bam_sort.c

#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"

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:")) >= 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;
		}
	}
	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\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;
		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:")) >= 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;
		}
	}
	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, "\n");
		return 1;
	}
	bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);
	return 0;
}