#include <stdlib.h>

#include <ctype.h>

#include <assert.h>

#include <errno.h>

#include <stdio.h>

#include <string.h>

#include <unistd.h>

#include "bam.h"

#include "ksort.h"

#include "globals.h"

static int g_is_by_qname = 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 0xffffffffffffffffull

typedef struct {

int i;

uint64_t pos, idx;

bam1_t *b;

} heap1_t;

#define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))

static inline int heap_lt(const heap1_t a, const heap1_t b)

{

if (g_is_by_qname) {

int t;

if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;

t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));

return (t > 0 || (t == 0 && (a.b->core.flag&0xc0) > (b.b->core.flag&0xc0)));

} else return __pos_cmp(a, b);

}

KSORT_INIT(heap, heap1_t, heap_lt)

static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)

{

bam_header_t t;

t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;

t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;

t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;

}

static void swap_header_text(bam_header_t *h1, bam_header_t *h2)

{

int tempi;

char *temps;

tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;

temps = h1->text, h1->text = h2->text, h2->text = temps;

}

#define MERGE_RG 1

#define MERGE_UNCOMP 2

#define MERGE_LEVEL1 4

#define MERGE_FORCE 8

/*!

@abstract Merge multiple sorted BAM.

@param is_by_qname whether to sort by query name

@param out output BAM file name

@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

@discussion Padding information may NOT correctly maintained. This

function is NOT thread safe.

*/

int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads, int level)

{

bamFile fpout, *fp;

heap1_t *heap;

bam_header_t *hout = 0;

bam_header_t *hheaders = NULL;

int i, j, *RG_len = 0;

uint64_t idx = 0;

char **RG = 0, mode[8];

bam_iter_t *iter = 0;

if (headers) {

tamFile fpheaders = sam_open(headers);

if (fpheaders == 0) {

const char *message = strerror(errno);

fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);

return -1;

}

hheaders = sam_header_read(fpheaders);

sam_close(fpheaders);

}

g_is_by_qname = by_qname;

fp = (bamFile*)calloc(n, sizeof(bamFile));

heap = (heap1_t*)calloc(n, sizeof(heap1_t));

iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));

// prepare RG tag

if (flag & MERGE_RG) {

RG = (char**)calloc(n, sizeof(void*));

RG_len = (int*)calloc(n, sizeof(int));

for (i = 0; i != n; ++i) {

int l = strlen(fn[i]);

const char *s = fn[i];

if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;

for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;

++j; l -= j;

RG[i] = calloc(l + 1, 1);

RG_len[i] = l;

strncpy(RG[i], s + j, l);

}

}

// read the first

for (i = 0; i != n; ++i) {

bam_header_t *hin;

fp[i] = bam_open(fn[i], "r");

if (fp[i] == 0) {

int j;

fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);

for (j = 0; j < i; ++j) bam_close(fp[j]);

free(fp); free(heap);

// FIXME: possible memory leak

return -1;

}

hin = bam_header_read(fp[i]);

if (i == 0) { // the first BAM

hout = hin;

} else { // validate multiple baf

int min_n_targets = hout->n_targets;

if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;

for (j = 0; j < min_n_targets; ++j)

if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {

fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",

hout->target_name[j], hin->target_name[j], fn[i]);

return -1;

}

// If this input file has additional target reference sequences,

// add them to the headers to be output

if (hin->n_targets > hout->n_targets) {

swap_header_targets(hout, hin);

// FIXME Possibly we should also create @SQ text headers

// for the newly added reference sequences

}

bam_header_destroy(hin);

}

}

if (hheaders) {

// If the text headers to be swapped in include any @SQ headers,

// check that they are consistent with the existing binary list

// of reference information.

if (hheaders->n_targets > 0) {

if (hout->n_targets != hheaders->n_targets) {

fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);

if (!reg) return -1;

}

for (j = 0; j < hout->n_targets; ++j)

if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {

fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers);

if (!reg) return -1;

