Release 1.4.1: summary

.gitignore

@@ -42,6 +42,7 @@ lib*.so.*
 /test/test-regidx
 /test/test-vcf-api
 /test/test-vcf-sweep
+/test/test-bcf-sr
 /test/test_view
 /test/thrash_threads[1-6]
 /test/*.tmp

Makefile

@@ -31,6 +31,8 @@ htslib_default_libs = -lz -lm -lbz2 -llzma
 
 CPPFLAGS =
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+#CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
 CFLAGS   = -g -Wall -O2
 EXTRA_CFLAGS_PIC = -fpic
 LDFLAGS  =
@@ -90,7 +92,7 @@ HTSPREFIX =
 include htslib_vars.mk
 
 
-PACKAGE_VERSION = 1.4
+PACKAGE_VERSION = 1.4.1
 LIBHTS_SOVERSION = 2
 
 
@@ -262,7 +264,7 @@ print-config:
 # file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
 
 libhts.so: $(LIBHTS_OBJS:.o=.pico)
-	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS)
+	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread
 	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
 
 # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
@@ -274,11 +276,11 @@ libhts.dylib: $(LIBHTS_OBJS)
 	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
 
 cyghts-$(LIBHTS_SOVERSION).dll: $(LIBHTS_OBJS)
-	$(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import -pthread $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS)
+	$(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
 
 
 .pico.so:
-	$(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS)
+	$(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< $(LIBS) -lpthread
 
 .o.bundle:
 	$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
@@ -335,13 +337,13 @@ cram/zfio.o cram/zfio.pico: cram/zfio.c config.h $(cram_os_h) cram/zfio.h
 
 
 bgzip: bgzip.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread
 
 htsfile: htsfile.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) -lpthread
 
 tabix: tabix.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
 
 bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h)
 htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
@@ -350,7 +352,7 @@ tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htsl
 
 # For tests that might use it, set $REF_PATH explicitly to use only reference
 # areas within the test suite (or set it to ':' to use no reference areas).
-check test: bgzip htsfile $(BUILT_TEST_PROGRAMS)
+check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
 	test/hts_endian
 	test/fieldarith test/fieldarith.sam
 	test/hfile
@@ -364,31 +366,31 @@ test/hts_endian: test/hts_endian.o
 	$(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)
 
 test/fieldarith: test/fieldarith.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LIBS) -lpthread
 
 test/hfile: test/hfile.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LIBS) -lpthread
 
 test/sam: test/sam.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/sam.o libhts.a $(LIBS) -lpthread
 
 test/test_bgzf: test/test_bgzf.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test_bgzf.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/test_bgzf.o libhts.a -lz $(LIBS) -lpthread
 
 test/test-regidx: test/test-regidx.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/test-regidx.o libhts.a $(LIBS) -lpthread
 
 test/test_view: test/test_view.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LIBS) -lpthread
 
 test/test-vcf-api: test/test-vcf-api.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LIBS) -lpthread
 
 test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LIBS) -lpthread
 
 test/test-bcf-sr: test/test-bcf-sr.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test-bcf-sr.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/test-bcf-sr.o libhts.a -lz $(LIBS) -lpthread
 
 test/hts_endian.o: test/hts_endian.c $(htslib_hts_endian_h)
 test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
@@ -403,22 +405,22 @@ test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_vcf_sweep_h) bcf_sr_sor
 
 
 test/thrash_threads1: test/thrash_threads1.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/thrash_threads1.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads1.o libhts.a -lz $(LIBS) -lpthread
 
 test/thrash_threads2: test/thrash_threads2.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/thrash_threads2.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads2.o libhts.a -lz $(LIBS) -lpthread
 
 test/thrash_threads3: test/thrash_threads3.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/thrash_threads3.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads3.o libhts.a -lz $(LIBS) -lpthread
 
 test/thrash_threads4: test/thrash_threads4.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/thrash_threads4.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads4.o libhts.a -lz $(LIBS) -lpthread
 
 test/thrash_threads5: test/thrash_threads5.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/thrash_threads5.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads5.o libhts.a -lz $(LIBS) -lpthread
 
 test/thrash_threads6: test/thrash_threads6.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/thrash_threads6.o libhts.a -lz $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ test/thrash_threads6.o libhts.a -lz $(LIBS) -lpthread
 
 test_thrash: $(BUILT_THRASH_PROGRAMS)
 

NEWS

@@ -1,4 +1,24 @@
-Noteworthy changes in release 1.4
+Noteworthy changes in release 1.4.1  (8th May 2017)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is primarily a security bug fix update.
+
+* Fixed SECURITY issue with buffer overruns with malicious data. (#514).
+
+* S3 support for non Amazon AWS endpoints. (#506)
+
+* Support for variant breakpoints in bcftools. (#516)
+
+* Improved handling of BCF NaNs. (#485)
+
+* Compilation / portability improvements. (#255, #423, #498, #488)
+
+* Miscellaneous bug fixes (#482, #521, #522, #523, #524).
+
+* Sanitise headers (#509)
+
+
+Release 1.4 (13 March 2017)
 
