X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_index.c;h=9610a2656031657b796abc68bf32c1b6f1564745;hp=a6278843583c605799360affb0b9c3c21fbd02c4;hb=d59366b97f0e6a0cbb0dfcdc5679f0ed88c8fe1e;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351

diff --git a/bam_index.c b/bam_index.c
index a627884..9610a26 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -42,6 +42,8 @@
 // 1<<14 is the size of minimum bin.
 #define BAM_LIDX_SHIFT    14
 
+#define BAM_MAX_BIN 37450 // =(8^6-1)/7+1
+
 typedef struct {
 	uint64_t u, v;
 } pair64_t;
@@ -63,6 +65,7 @@ KHASH_MAP_INIT_INT(i, bam_binlist_t)
 
 struct __bam_index_t {
 	int32_t n;
+	uint64_t n_no_coor; // unmapped reads without coordinate
 	khash_t(i) **index;
 	bam_lidx_t *index2;
 };
@@ -98,8 +101,12 @@ static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset
 		index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
 		memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
 	}
-	for (i = beg + 1; i <= end; ++i)
-		if (index2->offset[i] == 0) index2->offset[i] = offset;
+	if (beg == end) {
+		if (index2->offset[beg] == 0) index2->offset[beg] = offset;
+	} else {
+		for (i = beg; i <= end; ++i)
+			if (index2->offset[i] == 0) index2->offset[i] = offset;
+	}
 	index2->n = end + 1;
 }
 
@@ -113,7 +120,7 @@ static void merge_chunks(bam_index_t *idx)
 		index = idx->index[i];
 		for (k = kh_begin(index); k != kh_end(index); ++k) {
 			bam_binlist_t *p;
-			if (!kh_exist(index, k)) continue;
+			if (!kh_exist(index, k) || kh_key(index, k) == BAM_MAX_BIN) continue;
 			p = &kh_value(index, k);
 			m = 0;
 			for (l = 1; l < p->n; ++l) {
@@ -130,6 +137,17 @@ static void merge_chunks(bam_index_t *idx)
 #endif // defined(BAM_TRUE_OFFSET) || defined(BAM_BGZF)
 }
 
+static void fill_missing(bam_index_t *idx)
+{
+	int i, j;
+	for (i = 0; i < idx->n; ++i) {
+		bam_lidx_t *idx2 = &idx->index2[i];
+		for (j = 1; j < idx2->n; ++j)
+			if (idx2->offset[j] == 0)
+				idx2->offset[j] = idx2->offset[j-1];
+	}
+}
+
 bam_index_t *bam_index_core(bamFile fp)
 {
 	bam1_t *b;
@@ -139,7 +157,7 @@ bam_index_t *bam_index_core(bamFile fp)
 	uint32_t last_bin, save_bin;
 	int32_t last_coor, last_tid, save_tid;
 	bam1_core_t *c;
-	uint64_t save_off, last_off;
+	uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
 
 	idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
 	b = (bam1_t*)calloc(1, sizeof(bam1_t));
@@ -154,19 +172,33 @@ bam_index_t *bam_index_core(bamFile fp)
 
 	save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
 	save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
+	n_mapped = n_unmapped = n_no_coor = off_end = 0;
+	off_beg = off_end = bam_tell(fp);
 	while ((ret = bam_read1(fp, b)) >= 0) {
-		if (last_tid != c->tid) { // change of chromosomes
+		if (c->tid < 0) ++n_no_coor;
+		if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
 			last_tid = c->tid;
 			last_bin = 0xffffffffu;
-		} else if (last_coor > c->pos) {
+		} else if ((uint32_t)last_tid > (uint32_t)c->tid) {
+			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
+					bam1_qname(b), last_tid+1, c->tid+1);
+			return NULL;
+		} else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
 			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
 					bam1_qname(b), last_coor, c->pos, c->tid+1);
-			exit(1);
+			return NULL;
 		}
-		if (b->core.tid >= 0 && b->core.bin < 4681) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+		if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
 		if (c->bin != last_bin) { // then possibly write the binning index
 			if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
 				insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
+			if (last_bin == 0xffffffffu && save_tid != 0xffffffffu) { // write the meta element
+				off_end = last_off;
+				insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
+				insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
+				n_mapped = n_unmapped = 0;
+				off_beg = off_end;
+			}
 			save_off = last_off;
 			save_bin = last_bin = c->bin;
 			save_tid = c->tid;
@@ -175,15 +207,32 @@ bam_index_t *bam_index_core(bamFile fp)
 		if (bam_tell(fp) <= last_off) {
 			fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
 					(unsigned long long)bam_tell(fp), (unsigned long long)last_off);
-			exit(1);
+			return NULL;
 		}
+		if (c->flag & BAM_FUNMAP) ++n_unmapped;
+		else ++n_mapped;
 		last_off = bam_tell(fp);
 		last_coor = b->core.pos;
 	}
-	if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
+	if (save_tid >= 0) {
+		insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
+		insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
+		insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
+	}
 	merge_chunks(idx);
+	fill_missing(idx);
+	if (ret >= 0) {
+		while ((ret = bam_read1(fp, b)) >= 0) {
+			++n_no_coor;
+			if (c->tid >= 0 && n_no_coor) {
+				fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+				return NULL;
+			}
+		}
+	}
 	if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
 	free(b->data); free(b);
+	idx->n_no_coor = n_no_coor;
 	return idx;
 }
 