}

}

swap_header_text(hout, hheaders);

bam_header_destroy(hheaders);

}

if (reg) {

int tid, beg, end;

if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {

fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);

return -1;

}

for (i = 0; i < n; ++i) {

bam_index_t *idx;

idx = bam_index_load(fn[i]);

iter[i] = bam_iter_query(idx, tid, beg, end);

bam_index_destroy(idx);

}

}

for (i = 0; i < n; ++i) {

heap1_t *h = heap + i;

h->i = i;

h->b = (bam1_t*)calloc(1, sizeof(bam1_t));

if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {

h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);

h->idx = idx++;

}

else h->pos = HEAP_EMPTY;

}

if (flag & MERGE_UNCOMP) level = 0;

else if (flag & MERGE_LEVEL1) level = 1;

strcpy(mode, "w");

if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);

if ((fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w")) == 0) {

fprintf(stderr, "[%s] fail to create the output file.\n", __func__);

return -1;

}

bam_header_write(fpout, hout);

bam_header_destroy(hout);

if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256);

ks_heapmake(heap, n, heap);

while (heap->pos != HEAP_EMPTY) {

bam1_t *b = heap->b;

if (flag & MERGE_RG) {

uint8_t *rg = bam_aux_get(b, "RG");

if (rg) bam_aux_del(b, rg);

bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);

}

bam_write1_core(fpout, &b->core, b->data_len, b->data);

if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {

heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);

heap->idx = idx++;

} else if (j == -1) {

heap->pos = HEAP_EMPTY;

free(heap->b->data); free(heap->b);

heap->b = 0;

} else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);

ks_heapadjust(heap, 0, n, heap);

}

if (flag & MERGE_RG) {

for (i = 0; i != n; ++i) free(RG[i]);

free(RG); free(RG_len);

}

for (i = 0; i != n; ++i) {

bam_iter_destroy(iter[i]);

bam_close(fp[i]);

}

bam_close(fpout);

free(fp); free(heap); free(iter);

return 0;

}

int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)

{

return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0, -1);

}

int bam_merge(int argc, char *argv[])

{

int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0, level = -1;

char *fn_headers = NULL, *reg = 0;

while ((c = getopt(argc, argv, "h:nru1R:f@:l:z:")) >= 0) {

switch (c) {

case 'r': flag |= MERGE_RG; break;

case 'f': flag |= MERGE_FORCE; break;

case 'h': fn_headers = strdup(optarg); break;

case 'n': is_by_qname = 1; break;

case '1': flag |= MERGE_LEVEL1; break;

case 'u': flag |= MERGE_UNCOMP; break;

case 'R': reg = strdup(optarg); break;

case 'l': level = atoi(optarg); break;

case '@': n_threads = atoi(optarg); break;

case 'z': g_block_size = atoi(optarg); break;

}

}

if (optind + 2 >= argc) {

fprintf(stderr, "\n");

fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");

fprintf(stderr, "Options: -n sort by read names\n");

fprintf(stderr, " -r attach RG tag (inferred from file names)\n");

fprintf(stderr, " -u uncompressed BAM output\n");

fprintf(stderr, " -f overwrite the output BAM if exist\n");

fprintf(stderr, " -1 compress level 1\n");

fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n");

fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");

fprintf(stderr, " -R STR merge file in the specified region STR [all]\n");

fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n");

fprintf(stderr, " -z INT specify I/O buffer size in kB\n\n");

fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");

fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");

fprintf(stderr, " the header dictionary in merging.\n\n");

return 1;

}

if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {

FILE *fp = fopen(argv[optind], "rb");

if (fp != NULL) {

fclose(fp);

fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);

return 1;

}

}

if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads, level) < 0) ret = 1;

free(reg);

free(fn_headers);

return ret;

}

/***************

* BAM sorting *

***************/

#include <pthread.h>

typedef bam1_t *bam1_p;

static int change_SO(bam_header_t *h, const char *so)

