X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=index.c;h=15cd65e01b379e5ed3daf2ea9aa427996faa6176;hp=8eddcecb34bab21f8d4f6de7a88639f8c67d0358;hb=HEAD;hpb=f14cecb6523bd4275c2858c2d54167c94db25ede

diff --git a/index.c b/index.c
index 8eddcec..15cd65e 100644
--- a/index.c
+++ b/index.c
@@ -83,38 +83,7 @@ int ti_readline(BGZF *fp, kstring_t *str)
  * commented out above. */
 int ti_readline(BGZF *fp, kstring_t *str)
 {
-	int l, state = 0;
-	unsigned char *buf = (unsigned char*)fp->uncompressed_block;
-	str->l = 0;
-	do {
-		if (fp->block_offset >= fp->block_length) {
-			if (bgzf_read_block(fp) != 0) { state = -2; break; }
-			if (fp->block_length == 0) { state = -1; break; }
-		}
-		for (l = fp->block_offset; l < fp->block_length && buf[l] != '\n'; ++l);
-		if (l < fp->block_length) state = 1;
-		l -= fp->block_offset;
-		if (str->l + l + 1 >= str->m) {
-			str->m = str->l + l + 2;
-			kroundup32(str->m);
-			str->s = (char*)realloc(str->s, str->m);
-		}
-		memcpy(str->s + str->l, buf + fp->block_offset, l);
-		str->l += l;
-		fp->block_offset += l + 1;
-		if (fp->block_offset >= fp->block_length) {
-#ifdef _USE_KNETFILE
-			fp->block_address = knet_tell(fp->x.fpr);
-#else
-			fp->block_address = ftello(fp->file);
-#endif
-			fp->block_offset = 0;
-			fp->block_length = 0;
-		} 
-	} while (state == 0);
-	if (str->l == 0 && state < 0) return state;
-	str->s[str->l] = 0;
-	return str->l;
+	return bgzf_getline(fp, '\n', str);
 }
 
 /*************************************
@@ -156,32 +125,31 @@ static int get_tid(ti_index_t *idx, const char *ss)
 	return tid;
 }
 
-static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
+int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv)
 {
-	int i, b = 0, id = 1;
+	int i, b = 0, id = 1, ncols = 0;
 	char *s;
-	intv->tid = intv->beg = intv->end = intv->bin = -1;
-	for (i = 0; i <= str->l; ++i) {
-		if (str->s[i] == '\t' || str->s[i] == 0) {
-			if (id == idx->conf.sc) {
-				str->s[i] = 0;
-				intv->tid = get_tid(idx, str->s + b);
-				if (i != str->l) str->s[i] = '\t';
-			} else if (id == idx->conf.bc) {
+	intv->ss = intv->se = 0; intv->beg = intv->end = -1;
+	for (i = 0; i <= len; ++i) {
+		if (line[i] == '\t' || line[i] == 0) {
+            ++ncols;
+			if (id == conf->sc) {
+				intv->ss = line + b; intv->se = line + i;
+			} else if (id == conf->bc) {
 				// here ->beg is 0-based.
-				intv->beg = intv->end = strtol(str->s + b, &s, 0);
-				if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
+				intv->beg = intv->end = strtol(line + b, &s, 0);
+				if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg;
 				else ++intv->end;
 				if (intv->beg < 0) intv->beg = 0;
 				if (intv->end < 1) intv->end = 1;
 			} else {
-				if ((idx->conf.preset&0xffff) == TI_PRESET_GENERIC) {
-					if (id == idx->conf.ec) intv->end = strtol(str->s + b, &s, 0);
-				} else if ((idx->conf.preset&0xffff) == TI_PRESET_SAM) {
+				if ((conf->preset&0xffff) == TI_PRESET_GENERIC) {
+					if (id == conf->ec) intv->end = strtol(line + b, &s, 0);
+				} else if ((conf->preset&0xffff) == TI_PRESET_SAM) {
 					if (id == 6) { // CIGAR
 						int l = 0, op;
 						char *t;
-						for (s = str->s + b; s < str->s + i;) {
+						for (s = line + b; s < line + i;) {
 							long x = strtol(s, &t, 10);
 							op = toupper(*t);
 							if (op == 'M' || op == 'D' || op == 'N') l += x;
@@ -190,21 +158,21 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 						if (l == 0) l = 1;
 						intv->end = intv->beg + l;
 					}
-				} else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
+				} else if ((conf->preset&0xffff) == TI_PRESET_VCF) {
 					// FIXME: the following is NOT tested and is likely to be buggy
 					if (id == 4) {
 						if (b < i) intv->end = intv->beg + (i - b);
 					} else if (id == 8) { // look for "END="
-						int c = str->s[i];
-						str->s[i] = 0;
-						s = strstr(str->s + b, "END=");
-						if (s == str->s + b) s += 4;
+						int c = line[i];
+						line[i] = 0;
+						s = strstr(line + b, "END=");
+						if (s == line + b) s += 4;
 						else if (s) {
-							s = strstr(str->s + b, ";END=");
+							s = strstr(line + b, ";END=");
 							if (s) s += 5;
 						}
 						if (s) intv->end = strtol(s, &s, 0);
-						str->s[i] = c;
+						line[i] = c;
 					}
 				}
 			}
@@ -212,11 +180,33 @@ static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
 			++id;
 		}
 	}
-	if (intv->tid < 0 || intv->beg < 0 || intv->end < 0) return -1;
-	intv->bin = ti_reg2bin(intv->beg, intv->end);
+/*
+	if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) {
+		if (ncols == 1) fprintf(stderr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line);
+		else fprintf(stderr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line);
+		exit(1);
+	}
+*/
+	if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1;
 	return 0;
 }
 
