Merge pull request #850 from valeriuo/tabix-gz-841

Display an error message about the compression mismatch
samtools · Apr 10, 2019 · 75be032 · 75be032
1 parent 089eb16
commit 75be032
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Showing 3 changed files with 26 additions and 5 deletions.
diff --git a/htslib/tbx.h b/htslib/tbx.h
@@ -67,6 +67,9 @@ extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sa
     int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end);
 
     tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf);
+/*
+ * All tbx_index_build* methods return: 0 (success), -1 (general failure) or -2 (compression not BGZF)
+ */
     int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf);
     int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
     int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf);

diff --git a/tabix.c b/tabix.c
@@ -529,6 +529,7 @@ int main(int argc, char *argv[])
     }
     free(idx_fname);
 
+    int ret;
     if ( ftype==IS_CRAM )
     {
         if ( bam_index_build(fname, min_shift)!=0 ) error("bam_index_build failed: %s\n", fname);
@@ -546,12 +547,29 @@ int main(int argc, char *argv[])
             if ( bam_index_build(fname, min_shift)!=0 ) error("bam_index_build failed: %s\n", fname);
             return 0;
         }
-        if ( tbx_index_build(fname, min_shift, &conf)!=0 ) error("tbx_index_build failed: %s\n", fname);
-        return 0;
+
+        switch (ret = tbx_index_build(fname, min_shift, &conf))
+        {
+            case 0:
+                return 0;
+            case -2:
+                error("[tabix] the compression of '%s' is not BGZF\n", fname);
+            default:
+                error("tbx_index_build failed: %s\n", fname);
+        }
     }
     else    // TBI index
     {
-        if ( tbx_index_build(fname, min_shift, &conf) ) error("tbx_index_build failed: %s\n", fname);
-        return 0;
+        switch (ret = tbx_index_build(fname, min_shift, &conf))
+        {
+            case 0:
+                return 0;
+            case -2:
+                error("[tabix] the compression of '%s' is not BGZF\n", fname);
+            default:
+                error("tbx_index_build failed: %s\n", fname);
+        }
     }
+
+    return 0;
 }
diff --git a/tbx.c b/tbx.c
@@ -277,7 +277,7 @@ int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_thr
     int ret;
     if ((fp = bgzf_open(fn, "r")) == 0) return -1;
     if ( n_threads ) bgzf_mt(fp, n_threads, 256);
-    if ( bgzf_compression(fp) != bgzf ) { bgzf_close(fp); return -1; }
+    if ( bgzf_compression(fp) != bgzf ) { bgzf_close(fp); return -2; }
     tbx = tbx_index(fp, min_shift, conf);
     bgzf_close(fp);
     if ( !tbx ) return -1;