{

char *p, *q, *beg = 0, *end = 0, *newtext;

if (h->l_text > 3) {

if (strncmp(h->text, "@HD", 3) == 0) {

if ((p = strchr(h->text, '\n')) == 0) return -1;

*p = '\0';

if ((q = strstr(h->text, "\tSO:")) != 0) {

*p = '\n'; // change back

if (strncmp(q + 4, so, p - q - 4) != 0) {

beg = q;

for (q += 4; *q != '\n' && *q != '\t'; ++q);

end = q;

} else return 0; // no need to change

} else beg = end = p, *p = '\n';

}

}

if (beg == 0) { // no @HD

h->l_text += strlen(so) + 15;

newtext = malloc(h->l_text + 1);

sprintf(newtext, "@HD\tVN:1.3\tSO:%s\n", so);

strcat(newtext, h->text);

} else { // has @HD but different or no SO

h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);

newtext = malloc(h->l_text + 1);

strncpy(newtext, h->text, beg - h->text);

sprintf(newtext + (beg - h->text), "\tSO:%s", so);

strcat(newtext, end);

}

free(h->text);

h->text = newtext;

return 0;

}

static inline int bam1_lt(const bam1_p a, const bam1_p b)

{

if (g_is_by_qname) {

int t = strnum_cmp(bam1_qname(a), bam1_qname(b));

return (t < 0 || (t == 0 && (a->core.flag&0xc0) < (b->core.flag&0xc0)));

} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(b)));

}

KSORT_INIT(sort, bam1_p, bam1_lt)

typedef struct {

size_t buf_len;

const char *prefix;

bam1_p *buf;

const bam_header_t *h;

int index;

} worker_t;

static void write_buffer(const char *fn, const char *mode, size_t l, bam1_p *buf, const bam_header_t *h, int n_threads)

{

size_t i;

bamFile fp;

fp = strcmp(fn, "-")? bam_open(fn, mode) : bam_dopen(fileno(stdout), mode);

if (fp == 0) return;

bam_header_write(fp, h);

if (n_threads > 1) bgzf_mt(fp, n_threads, 256);

for (i = 0; i < l; ++i)

bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);

bam_close(fp);

}

static void *worker(void *data)

{

worker_t *w = (worker_t*)data;

char *name;

ks_mergesort(sort, w->buf_len, w->buf, 0);

name = (char*)calloc(strlen(w->prefix) + 20, 1);

sprintf(name, "%s.%.4d.bam", w->prefix, w->index);

write_buffer(name, "w1", w->buf_len, w->buf, w->h, 0);

free(name);

return 0;

}

static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, const bam_header_t *h, int n_threads)

{

int i;

size_t rest;

bam1_p *b;

pthread_t *tid;

pthread_attr_t attr;

worker_t *w;

if (n_threads < 1) n_threads = 1;

if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records

pthread_attr_init(&attr);

pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);

w = calloc(n_threads, sizeof(worker_t));

tid = calloc(n_threads, sizeof(pthread_t));

b = buf; rest = k;

for (i = 0; i < n_threads; ++i) {

w[i].buf_len = rest / (n_threads - i);

w[i].buf = b;

w[i].prefix = prefix;

w[i].h = h;

w[i].index = n_files + i;

b += w[i].buf_len; rest -= w[i].buf_len;

pthread_create(&tid[i], &attr, worker, &w[i]);

}

for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);

free(tid); free(w);

return n_files + n_threads;

}

/*!

@abstract Sort an unsorted BAM file based on the chromosome order

and the leftmost position of an alignment

@param is_by_qname whether to sort by query name

@param fn name of the file to be sorted

@param prefix prefix of the output and the temporary files; upon

sucessess, prefix.bam will be written.

@param max_mem approxiate maximum memory (very inaccurate)

@discussion It may create multiple temporary subalignment files

and then merge them by calling bam_merge_core(). This function is

NOT thread safe.

