* samtools-0.1.4-21 (r368)

 * propagate errors rather than exit or complain assertion failure. Assertion
   should be only used for checking internal bugs, but not for external input
   inconsistency. I was just a bit lazy.
 * small memory leak may be present on failure, though

bam.c

@@ -1,5 +1,6 @@
 #include <stdio.h>
 #include <ctype.h>
+#include <assert.h>
 #include "bam.h"
 #include "bam_endian.h"
 #include "kstring.h"

bam.h

@@ -41,7 +41,6 @@
  */
 
 #include <stdint.h>
-#include <assert.h>
 #include <stdlib.h>
 #include <string.h>
 #include <stdio.h>
@@ -600,8 +599,9 @@ extern "C" {
 	  @param  ref_id  the returned chromosome ID
 	  @param  begin   the returned start coordinate
 	  @param  end     the returned end coordinate
+	  @return         0 on success; -1 on failure
 	 */
-	void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
+	int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
 
 	/*!
 	  @abstract       Retrieve data of a tag

bam_aux.c

@@ -72,7 +72,7 @@ int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
 	return k == kh_end(h)? -1 : kh_value(h, k);
 }
 
-void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
+int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
 {
 	char *s, *p;
 	int i, l, k;
@@ -93,12 +93,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
 	iter = kh_get(s, h, s); /* get the ref_id */
 	if (iter == kh_end(h)) { // name not found
 		*ref_id = -1; free(s);
-		return;
+		return -1;
 	}
 	*ref_id = kh_value(h, iter);
 	if (i == k) { /* dump the whole sequence */
 		*begin = 0; *end = 1<<29; free(s);
-		return;
+		return -1;
 	}
 	for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
 	*begin = atoi(p);
@@ -107,8 +107,12 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
 		*end = atoi(p);
 	} else *end = 1<<29;
 	if (*begin > 0) --*begin;
-	assert(*begin <= *end);
 	free(s);
+	if (*begin > *end) {
+		fprintf(stderr, "[bam_parse_region] invalid region.\n");
+		return -1;
+	}
+	return 0;
 }
 
 int32_t bam_aux2i(const uint8_t *s)

bam_index.c

@@ -1,4 +1,5 @@
 #include <ctype.h>
+#include <assert.h>
 #include "bam.h"
 #include "khash.h"
 #include "ksort.h"
@@ -324,7 +325,6 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 
 bam_index_t *bam_index_load_local(const char *_fn)
 {
-	bam_index_t *idx;
 	FILE *fp;
 	char *fnidx, *fn;
 
@@ -347,9 +347,11 @@ bam_index_t *bam_index_load_local(const char *_fn)
 		}
 	}
 	free(fnidx); free(fn);
-	idx = bam_index_load_core(fp);
-	fclose(fp);
-	return idx;
+	if (fp) {
+		bam_index_t *idx = bam_index_load_core(fp);
+		fclose(fp);
+		return idx;
+	} else return 0;
 }
 
 static void download_from_remote(const char *url)
@@ -394,6 +396,7 @@ bam_index_t *bam_index_load(const char *fn)
 		download_from_remote(fnidx);
 		idx = bam_index_load_local(fn);
 	}
+	if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
 	return idx;
 }
 
@@ -403,7 +406,10 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	FILE *fpidx;
 	bamFile fp;
 	bam_index_t *idx;
-	assert(fp = bam_open(fn, "r"));
+	if ((fp = bam_open(fn, "r")) == 0) {
+		fprintf(stderr, "[bam_index_build2] fail to open the BAM file.\n");
+		return -1;
+	}
 	idx = bam_index_core(fp);
 	bam_close(fp);
 	if (_fnidx == 0) {
@@ -414,7 +420,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	if (fpidx == 0) {
 		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
 		free(fnidx);
-		return 1;
+		return -1;
 	}
 	bam_index_save(idx, fpidx);
 	bam_index_destroy(idx);

