Fix warnings

lib/flash/combine_reads.cpp

@@ -54,16 +54,15 @@
 #	define __noreturn __attribute__((noreturn))
 #	define __format(type, format_str, args_start) \
 			__attribute__((format(type, format_str, args_start)))
-#	define max(a,b) ({ __typeof__(a) _a = (a); __typeof__(b) _b = (b); _a > _b ? _a : _b; })
-#	define min(a,b) ({ __typeof__(a) _a = (a); __typeof__(b) _b = (b); _a < _b ? _a : _b; })
-#	define inline inline __attribute__((always_inline))
+
 #else
 #	define __noreturn
 #	define __cold
 #	define __format(type, format_str, args_start)
+#endif
+
 #	define max(a,b) (((a) > (b)) ? (a) : (b))
 #	define min(a,b) (((a) < (b)) ? (a) : (b))
-#endif
 
 /* Sum the values an 8 x 8 bit vector and return a 32-bit result.  */
 static inline uint32_t
@@ -360,12 +359,12 @@ generate_combined_read(const struct read *read_1,
     char * combined_seq;
     char * combined_qual;
 
-    if (combined_read->seq_bufsz < combined_seq_len) {
+    if (combined_read->seq_bufsz < static_cast<size_t >(combined_seq_len)) {
         combined_read->seq = (char *)xrealloc(combined_read->seq,
                                       combined_seq_len);
         combined_read->seq_bufsz = combined_seq_len;
     }
-    if (combined_read->qual_bufsz < combined_seq_len) {
+    if (combined_read->qual_bufsz < static_cast<size_t >(combined_seq_len)) {
         combined_read->qual = (char *)xrealloc(combined_read->qual,
                                        combined_seq_len);
         combined_read->qual_bufsz = combined_seq_len;

lib/flash/util.cpp

@@ -60,6 +60,7 @@ xmalloc(size_t size)
             return p;
     }
     fprintf(stderr, "Out of memory: tried to allocate %zu bytes", size);
+    return NULL;
 }
 
 
@@ -78,5 +79,6 @@ xrealloc(void *ptr, size_t size)
             return p;
     }
     fprintf(stderr, "Out of memory: tried to reallocate %zu bytes", size);
+    return NULL;
 }
 

src/LocalCommandDeclarations.h

@@ -11,7 +11,6 @@ extern int hybridassembleresults(int argc, const char** argv, const Command &com
 extern int filternoncoding(int argc, const char** argv, const Command &command);
 extern int mergereads(int argc, const char** argv, const Command &command);
 extern int findassemblystart(int argc, const char** argv, const Command &command);
-extern int correctreads(int argc, const char** argv, const Command &command);
 extern int cyclecheck(int argc, const char** argv, const Command &command);
 extern int createhdb(int argc, const char** argv, const Command &command);
 #endif

src/assembler/CMakeLists.txt

@@ -1,7 +1,6 @@
 set(assembler_source_files
         assembler/assembleresult.cpp
         assembler/hybridassembleresult.cpp
-        assembler/correctreads.cpp
         assembler/findassemblystart.cpp
         assembler/filternoncoding.cpp
         assembler/mergereads.cpp

src/assembler/assembleresult.cpp

@@ -45,8 +45,8 @@ Matcher::result_t selectFragmentToExtend(QueueByScore &alignments,
         alignments.pop();
         size_t dbKey = res.dbKey;
         const bool notRightStartAndLeftStart = !(res.dbStartPos == 0 &&  res.qStartPos == 0 );
-        const bool rightStart = res.dbStartPos == 0 && (res.dbEndPos != res.dbLen-1);
-        const bool leftStart = res.qStartPos == 0   && (res.qEndPos != res.qLen-1);
+        const bool rightStart = res.dbStartPos == 0 && (res.dbEndPos != static_cast<int>(res.dbLen)-1);
+        const bool leftStart = res.qStartPos == 0   && (res.qEndPos != static_cast<int>(res.qLen)-1);
         const bool isNotIdentity = (dbKey != queryKey);
 
         if ((rightStart || leftStart) && notRightStartAndLeftStart && isNotIdentity){
@@ -205,7 +205,7 @@ int doassembly(LocalParameters &par) {
                             continue;
                         }
                     } else if (besttHitToExtend.qStartPos == 0) {
-                        if (besttHitToExtend.dbStartPos <= leftQueryOffsetToUse) {
+                        if (besttHitToExtend.dbStartPos <= static_cast<int>(leftQueryOffsetToUse)) {
                             continue;
                         }
                     }
@@ -236,7 +236,7 @@ int doassembly(LocalParameters &par) {
                     }
 
                     // check right extension or reverse left
-                    if (dbStartPos == 0 && qEndPos == (querySeqLen - 1) ) {
+                    if (dbStartPos == 0 && qEndPos == (static_cast<int>(querySeqLen) - 1) ) {
                         if((!isReverse && queryCouldBeExtendedRight == true) || (isReverse && queryCouldBeExtendedLeft == true)) {
                             float alnLen = qEndPos - qStartPos;
                             float scorePerCol = static_cast<float>(score) / (alnLen+0.5);
@@ -278,7 +278,7 @@ int doassembly(LocalParameters &par) {
                         }
 
                         //check left extension
-                    } else if (qStartPos == 0 && dbEndPos == (targetSeqLen - 1)) {
+                    } else if (qStartPos == 0 && dbEndPos == (static_cast<int>(targetSeqLen) - 1)) {
                         if ((!isReverse && queryCouldBeExtendedLeft == true)|| (isReverse && queryCouldBeExtendedRight == true)) {
                             float alnLen = qEndPos - qStartPos;
                             float scorePerCol = static_cast<float>(score) / (alnLen+0.5);