Silence compiler warnings.

Author: jkbonfield

io_lib/cram_codecs.c

@@ -1187,7 +1187,7 @@ static uint8_t  zigzag8 (int8_t  x) { return (x << 1) ^ (x >>  7); }
 static uint16_t zigzag16(int16_t x) { return (x << 1) ^ (x >> 15); }
 static uint32_t zigzag32(int32_t x) { return (x << 1) ^ (x >> 31); }
 
-static int8_t  unzigzag8 (uint8_t  x) { return (x >> 1) ^ -(x & 1); }
+//static int8_t  unzigzag8 (uint8_t  x) { return (x >> 1) ^ -(x & 1); }
 static int16_t unzigzag16(uint16_t x) { return (x >> 1) ^ -(x & 1); }
 static int32_t unzigzag32(uint32_t x) { return (x >> 1) ^ -(x & 1); }
 

io_lib/crc32.c

@@ -19,6 +19,7 @@
 #include "io_lib/os.h"
 
 #ifdef HAVE_LIBDEFLATE
+#include <libdeflate.h>
 uint32_t iolib_crc32(uint32_t previousCrc32, unsigned char *buf, unsigned int len) {
     return libdeflate_crc32(previousCrc32, buf, len);
 }

io_lib/open_trace_file.c

@@ -491,7 +491,7 @@ mFILE *find_file_url(char *file, char *url) {
     int pid;
     int maxlen = 8190 - strlen(file);
     char *fname = tempnam(NULL, NULL);
-    int status;
+    int status = 0;
 
     /* Expand %s for the trace name */
     for (cp = buf; *url && cp - buf < maxlen; url++) {

io_lib/string_alloc.c

@@ -148,7 +148,7 @@ char *string_ndup(string_alloc_t *a_str, char *instr, size_t len) {
 
     if (NULL == str) return NULL;
 
-    strncpy(str, instr, len);
+    memcpy(str, instr, len);
     str[len] = 0;
 
     return str;

progs/cram_filter.c

@@ -745,9 +745,14 @@ int index_start(cram_fd *fd, char *fn, int container) {
 	return -1;
     }
 
-    strtol(cp, &cp, 10);
-    strtol(cp, &cp, 10);
-    strtol(cp, &cp, 10);
+    long dummy = 0;
+    dummy |= strtol(cp, &cp, 10);
+    dummy |= strtol(cp, &cp, 10);
+    dummy |= strtol(cp, &cp, 10);
+    if (dummy == LONG_MIN || dummy == LONG_MAX) {
+	free(buf);
+	return -1;
+    }
     if (cram_seek(fd, strtoll(cp, &cp, 10), SEEK_SET) != 0) {
 	free(buf);
 	return -1;

progs/srf_dump_all.c

@@ -846,7 +846,7 @@ void dump_destination_mode(char mode) {
  * Returns the successfully opened file or NULL.
  */
 FILE *fopen_slx(char *dir, char *type, int lane, int tile) {
-    char fn[1024];
+    char fn[2048];
     FILE *fp;
 
     sprintf(fn, "%s/s_%d_%04d_%s.txt", dir, lane, tile, type);
@@ -948,7 +948,7 @@ int process_srf_to_solexa_files(char *ar_name, char chunk_mode, int num_reads_on
  * Returns the successfully opened file or NULL.
  */
 FILE *fopen_text(char *dir, int lane, int tile) {
-    char fn[1024];
+    char fn[2048];
     FILE *fp;
 
     sprintf(fn, "%s/s_%d_%04d_dump.txt", dir, lane, tile);