bam_lpileup.c

@@ -1,5 +1,6 @@
 #include <stdlib.h>
 #include <stdio.h>
+#include <assert.h>
 #include "bam.h"
 #include "ksort.h"
 

bam_md.c

@@ -1,4 +1,5 @@
 #include <unistd.h>
+#include <assert.h>
 #include <string.h>
 #include <ctype.h>
 #include "faidx.h"

bam_pileup.c

@@ -1,6 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <ctype.h>
+#include <assert.h>
 #include "sam.h"
 
 typedef struct __linkbuf_t {
@@ -61,7 +62,7 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
 	int ret = 1, is_restart = 1;
 
 	if (c->flag&BAM_FUNMAP) return 0; // unmapped read
-	assert(x <= pos);
+	assert(x <= pos); // otherwise a bug
 	p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0;
 	for (k = 0; k < c->n_cigar; ++k) {
 		int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
@@ -97,7 +98,7 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
 			break;
 		}
 	}
-	assert(x > pos);
+	assert(x > pos); // otherwise a bug
 	return ret;
 }
 
@@ -196,7 +197,12 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
 			buf->func(buf->tid, buf->pos, n_pu, buf->pu, buf->func_data);
 		}
 		// update tid and pos
-		if (buf->head->next) assert(buf->tid <= buf->head->b.core.tid); // otherwise, not sorted
+		if (buf->head->next) {
+			if (buf->tid > buf->head->b.core.tid) {
+				fprintf(stderr, "[bam_plbuf_push] unsorted input. Pileup aborts.\n");
+				return 1;
+			}
+		}
 		if (buf->tid < buf->head->b.core.tid) { // come to a new reference sequence
 			buf->tid = buf->head->b.core.tid; buf->pos = buf->head->beg; // jump to the next reference
 		} else if (buf->pos < buf->head->beg) { // here: tid == head->b.core.tid

bam_rmdup.c

@@ -1,7 +1,6 @@
 #include <stdlib.h>
 #include <string.h>
 #include <stdio.h>
-#include <assert.h>
 #include <zlib.h>
 #include "bam.h"
 

bam_stat.c

@@ -1,4 +1,5 @@
 #include <unistd.h>
+#include <assert.h>
 #include "bam.h"
 
 typedef struct {

bam_tview.c

@@ -161,6 +161,7 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
 	tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
 	tv->is_dot = 1;
 	tv->idx = bam_index_load(fn);
+	if (tv->idx == 0) exit(1);
 	tv->fp = bam_open(fn, "r");
 	bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
 	assert(tv->fp);

bamtk.c

@@ -1,9 +1,10 @@
 #include <stdio.h>
 #include <unistd.h>
+#include <assert.h>
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.4-20 (r365)"
+#define PACKAGE_VERSION "0.1.4-21 (r368)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

faidx.c

@@ -1,5 +1,4 @@
 #include <ctype.h>
-#include <assert.h>
 #include <string.h>
 #include <stdlib.h>
 #include <stdio.h>
@@ -85,14 +84,19 @@ faidx_t *fai_build_core(RAZF *rz)
 				name[l_name++] = c;
 			}
 			name[l_name] = '\0';
-			assert(ret);
+			if (ret == 0) {
+				fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
+				free(name); fai_destroy(idx);
+				return 0;
+			}
 			if (c != '\n') while (razf_read(rz, &c, 1) && c != '\n');
 			state = 1; len = 0;
 			offset = razf_tell(rz);
 		} else {
 			if (state == 3) {
-				fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'. Abort!\n", name);
-				exit(1);
+				fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
 			}
 			if (state == 2) state = 3;
 			l1 = l2 = 0;
@@ -101,13 +105,15 @@ faidx_t *fai_build_core(RAZF *rz)
 				if (isgraph(c)) ++l2;
 			} while ((ret = razf_read(rz, &c, 1)) && c != '\n');
 			if (state == 3 && l2) {
-				fprintf(stderr, "[fai_build_core] different line length in sequence '%s'. Abort!\n", name);
-				exit(1);
+				fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
 			}
 			++l1; len += l2;
 			if (l2 >= 0x10000) {
-				fprintf(stderr, "[fai_build_core] line length exceeds 65535 in sequence '%s'. Abort!\n", name);
-				exit(1);
+				fprintf(stderr, "[fai_build_core] line length exceeds 65535 in sequence '%s'.\n", name);
+				free(name); fai_destroy(idx);
+				return 0;
 			}
 			if (state == 1) line_len = l1, line_blen = l2, state = 0;
 			else if (state == 0) {
@@ -161,7 +167,7 @@ void fai_destroy(faidx_t *fai)
 	free(fai);
 }
 