@@ -261,6 +310,11 @@ void bam_index_save(const bam_index_t *idx, FILE *fp)
 				bam_swap_endian_8p(&index2->offset[x]);
 		} else fwrite(index2->offset, 8, index2->n, fp);
 	}
+	{ // write the number of reads coor-less records.
+		uint64_t x = idx->n_no_coor;
+		if (bam_is_be) bam_swap_endian_8p(&x);
+		fwrite(&x, 8, 1, fp);
+	}
 	fflush(fp);
 }
 
@@ -322,6 +376,8 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 		if (bam_is_be)
 			for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
 	}
+	if (fread(&idx->n_no_coor, 8, 1, fp) == 0) idx->n_no_coor = 0;
+	if (bam_is_be) bam_swap_endian_8p(&idx->n_no_coor);
 	return idx;
 }
 
@@ -339,13 +395,13 @@ bam_index_t *bam_index_load_local(const char *_fn)
 	} else fn = strdup(_fn);
 	fnidx = (char*)calloc(strlen(fn) + 5, 1);
 	strcpy(fnidx, fn); strcat(fnidx, ".bai");
-	fp = fopen(fnidx, "r");
+	fp = fopen(fnidx, "rb");
 	if (fp == 0) { // try "{base}.bai"
 		char *s = strstr(fn, "bam");
 		if (s == fn + strlen(fn) - 3) {
 			strcpy(fnidx, fn);
 			fnidx[strlen(fn)-1] = 'i';
-			fp = fopen(fnidx, "r");
+			fp = fopen(fnidx, "rb");
 		}
 	}
 	free(fnidx); free(fn);
@@ -375,7 +431,7 @@ static void download_from_remote(const char *url)
 		fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
 		return;
 	}
-	if ((fp = fopen(fn, "w")) == 0) {
+	if ((fp = fopen(fn, "wb")) == 0) {
 		fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
 		knet_close(fp_remote);
 		return;
@@ -421,11 +477,15 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	}
 	idx = bam_index_core(fp);
 	bam_close(fp);
+	if(idx == 0) {
+		fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
+		return -1;
+	}
 	if (_fnidx == 0) {
 		fnidx = (char*)calloc(strlen(fn) + 5, 1);
 		strcpy(fnidx, fn); strcat(fnidx, ".bai");
 	} else fnidx = strdup(_fnidx);
-	fpidx = fopen(fnidx, "w");
+	fpidx = fopen(fnidx, "wb");
 	if (fpidx == 0) {
 		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
 		free(fnidx);
@@ -446,7 +506,7 @@ int bam_index_build(const char *fn)
 int bam_index(int argc, char *argv[])
 {
 	if (argc < 2) {
-		fprintf(stderr, "Usage: samtools index <in.bam> [<out.index>]\n");
+		fprintf(stderr, "Usage: samtools index <in.bam> [out.index]\n");
 		return 1;
 	}
 	if (argc >= 3) bam_index_build2(argv[1], argv[2]);
@@ -454,11 +514,43 @@ int bam_index(int argc, char *argv[])
 	return 0;
 }
 
-#define MAX_BIN 37450 // =(8^6-1)/7+1
+int bam_idxstats(int argc, char *argv[])
+{
+	bam_index_t *idx;
+	bam_header_t *header;
+	bamFile fp;
+	int i;
+	if (argc < 2) {
+		fprintf(stderr, "Usage: samtools idxstats <in.bam>\n");
+		return 1;
+	}
+	fp = bam_open(argv[1], "r");
+	if (fp == 0) { fprintf(stderr, "[%s] fail to open BAM.\n", __func__); return 1; }
+	header = bam_header_read(fp);
+	bam_close(fp);
+	idx = bam_index_load(argv[1]);
+	if (idx == 0) { fprintf(stderr, "[%s] fail to load the index.\n", __func__); return 1; }
+	for (i = 0; i < idx->n; ++i) {
+		khint_t k;
+		khash_t(i) *h = idx->index[i];
+		printf("%s\t%d", header->target_name[i], header->target_len[i]);
+		k = kh_get(i, h, BAM_MAX_BIN);
+		if (k != kh_end(h))
+			printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v);
+		else printf("\t0\t0");
+		putchar('\n');
+	}
+	printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);
+	bam_header_destroy(header);
+	bam_index_destroy(idx);
+	return 0;
+}
 
-static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
+static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[BAM_MAX_BIN])
 {
 	int i = 0, k;
+	if (beg >= end) return 0;
+	if (end >= 1u<<29) end = 1u<<29;
 	--end;
 	list[i++] = 0;
 	for (k =    1 + (beg>>26); k <=    1 + (end>>26); ++k) list[i++] = k;
@@ -476,8 +568,15 @@ static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
 	return (rend > beg && rbeg < end);
 }
 
