many changes that fix LFS bugs and make implicit casts explicit

Makefile

@@ -100,16 +100,17 @@ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
 VERSION = $(shell cat VERSION)
 
 BITS=32
-# cygwin will stay 32 bit for now.
-ifeq (1,$(MINGW))
-    # msys will always be 32 bit so look at the cpu arch.
-    ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
-        BITS=64
-    else
-        ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITECTURE)))
-            BITS=64
-        endif
-    endif
+ifeq (x86_64,$(shell uname -m))
+	BITS=64
+endif
+# msys will always be 32 bit so look at the cpu arch instead.
+ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
+	ifeq (1,$(MINGW))
+		BITS=64
+	endif
+endif
+ifeq (32,$(BITS))
+  $(error bowtie2 compilation requires a 64-bit platform )
 endif
 
 ifeq (1,$(LINUX))

SeqAn-1.1/seqan/index/index_sa_lss.h

@@ -57,7 +57,7 @@ struct _Context_LSS
 	{
 	   TValue g;
 
-	   g=pm-I;                      /* group number.*/
+	   g=(TValue)(pm-I);                      /* group number.*/
 	   V[*pl]=g;                    /* update group number of first position.*/
 	   if (pl==pm)
 		  *pl=-1;                   /* one element, sorted group.*/
@@ -90,7 +90,7 @@ struct _Context_LSS
 		  pa=pb;                    /* continue sorting rest of the subarray.*/
 	   }
 	   if (pa==pn) {                /* check if last part is single element.*/
-		  V[*pa]=pa-I;
+		  V[*pa]=(TValue)(pa-I);
 		  *pa=-1;                   /* sorted group.*/
 	   }
 	}
@@ -157,17 +157,17 @@ struct _Context_LSS
 		  --pc;
 	   }
 	   pn=p+n;
-	   if ((s=pa-p)>(t=pb-pa))
+	   if ((s=(TValue)(pa-p))>(t=(TValue)(pb-pa)))
 		  s=t;
 	   for (pl=p, pm=pb-s; s; --s, ++pl, ++pm)
 		  SEQAN_LSSSWAP(pl, pm);
-	   if ((s=pd-pc)>(t=pn-pd-1))
+	   if ((s=(TValue)(pd-pc))>(t=(TValue)(pn-pd-1)))
 		  s=t;
 	   for (pl=pb, pm=pn-s; s; --s, ++pl, ++pm)
 		  SEQAN_LSSSWAP(pl, pm);
 
-	   s=pb-pa;
-	   t=pd-pc;
+	   s=(TValue)(pb-pa);
+	   t=(TValue)(pd-pc);
 	   if (s>0)
 		  sort_split(p, s);
 	   update_group(p+s, p+n-t-1);
@@ -197,13 +197,13 @@ struct _Context_LSS
 	   for (pi=p+k-1, i=n; pi>=p; --pi) {
 		  d=x[c=*pi];               /* c is position, d is next in list.*/
 		  x[c]=g=i;                 /* last position equals group number.*/
-		  if (d>=0) {               /* if more than one element in group.*/
+		  if (d == 0 || d > 0) {               /* if more than one element in group.*/
 			 p[i--]=c;              /* p is permutation for the sorted x.*/
 			 do {
 				d=x[c=d];           /* next in linked list.*/
 				x[c]=g;             /* group number in x.*/
 				p[i--]=c;           /* permutation in p.*/
-			 } while (d>=0);
+			 } while (d == 0 || d > 0);
 		  } else
 			 p[i--]=-1;             /* one element, sorted group.*/
 	   }
@@ -305,7 +305,7 @@ struct _Context_LSS
 		  pi=I;                     /* pi is first position of group.*/
 		  sl=0;                     /* sl is negated length of sorted groups.*/
 		  do {
-			 if ((s=*pi)<0) {
+			 if ((s=*pi) <= 0 && (s=*pi) != 0) {
 				pi-=s;              /* skip over sorted group.*/
 				sl+=s;              /* add negated length to sl.*/
 			 } else {
@@ -314,7 +314,7 @@ struct _Context_LSS
 				   sl=0;
 				}
 				pk=I+V[s]+1;        /* pk-1 is last position of unsorted group.*/
-				sort_split(pi, pk-pi);
+				sort_split(pi, (TValue)(pk-pi));
 				pi=pk;              /* next group.*/
 			 }
 		  } while (pi<=I+n);

