From 6363198a0cc78a525c0ec0672f2030d3a3232adb Mon Sep 17 00:00:00 2001
From: James Bonfield <jkb@sanger.ac.uk>
Date: Thu, 16 Nov 2023 17:30:24 +0000
Subject: [PATCH] Improve the SAM/BAM/CRAM fuzzer to write BAM and CRAM too.

TODO: add BCF as well.
---
 Makefile                    |  4 +++
 test/fuzz/hts_open_fuzzer.c | 51 +++++++++++++++++++++++++++++++------
 2 files changed, 47 insertions(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index 9a0c86c477..643f5fbbaf 100644
--- a/Makefile
+++ b/Makefile
@@ -623,6 +623,10 @@ check test: all $(HTSCODECS_TEST_TARGETS)
 test/hts_endian: test/hts_endian.o
 	$(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)
 
+# To build the fuzzer, try:
+# make  CC="clang16 -fsanitize=address,undefined,fuzzer" \
+#     CFLAGS="-g -O3 -DFUZZING_BUILD_MODE_UNSAFE_FOR_PRODUCTION" \
+#     test/fuzz/hts_open_fuzzer
 test/fuzz/hts_open_fuzzer: test/fuzz/hts_open_fuzzer.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ test/fuzz/hts_open_fuzzer.o libhts.a $(LIBS) -lpthread
 
diff --git a/test/fuzz/hts_open_fuzzer.c b/test/fuzz/hts_open_fuzzer.c
index 355f790a57..7bd34e6717 100644
--- a/test/fuzz/hts_open_fuzzer.c
+++ b/test/fuzz/hts_open_fuzzer.c
@@ -47,39 +47,74 @@ static void view_sam(htsFile *in) {
     if (!in) {
         return;
     }
-    samFile *out = sam_open("/dev/null", "w");
-    if (!out) {
+    samFile *outS = sam_open("/dev/null", "w");
+    samFile *outB = sam_open("/dev/null", "wb");
+    samFile *outC = sam_open("/dev/null", "wC");
+    if (!outS || !outB || !outC) {
         abort();
     }
+    // Not critical if this doesn't work, but can test more if
+    // we're in the right location.
+    if (hts_set_fai_filename(outC, "../c2.fa") < 0) {
+        static int warned = 0;
+        if (!warned) {
+            warned = 1;
+            fprintf(stderr, "Warning couldn't find the c2.fa file\n");
+        }
+    }
     sam_hdr_t *hdr = sam_hdr_read(in);
     if (hdr == NULL) {
-        hts_close_or_abort(out);
+        hts_close_or_abort(outS);
+        hts_close_or_abort(outB);
+        hts_close_or_abort(outC);
         return;
     }
 
     // This will force the header to be parsed.
     (void) sam_hdr_count_lines(hdr, "SQ");
 
-    if (sam_hdr_write(out, hdr) != 0) {
+    if (sam_hdr_write(outS, hdr) != 0) {
         sam_hdr_destroy(hdr);
-        hts_close_or_abort(out);
+        hts_close_or_abort(outS);
+        hts_close_or_abort(outB);
+        hts_close_or_abort(outC);
+        return;
+    }
+    if (sam_hdr_write(outB, hdr) != 0) {
+        sam_hdr_destroy(hdr);
+        hts_close_or_abort(outS);
+        hts_close_or_abort(outB);
+        hts_close_or_abort(outC);
+        return;
+    }
+    if (sam_hdr_write(outC, hdr) != 0) {
+        sam_hdr_destroy(hdr);
+        hts_close_or_abort(outS);
+        hts_close_or_abort(outB);
+        hts_close_or_abort(outC);
         return;
     }
     bam1_t *b = bam_init1();
     if (b == NULL) {
         sam_hdr_destroy(hdr);
-        hts_close_or_abort(out);
+        hts_close_or_abort(outS);
+        hts_close_or_abort(outB);
+        hts_close_or_abort(outC);
         return;
     }
     while (sam_read1(in, hdr, b) >= 0) {
-        if (sam_write1(out, hdr, b) < 0) {
+        if (sam_write1(outS, hdr, b) < 0 ||
+            sam_write1(outB, hdr, b) < 0 ||
+            sam_write1(outC, hdr, b) < 0) {
             break;
         }
     }
     bam_destroy1(b);
 
     sam_hdr_destroy(hdr);
-    hts_close_or_abort(out);
+    hts_close_or_abort(outS);
+    hts_close_or_abort(outB);
+    hts_close_or_abort(outC);
 }
 
 static void view_vcf(htsFile *in) {