* samtools-0.1.4-21 (r368)

[samtools.git] / faidx.c

diff --git a/faidx.c b/faidx.c
index 6b4514ffa2f24946bdfed2228c8044cd8268e692..36366c20db595ee9ffeaac4d87628dc40c3690d2 100644 (file)
--- a/faidx.c
+++ b/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)
@@ -194,6 +209,7 @@ 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;
                }
@@ -201,9 +217,11 @@ faidx_t *fai_load(const char *fn)
        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);