-void fai_build(const char *fn)
+int fai_build(const char *fn)
 {
 	char *str;
 	RAZF *rz;
@@ -170,15 +176,24 @@ void fai_build(const char *fn)
 	str = (char*)calloc(strlen(fn) + 5, 1);
 	sprintf(str, "%s.fai", fn);
 	rz = razf_open(fn, "r");
-	assert(rz);
+	if (rz == 0) {
+		fprintf(stderr, "[fai_build] fail to open the FASTA file.\n");
+		free(str);
+		return -1;
+	}
 	fai = fai_build_core(rz);
 	razf_close(rz);
 	fp = fopen(str, "w");
-	assert(fp);
+	if (fp == 0) {
+		fprintf(stderr, "[fai_build] fail to write FASTA index.\n");
+		fai_destroy(fai); free(str);
+		return -1;
+	}
 	fai_save(fai, fp);
 	fclose(fp);
 	free(str);
 	fai_destroy(fai);
+	return 0;
 }
 
 faidx_t *fai_load(const char *fn)
@@ -194,16 +209,19 @@ faidx_t *fai_load(const char *fn)
 		fai_build(fn);
 		fp = fopen(str, "r");
 		if (fp == 0) {
+			fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
 			free(str);
 			return 0;
 		}
 	}
 	fai = fai_read(fp);
 	fclose(fp);
 	fai->rz = razf_open(fn, "r");
-	if (fai->rz == 0) return 0;
-	assert(fai->rz);
 	free(str);
+	if (fai->rz == 0) {
+		fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
+		return 0;
+	}
 	return fai;
 }
 
@@ -271,7 +289,7 @@ int faidx_main(int argc, char *argv[])
 			char *s;
 			faidx_t *fai;
 			fai = fai_load(argv[1]);
-			assert(fai);
+			if (fai == 0) return 1;
 			for (i = 2; i != argc; ++i) {
 				printf(">%s\n", argv[i]);
 				s = fai_fetch(fai, argv[i], &l);

faidx.h

@@ -46,9 +46,10 @@ extern "C" {
 	/*!
 	  @abstract   Build index for a FASTA or razip compressed FASTA file.
 	  @param  fn  FASTA file name
+	  @return     0 on success; or -1 on failure
 	  @discussion File "fn.fai" will be generated.
 	 */
-	void fai_build(const char *fn);
+	int fai_build(const char *fn);
 
 	/*!
 	  @abstract    Distroy a faidx_t struct.

glf.c

@@ -38,8 +38,9 @@ glf3_header_t *glf3_header_read(glfFile fp)
 	h = glf3_header_init();
 	bgzf_read(fp, magic, 4);
 	if (strncmp(magic, "GLF\3", 4)) {
-		fprintf(stderr, "[glf3_header_read] invalid magic. Abort.\n");
-		exit(1);
+		fprintf(stderr, "[glf3_header_read] invalid magic.\n");
+		glf3_header_destroy(h);
+		return 0;
 	}
 	bgzf_read(fp, &h->l_text, 4);
 	if (glf3_is_BE) h->l_text = bam_swap_endian_4(h->l_text);