 * Incompatible changes: several functions and data types have been changed
   in this release, and the shared library soversion has been bumped to 2.

bcf_sr_sort.c

@@ -22,6 +22,8 @@
     THE SOFTWARE.
 */
 
+#include <strings.h>
+
 #include "bcf_sr_sort.h"
 #include "htslib/khash_str2int.h"
 

bgzf.c

@@ -220,7 +220,7 @@ static BGZF *bgzf_read_init(hFILE *hfpr)
 }
 
 // get the compress level from the mode string: compress_level==-1 for the default level, -2 plain uncompressed
-static int mode2level(const char *__restrict mode)
+static int mode2level(const char *mode)
 {
     int i, compress_level = -1;
     for (i = 0; mode[i]; ++i)
@@ -837,6 +837,11 @@ int bgzf_read_block(BGZF *fp)
         }
         size = count;
         block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1"
+        if (block_length < BLOCK_HEADER_LENGTH)
+        {
+            fp->errcode |= BGZF_ERR_HEADER;
+            return -1;
+        }
         compressed_block = (uint8_t*)fp->compressed_block;
         memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
         remaining = block_length - BLOCK_HEADER_LENGTH;
@@ -1049,6 +1054,10 @@ int bgzf_mt_read_block(BGZF *fp, bgzf_job *j)
 
     size = count;
     block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1"
+    if (block_length < BLOCK_HEADER_LENGTH) {
+        j->errcode |= BGZF_ERR_HEADER;
+        return -1;
+    }
     compressed_block = (uint8_t*)j->comp_data;
     memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
     remaining = block_length - BLOCK_HEADER_LENGTH;

bgzip.c

@@ -333,5 +333,4 @@ int main(int argc, char **argv)
         if (!pstdout) unlink(argv[optind]);
         return 0;
     }
-    return 0;
 }

configure.ac

@@ -182,6 +182,11 @@ is installed.
 FAILED.  This error must be resolved in order to build HTSlib successfully.])
 fi
 
+dnl connect() etc. fns are in libc on linux, but libsocket on illumos/Solaris
+libsocket=unneeded
+AC_SEARCH_LIBS(connect, socket, [libsocket=needed], [])
+
+
 if test "$enable_bz2" != no; then
   bz2_devel=ok
   AC_CHECK_HEADER([bzlib.h], [], [bz2_devel=missing], [;])

cram/cram_codecs.c

@@ -39,6 +39,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <string.h>
 #include <assert.h>
 #include <limits.h>
+#include <stdint.h>
+#include <errno.h>
 
 #include "cram/cram.h"
 
@@ -991,6 +993,15 @@ cram_codec *cram_huffman_decode_init(char *data, int size,
     }
 
     cp += safe_itf8_get(cp, data_end, &ncodes);
+    if (ncodes < 0) {
+        fprintf(stderr, "Invalid number of symbols in huffman stream\n");
+        return NULL;
+    }
+    if (ncodes >= SIZE_MAX / sizeof(*codes)) {
+        errno = ENOMEM;
+        return NULL;
+    }
+
     h = calloc(1, sizeof(*h));
     if (!h)
 	return NULL;
@@ -999,10 +1010,14 @@ cram_codec *cram_huffman_decode_init(char *data, int size,
     h->free   = cram_huffman_decode_free;
 
     h->huffman.ncodes = ncodes;
-    codes = h->huffman.codes = malloc(ncodes * sizeof(*codes));
-    if (!codes) {
-	free(h);
-	return NULL;
+    if (ncodes) {
+        codes = h->huffman.codes = malloc(ncodes * sizeof(*codes));
+        if (!codes) {
+            free(h);
+            return NULL;
+        }
+    } else {
+        codes = h->huffman.codes = NULL;
     }
 
     /* Read symbols and bit-lengths */

cram/cram_decode.c

@@ -2279,6 +2279,10 @@ int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
 	    s->ref = (char *)BLOCK_DATA(b);
 	    s->ref_start = s->hdr->ref_seq_start;
 	    s->ref_end   = s->hdr->ref_seq_start + s->hdr->ref_seq_span-1;
+	    if (s->ref_end - s->ref_start > b->uncomp_size) {
+		fprintf(stderr, "Embedded reference is too small.\n");
+		return -1;
+	    }
 	} else if (!fd->no_ref) {
 	    //// Avoid Java cramtools bug by loading entire reference seq 
 	    //s->ref = cram_get_ref(fd, s->hdr->ref_seq_id, 1, 0);