+static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
+{
+	ti_interval_t x;
+	intv->tid = intv->beg = intv->end = intv->bin = -1;
+	if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) {
+		int c = *x.se;
+		*x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c;
+		intv->beg = x.beg; intv->end = x.end;
+		intv->bin = ti_reg2bin(intv->beg, intv->end);
+		return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1;
+	} else {
+		fprintf(stderr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s);
+		return -1;
+	}
+}
+
 /************
  * indexing *
  ************/
@@ -240,7 +230,7 @@ static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t
 	l->list[l->n].u = beg; l->list[l->n++].v = end;
 }
 
-static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
+static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
 {
 	int i, beg, end;
 	beg = _beg >> TAD_LIDX_SHIFT;
@@ -259,6 +249,7 @@ static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_
 			if (index2->offset[i] == 0) index2->offset[i] = offset;
 	}
 	if (index2->n < end + 1) index2->n = end + 1;
+	return (uint64_t)beg<<32 | end;
 }
 
 static void merge_chunks(ti_index_t *idx)
@@ -299,7 +290,7 @@ ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
 	ti_index_t *idx;
 	uint32_t last_bin, save_bin;
 	int32_t last_coor, last_tid, save_tid;
-	uint64_t save_off, last_off, lineno = 0;
+	uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp;
 	kstring_t *str;
 
 	str = calloc(1, sizeof(kstring_t));
@@ -321,14 +312,25 @@ ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
 			continue;
 		}
 		get_intv(idx, str, &intv);
+        if ( intv.beg<0 || intv.end<0 )
+        {
+            fprintf(stderr,"[ti_index_core] the indexes overlap or are out of bounds\n");
+            exit(1);
+        }
 		if (last_tid != intv.tid) { // change of chromosomes
+            if (last_tid>intv.tid )
+            {
+                fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1);
+                exit(1);
+            }
 			last_tid = intv.tid;
 			last_bin = 0xffffffffu;
 		} else if (last_coor > intv.beg) {
 			fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
 			exit(1);
 		}
-		insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+		tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+		if (last_off == 0) offset0 = tmp;
 		if (intv.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);
@@ -348,6 +350,10 @@ ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
 	if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
 	merge_chunks(idx);
 	fill_missing(idx);
+	if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) {
+		int i, beg = offset0>>32, end = offset0&0xffffffffu;
+		for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0;
+	}
 
 	free(str->s); free(str);
 	return idx;
@@ -645,8 +651,8 @@ ti_index_t *ti_index_load(const char *fn)
     char *fname = get_local_version(fn);
 	if (fname == 0) return 0;
 	idx = ti_index_load_local(fname);
+	if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load the index: %s\n", fname);
     free(fname);
-	if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load BAM index.\n");
 	return idx;
 }
 
@@ -656,7 +662,7 @@ int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
 	BGZF *fp, *fpidx;
 	ti_index_t *idx;
 	if ((fp = bgzf_open(fn, "r")) == 0) {
-		fprintf(stderr, "[ti_index_build2] fail to open the BAM file.\n");
+		fprintf(stderr, "[ti_index_build2] fail to open the file: %s\n", fn);
 		return -1;
 	}
 	idx = ti_index_core(fp, conf);
@@ -803,6 +809,9 @@ ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
 				if (p->list[j].v > min_off) off[n_off++] = p->list[j];
 		}
 	}
+	if (n_off == 0) {
+		free(bins); free(off); return iter;
+	}
 	free(bins);
 	{
 		int l;
@@ -888,6 +897,8 @@ int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *d
 	return 0;
 }
 
+const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; }
+
 /*******************
  * High-level APIs *
  *******************/