Add NULL checks to sam_hdr_read(), sam_hdr_write(); add checks to test/sam.c copy_check_alignment() (#730)

* Check for NULL fp in sam_hdr_read(), sam_hdr_write()

* Add more tests for failure in copy_check_alignment()

Catch problems like sam_open() and sam_read1() failing.  Prevents
a seg fault if sam_open() fails on either the input or output file.

Fixes #728 (A SEGV signal occurred when running program sam in test
directory).

Author: daviesrob

sam.c

@@ -1007,6 +1007,11 @@ static bam_hdr_t *sam_hdr_sanitise(bam_hdr_t *h) {
 
 bam_hdr_t *sam_hdr_read(htsFile *fp)
 {
+    if (!fp) {
+        errno = EINVAL;
+        return NULL;
+    }
+
     switch (fp->format.format) {
     case bam:
         return sam_hdr_sanitise(bam_hdr_read(fp->fp.bgzf));
@@ -1061,7 +1066,7 @@ bam_hdr_t *sam_hdr_read(htsFile *fp)
 
 int sam_hdr_write(htsFile *fp, const bam_hdr_t *h)
 {
-    if (!h) {
+    if (!fp || !h) {
         errno = EINVAL;
         return -1;
     }

test/sam.c

@@ -459,29 +459,53 @@ static void copy_check_alignment(const char *infname, const char *informat,
     samFile *in = sam_open(infname, "r");
     samFile *out = sam_open(outfname, outmode);
     bam1_t *aln = bam_init1();
-    bam_hdr_t *header;
+    bam_hdr_t *header = NULL;
+    int res;
+
+    if (!in) {
+        fail("couldn't open %s", infname);
+        goto err;
+    }
+    if (!out) {
+        fail("couldn't open %s with mode %s", outfname, outmode);
+        goto err;
+    }
+    if (!aln) {
+        fail("bam_init1() failed");
+        goto err;
+    }
 
     if (outref) {
-        if (hts_set_opt(out, CRAM_OPT_REFERENCE, outref) < 0)
+        if (hts_set_opt(out, CRAM_OPT_REFERENCE, outref) < 0) {
             fail("setting reference %s for %s", outref, outfname);
+            goto err;
+        }
     }
 
     header = sam_hdr_read(in);
+    if (!header) {
+        fail("reading header from %s", infname);
+        goto err;
+    }
     if (sam_hdr_write(out, header) < 0) fail("writing headers to %s", outfname);
 
-    while (sam_read1(in, header, aln) >= 0) {
+    while ((res = sam_read1(in, header, aln)) >= 0) {
         int mod4 = ((intptr_t) bam_get_cigar(aln)) % 4;
         if (mod4 != 0)
             fail("%s CIGAR not 4-byte aligned; offset is 4k+%d for \"%s\"",
                  informat, mod4, bam_get_qname(aln));
 
         if (sam_write1(out, header, aln) < 0) fail("writing to %s", outfname);
     }
+    if (res < -1) {
+        fail("failed to read alignment from %s", infname);
+    }
 
+ err:
     bam_destroy1(aln);
     bam_hdr_destroy(header);
-    sam_close(in);
-    sam_close(out);
+    if (in) sam_close(in);
+    if (out) sam_close(out);
 }
 
 static void samrecord_layout(void)