*/

void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level)

{

int ret, i, n_files = 0;

size_t mem, max_k, k, max_mem;

bam_header_t *header;

bamFile fp;

bam1_t *b, **buf;

char *fnout = 0;

if (n_threads < 2) n_threads = 1;

g_is_by_qname = is_by_qname;

max_k = k = 0; mem = 0;

max_mem = _max_mem * n_threads;

buf = 0;

fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");

if (fp == 0) {

fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);

return;

}

header = bam_header_read(fp);

if (is_by_qname) change_SO(header, "queryname");

else change_SO(header, "coordinate");

// write sub files

for (;;) {

if (k == max_k) {

size_t old_max = max_k;

max_k = max_k? max_k<<1 : 0x10000;

buf = realloc(buf, max_k * sizeof(void*));

memset(buf + old_max, 0, sizeof(void*) * (max_k - old_max));

}

if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));

b = buf[k];

if ((ret = bam_read1(fp, b)) < 0) break;

if (b->data_len < b->m_data>>2) { // shrink

b->m_data = b->data_len;

kroundup32(b->m_data);

b->data = realloc(b->data, b->m_data);

}

mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays

++k;

if (mem >= max_mem) {

n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);

mem = k = 0;

}

}

if (ret != -1)

fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");

// output file name

fnout = calloc(strlen(prefix) + 20, 1);

if (is_stdout) sprintf(fnout, "-");

else sprintf(fnout, "%s.bam", prefix);

// write the final output

if (n_files == 0) { // a single block

char mode[8];

strcpy(mode, "w");

if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);

ks_mergesort(sort, k, buf, 0);

write_buffer(fnout, mode, k, buf, header, n_threads);

} else { // then merge

char **fns;

n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);

fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n_files);

fns = (char**)calloc(n_files, sizeof(char*));

for (i = 0; i < n_files; ++i) {

fns[i] = (char*)calloc(strlen(prefix) + 20, 1);

sprintf(fns[i], "%s.%.4d.bam", prefix, i);

}

bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);

for (i = 0; i < n_files; ++i) {

unlink(fns[i]);

free(fns[i]);

}

free(fns);

}

free(fnout);

// free

for (k = 0; k < max_k; ++k) {

if (!buf[k]) continue;

free(buf[k]->data);

free(buf[k]);

}

free(buf);

bam_header_destroy(header);

bam_close(fp);

}

void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)

{

bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1);

}

int bam_sort(int argc, char *argv[])

{

size_t max_mem = 768<<20; // 512MB

int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1;

while ((c = getopt(argc, argv, "nom:@:l:z:")) >= 0) {

switch (c) {

case 'o': is_stdout = 1; break;

case 'n': is_by_qname = 1; break;

case 'm': {

char *q;

max_mem = strtol(optarg, &q, 0);

if (*q == 'k' || *q == 'K') max_mem <<= 10;

else if (*q == 'm' || *q == 'M') max_mem <<= 20;

else if (*q == 'g' || *q == 'G') max_mem <<= 30;

break;

}

case '@': n_threads = atoi(optarg); break;

case 'l': level = atoi(optarg); break;

case 'z': g_block_size = atoi(optarg); break;

}

}

if (optind + 2 > argc) {

fprintf(stderr, "\n");

fprintf(stderr, "Usage: samtools sort [options] <in.bam> <out.prefix>\n\n");

fprintf(stderr, "Options: -n sort by read name\n");

fprintf(stderr, " -o final output to stdout\n");

fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n");

fprintf(stderr, " -@ INT number of sorting and compression threads [1]\n");

fprintf(stderr, " -m INT max memory per thread; suffix K/M/G recognized [768M]\n");

fprintf(stderr, " -z INT specify I/O buffer size in kB\n\n");

fprintf(stderr, "\n");

return 1;

}

bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);

return 0;

}