[med-svn] samtools 01/01: Fix Mayhem issues caused by unlimited reads of gz input

[Andreas Tille]

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tille pushed a commit to branch debian/unstable
in repository samtools.

commit 0777f64201bd5b2f3ec128a771351f840bebd9aa
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 21 13:24:01 2015 +0100

    Fix Mayhem issues caused by unlimited reads of gz input
---
 debian/changelog            |  4 ++-
 debian/patches/mayhem.patch | 69 +++++++++++++++++++++++++++++++++++++++++++++
 debian/patches/series       |  1 +
 3 files changed, 73 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index f706a65..347fe77 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,8 +6,10 @@ samtools (1.2-4) UNRELEASED; urgency=medium
   * Add lintian-override to document that the language extensions are used
     internally
   * Fix spelling
+  * Fix Mayhem issues caused by unlimited reads of gz input
+    Closes: #716199, #716197
 
- -- Andreas Tille <tille at debian.org>  Tue, 22 Sep 2015 16:14:20 +0200
+ -- Andreas Tille <tille at debian.org>  Mon, 21 Dec 2015 13:20:46 +0100
 
 samtools (1.2-3) unstable; urgency=medium
 
diff --git a/debian/patches/mayhem.patch b/debian/patches/mayhem.patch
new file mode 100644
index 0000000..08b745c
--- /dev/null
+++ b/debian/patches/mayhem.patch
@@ -0,0 +1,69 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 21 Dec 2015 13:20:46 +0100
+Bug-Debian: https://bugs.debian.org/716197
+            https://bugs.debian.org/716199
+Description: Fix Mayhem issues caused by unlimited reads of gz input
+
+
+--- a/misc/maq2sam.c
++++ b/misc/maq2sam.c
+@@ -98,14 +98,37 @@ maqmap_t *maqmap_read_header(gzFile fp)
+         }
+         assert(mm->format == MAQMAP_FORMAT_NEW);
+     }
+-    gzread(fp, &mm->n_ref, sizeof(int));
++    if ( gzread(fp, &mm->n_ref, sizeof(int)) < sizeof(int)) {
++        fprintf(stderr, "To few bytes in input file");
++        return NULL;
++    }
++    if (mm->n_ref < 0) {
++        fprintf(stderr, "Incorrect n_ref read from input file\n");
++        return NULL;
++    }
++    if ( gzeof(fp) ) {
++        fprintf(stderr, "Unexpected end of file.");
++        return NULL;
++    }
+     mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));
+     for (k = 0; k != mm->n_ref; ++k) {
++        if ( gzeof(fp) ) {
++            fprintf(stderr, "Unexpected end of file.");
++            return NULL;
++        }
+         gzread(fp, &len, sizeof(int));
+         mm->ref_name[k] = (char*)malloc(len * sizeof(char));
++        if ( gzeof(fp) ) {
++            fprintf(stderr, "Unexpected end of file.");
++            return NULL;
++        }
+         gzread(fp, mm->ref_name[k], len);
+     }
+     /* read number of mapped reads */
++    if ( gzeof(fp) ) {
++        fprintf(stderr, "Unexpected end of file.");
++        return NULL;
++    }
+     gzread(fp, &mm->n_mapped_reads, sizeof(uint64_t));
+     return mm;
+ }
+@@ -117,6 +140,8 @@ void maq2tam_core(gzFile fp, const char
+     int ret;
+     m1 = &mm1;
+     mm = maqmap_read_header(fp);
++    if (!mm) exit(1);
++
+     while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {
+         int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];
+         if (m1->flag) flag |= 1;
+@@ -191,6 +216,11 @@ int main(int argc, char *argv[])
+         return 1;
+     }
+     fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
++    if (!fp ) {
++        fprintf(stderr, "Unable to open file %s", argv[1]);
++        fprintf(stderr, "Usage: maq2sam <in.map> [<readGroup>]\n");
++        return 1;
++    }
+     maq2tam_core(fp, argc > 2? argv[2] : 0);
+     gzclose(fp);
+     return 0;
diff --git a/debian/patches/series b/debian/patches/series
index b9ad524..02347fd 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 fix_segfault_with_small_ref.patch
 dynamic-build.patch
 i386-build.patch
+mayhem.patch

-- 
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