
// If we have a RG update it
uint8_t *rg = bam_aux_get(b, "RG");
if (rg) {
char* decoded_rg = bam_aux2Z(rg);
khiter_t k = kh_get(c2c, tbl->rg_trans, decoded_rg);
if (k != kh_end(tbl->rg_trans)) {
char* translate_rg = kh_value(tbl->rg_trans,k);
bam_aux_del(b, rg);
if (translate_rg) {
bam_aux_append(b, "RG", 'Z', strlen(translate_rg) + 1,
(uint8_t*)translate_rg);
}
} else {
char *tmp = strdup(decoded_rg);
fprintf(stderr,
"[bam_translate] RG tag \"%s\" on read \"%s\" encountered "
"with no corresponding entry in header, tag lost. "
"Unknown tags are only reported once per input file for "
"each tag ID.\n",
decoded_rg, bam_get_qname(b));
bam_aux_del(b, rg);
// Prevent future whinges
if (tmp) {
int in_there = 0;
k = kh_put(c2c, tbl->rg_trans, tmp, &in_there);
if (in_there > 0) kh_value(tbl->rg_trans, k) = NULL;
}
}
}
// If we have a PG update it
uint8_t *pg = bam_aux_get(b, "PG");
if (pg) {
char* decoded_pg = bam_aux2Z(pg);
khiter_t k = kh_get(c2c, tbl->pg_trans, decoded_pg);
if (k != kh_end(tbl->pg_trans)) {
char* translate_pg = kh_value(tbl->pg_trans,k);
bam_aux_del(b, pg);
if (translate_pg) {
bam_aux_append(b, "PG", 'Z', strlen(translate_pg) + 1,
(uint8_t*)translate_pg);
}
} else {
char *tmp = strdup(decoded_pg);
fprintf(stderr,
"[bam_translate] PG tag \"%s\" on read \"%s\" encountered "
"with no corresponding entry in header, tag lost. "
"Unknown tags are only reported once per input file for "
"each tag ID.\n",
decoded_pg, bam_get_qname(b));
bam_aux_del(b, pg);
// Prevent future whinges
if (tmp) {
int in_there = 0;
k = kh_put(c2c, tbl->pg_trans, tmp, &in_there);
if (in_there > 0) kh_value(tbl->pg_trans, k) = NULL;
}
}
}
}
int* rtrans_build(int n, int n_targets, trans_tbl_t* translation_tbl)
{
// Create reverse translation table for tids
int* rtrans = (int*)malloc(sizeof(int32_t)*n*n_targets);
const int32_t NOTID = INT32_MIN;
if (!rtrans) return NULL;
memset_pattern4((void*)rtrans, &NOTID, sizeof(int32_t)*n*n_targets);
int i;
for (i = 0; i < n; ++i) {
int j;
for (j = 0; j < (translation_tbl+i)->n_targets; ++j) {
if ((translation_tbl+i)->tid_trans[j] != -1) {
rtrans[i*n_targets + (translation_tbl+i)->tid_trans[j]] = j;
}
}
}
return rtrans;
}
#define MERGE_RG 1 // Attach RG tag based on filename
#define MERGE_UNCOMP 2 // Generate uncompressed BAM
#define MERGE_LEVEL1 4 // Compress the BAM at level 1 (fast) mode
#define MERGE_FORCE 8 // Overwrite output BAM if it exists
#define MERGE_COMBINE_RG 16 // Combine RG tags frather than redefining them
#define MERGE_COMBINE_PG 32 // Combine PG tags frather than redefining them
#define MERGE_FIRST_CO 64 // Use only first file's @CO headers (sort cmd only)
static hts_reglist_t *duplicate_reglist(const hts_reglist_t *rl, int rn) {
if (!rl)
return NULL;
hts_reglist_t *new_rl = calloc(rn, sizeof(hts_reglist_t));
if (!new_rl)
return NULL;
int i;
for (i=0; i < rn; i++) {
new_rl[i].tid = rl[i].tid;
new_rl[i].count = rl[i].count;
new_rl[i].min_beg = rl[i].min_beg;
new_rl[i].max_end = rl[i].max_end;
new_rl[i].reg = rl[i].reg;
new_rl[i].intervals = malloc(new_rl[i].count * sizeof(hts_pair_pos_t));
if (!new_rl[i].intervals) {
hts_reglist_free(new_rl, i);
return NULL;
}
memcpy(new_rl[i].intervals, rl[i].intervals, new_rl[i].count * sizeof(hts_pair_pos_t));
}
return new_rl;
}
/*
* How merging is handled
*
* If a header is defined use we will use that as our output header
* otherwise we use the first header from the first input file.
*
* Now go through each file and create a translation table for that file for:
* -RG
* -tid
* -PG tags
*
* Then whenever we read a record from a bam we translate that read before
* stashing it in the hash.
*
* In the actual merge, a read is read from each input file, translated and
* stashed in the hash. This assumes that all input files are sorted in the
* same way. Next we just extract the next position ordered read from the
* hash, and replace it if there are still reads left in it's source input
* file. Finally we write our chosen read it to the output file.
*/
/*!
@abstract Merge multiple sorted BAM.
@param by_qname whether to sort by query name
@param sort_tag if non-null, sort by the given tag
@param out output BAM file name
@param mode sam_open() mode to be used to create the final output file
(overrides level settings from UNCOMP and LEVEL1 flags)
@param headers name of SAM file from which to copy '@' header lines,
or NULL to copy them from the first file to be merged
@param n number of files to be merged
@param fn names of files to be merged
@param flag flags that control how the merge is undertaken
@param reg region to merge
@param n_threads number of threads to use (passed to htslib)
@param cmd command name (used in print_error() etc)
@param in_fmt format options for input files
@param out_fmt output file format and options
@param write_index create the index, together with the output file
@param arg_list command string for PG line
@param no_pg if 1, do not add a new PG line
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
int bam_merge_core2(int by_qname, char* sort_tag, const char *out, const char *mode,
const char *headers, int n, char * const *fn, char * const *fn_idx,