+struct __bam_iter_t {
+	int from_first; // read from the first record; no random access
+	int tid, beg, end, n_off, i, finished;
+	uint64_t curr_off;
+	pair64_t *off;
+};
+
 // bam_fetch helper function retrieves 
-pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off)
+bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
 {
 	uint16_t *bins;
 	int i, n_bins, n_off;
@@ -485,17 +584,34 @@ pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int e
 	khint_t k;
 	khash_t(i) *index;
 	uint64_t min_off;
-
-	bins = (uint16_t*)calloc(MAX_BIN, 2);
+	bam_iter_t iter = 0;
+
+	if (beg < 0) beg = 0;
+	if (end < beg) return 0;
+	// initialize iter
+	iter = calloc(1, sizeof(struct __bam_iter_t));
+	iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
+	//
+	bins = (uint16_t*)calloc(BAM_MAX_BIN, 2);
 	n_bins = reg2bins(beg, end, bins);
 	index = idx->index[tid];
-	min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? 0 : idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
+	if (idx->index2[tid].n > 0) {
+		min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
+			: idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
+		if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
+			int n = beg>>BAM_LIDX_SHIFT;
+			if (n > idx->index2[tid].n) n = idx->index2[tid].n;
+			for (i = n - 1; i >= 0; --i)
+				if (idx->index2[tid].offset[i] != 0) break;
+			if (i >= 0) min_off = idx->index2[tid].offset[i];
+		}
+	} else min_off = 0; // tabix 0.1.2 may produce such index files
 	for (i = n_off = 0; i < n_bins; ++i) {
 		if ((k = kh_get(i, index, bins[i])) != kh_end(index))
 			n_off += kh_value(index, k).n;
 	}
 	if (n_off == 0) {
-		free(bins); return 0;
+		free(bins); return iter;
 	}
 	off = (pair64_t*)calloc(n_off, 16);
 	for (i = n_off = 0; i < n_bins; ++i) {
@@ -507,6 +623,9 @@ pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int e
 		}
 	}
 	free(bins);
+	if (n_off == 0) {
+		free(off); return iter;
+	}
 	{
 		bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
 		int l;
@@ -534,41 +653,67 @@ pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int e
 		}
 		bam_destroy1(b);
 	}
-	*cnt_off = n_off;
+	iter->n_off = n_off; iter->off = off;
+	return iter;
+}
+
+pair64_t *get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int *cnt_off)
+{ // for pysam compatibility
+	bam_iter_t iter;
+	pair64_t *off;
+	iter = bam_iter_query(idx, tid, beg, end);
+	off = iter->off; *cnt_off = iter->n_off;
+	free(iter);
 	return off;
 }
 
-int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+void bam_iter_destroy(bam_iter_t iter)
 {
-	int n_off;
-	pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
-	if (off == 0) return 0;
-	{
-		// retrive alignments
-		uint64_t curr_off;
-		int i, ret, n_seeks;
-		n_seeks = 0; i = -1; curr_off = 0;
-		bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
-		for (;;) {
-			if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
-				if (i == n_off - 1) break; // no more chunks
-				if (i >= 0) assert(curr_off == off[i].v); // otherwise bug
-				if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek
-					bam_seek(fp, off[i+1].u, SEEK_SET);
-					curr_off = bam_tell(fp);
-					++n_seeks;
-				}
-				++i;
+	if (iter) { free(iter->off); free(iter); }
+}
+
+int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
+{
+	int ret;
+	if (iter && iter->finished) return -1;
+	if (iter == 0 || iter->from_first) {
+		ret = bam_read1(fp, b);
+		if (ret < 0 && iter) iter->finished = 1;
+		return ret;
+	}
+	if (iter->off == 0) return -1;
+	for (;;) {
+		if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
+			if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks
+			if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
+			if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
+				bam_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
+				iter->curr_off = bam_tell(fp);
 			}
-			if ((ret = bam_read1(fp, b)) > 0) {
-				curr_off = bam_tell(fp);
-				if (b->core.tid != tid || b->core.pos >= end) break; // no need to proceed
-				else if (is_overlap(beg, end, b)) func(b, data);
-			} else break; // end of file
+			++iter->i;
 		}
-//		fprintf(stderr, "[bam_fetch] # seek calls: %d\n", n_seeks);
-		bam_destroy1(b);
+		if ((ret = bam_read1(fp, b)) >= 0) {
+			iter->curr_off = bam_tell(fp);
+			if (b->core.tid != iter->tid || b->core.pos >= iter->end) { // no need to proceed
+				ret = bam_validate1(NULL, b)? -1 : -5; // determine whether end of region or error
+				break;
+			}
+			else if (is_overlap(iter->beg, iter->end, b)) return ret;
+		} else break; // end of file or error
 	}
-	free(off);
-	return 0;
+	iter->finished = 1;
+	return ret;
+}
+
+int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+{
+	int ret;
+	bam_iter_t iter;
+	bam1_t *b;
+	b = bam_init1();
+	iter = bam_iter_query(idx, tid, beg, end);
+	while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+	bam_iter_destroy(iter);
+	bam_destroy1(b);
+	return (ret == -1)? 0 : ret;
 }