* samtools-0.1.6-2 (r457)

 * get rid of three assert() in bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index a2d3d09473730715b78f38d6abb2b0123589daca..225988825139d8decc112df2c3aa7063ce053d03 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -93,7 +93,15 @@ void bam_merge_core(int by_qname, const char *out, const char *headers, int n, c
        for (i = 0; i != n; ++i) {
                heap1_t *h;
                bam_header_t *hin;
-               assert(fp[i] = bam_open(fn[i], "r"));
+               fp[i] = bam_open(fn[i], "r");
+               if (fp[i] == 0) {
+                       int j;
+                       fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
+                       for (j = 0; j < i; ++j) bam_close(fp[j]);
+                       free(fp); free(heap);
+                       // FIXME: possible memory leak
+                       return;
+               }
                hin = bam_header_read(fp[i]);
                if (i == 0) { // the first SAM
                        hout = hin;
@@ -202,7 +210,13 @@ static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam
        name = (char*)calloc(strlen(prefix) + 20, 1);
        if (n >= 0) sprintf(name, "%s.%.4d.bam", prefix, n);
        else sprintf(name, "%s.bam", prefix);
-       assert(fp = bam_open(name, "w"));
+       fp = bam_open(name, "w");
+       if (fp == 0) {
+               fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
+               free(name);
+               // FIXME: possible memory leak
+               return;
+       }
        free(name);
        bam_header_write(fp, h);
        for (i = 0; i < k; ++i)
@@ -235,7 +249,10 @@ void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t m
        g_is_by_qname = is_by_qname;
        n = k = 0; mem = 0;
        fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
-       assert(fp);
+       if (fp == 0) {
+               fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
+               return;
+       }
        header = bam_header_read(fp);
        buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*));
        // write sub files

diff --git a/bamtk.c b/bamtk.c
index ea6667205c9b642e9e5540470d33b5ab274d727a..8db8bcb30b368fde4351c72cbada5f5984d8b410 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.6 (r453)"
+#define PACKAGE_VERSION "0.1.6-2 (r457)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);