aligner.h

@@ -944,7 +944,7 @@ class PairedBWAlignerV1 : public Aligner {
 		                                        patsrc_->bufa().qual) :
 		                                (off1 ? patsrc_->bufb().qualRev  :
 		                                        patsrc_->bufa().qualRev);
-		uint32_t qlen = seqan::length(seq);  // length of outstanding mate
+		uint32_t qlen = (uint32_t)seqan::length(seq);  // length of outstanding mate
 		uint32_t alen = (off1 ? patsrc_->bufa().length() :
 		                        patsrc_->bufb().length());
 		int minins = minInsert_;
@@ -1894,7 +1894,7 @@ class PairedBWAlignerV2 : public Aligner {
 			                    patsrc_->bufa().qual) :
 			     (range.mate1 ? patsrc_->bufb().qualRev :
 			                    patsrc_->bufa().qualRev);
-		uint32_t qlen = seqan::length(seq);  // length of outstanding mate
+		uint32_t qlen = (uint32_t)seqan::length(seq);  // length of outstanding mate
 		uint32_t alen = (range.mate1 ? patsrc_->bufa().length() :
 		                               patsrc_->bufb().length());
 		int minins = minInsert_;

binary_sa_search.h

@@ -30,7 +30,7 @@ TIndexOffU binarySASearch(const TStr& host,
             const String<TSufElt>& sa)
 {
 	TIndexOffU lLcp = 0, rLcp = 0; // greatest observed LCPs on left and right
-	TIndexOffU l = 0, r = length(sa)+1; // binary-search window
+	TIndexOffU l = 0, r = (TIndexOffU)length(sa)+1; // binary-search window
 	TIndexOffU hostLen = TIndexOffU(length(host));
 	while(true) {
 		assert_gt(r, l);

blockwise_sa.h

@@ -25,19 +25,19 @@ using namespace seqan;
 // Helpers for printing verbose messages
 
 #ifndef VMSG_NL
-#define VMSG_NL(args...) \
+#define VMSG_NL(...) \
 if(this->verbose()) { \
 	stringstream tmp; \
-	tmp << args << endl; \
+	tmp << __VA_ARGS__ << endl; \
 	this->verbose(tmp.str()); \
 }
 #endif
 
 #ifndef VMSG
-#define VMSG(args...) \
+#define VMSG(...) \
 if(this->verbose()) { \
 	stringstream tmp; \
-	tmp << args; \
+	tmp << __VA_ARGS__; \
 	this->verbose(tmp.str()); \
 }
 #endif
@@ -49,7 +49,7 @@ template<typename TStr>
 class BlockwiseSA {
 public:
 	BlockwiseSA(const TStr& __text,
-				TIndexOffU __bucketSz,
+	            TIndexOffU __bucketSz,
 	            bool __sanityCheck = false,
 	            bool __passMemExc = false,
 	            bool __verbose = false,
@@ -130,7 +130,7 @@ class BlockwiseSA {
 	bool sanityCheck()  const { return _sanityCheck; }
 	bool verbose()      const { return _verbose; }
 	ostream& log()      const { return _logger; }
-	uint32_t size()     const { return length(_text)+1; }
+	size_t size()       const { return length(_text)+1; }
 
 protected:
 	/// Reset back to the first block
@@ -148,7 +148,7 @@ class BlockwiseSA {
 	/// Optionally output a verbose message
 	void verbose(const string& s) const {
 		if(this->verbose()) {
-			this->log() << s;
+			this->log() << s.c_str();
 			this->log().flush();
 		}
 	}
@@ -172,7 +172,7 @@ template<typename TStr>
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
 public:
 	InorderBlockwiseSA(const TStr& __text,
-					   TIndexOffU __bucketSz,
+	                   TIndexOffU __bucketSz,
 	                   bool __sanityCheck = false,
 	   	               bool __passMemExc = false,
 	                   bool __verbose = false,
@@ -191,7 +191,7 @@ class KarkkainenBlockwiseSA : public InorderBlockwiseSA<TStr> {
 	typedef DifferenceCoverSample<TStr> TDC;
 
 	KarkkainenBlockwiseSA(const TStr& __text,
-						  TIndexOffU __bucketSz,
+	                      TIndexOffU __bucketSz,
 	                      uint32_t __dcV,
 	                      uint32_t __seed = 0,
 	      	              bool __sanityCheck = false,
@@ -288,15 +288,15 @@ class KarkkainenBlockwiseSA : public InorderBlockwiseSA<TStr> {
 	 * Defined in blockwise_sa.cpp
 	 */
 	inline bool tieBreakingLcp(TIndexOffU aOff,
-							   TIndexOffU bOff,
-							   TIndexOffU& lcp,
+	                           TIndexOffU bOff,
+	                           TIndexOffU& lcp,
 	                           bool& lcpIsSoft);
 
 	/**
 	 * Compare two suffixes using the difference-cover sample.
 	 */
 	inline bool suffixCmp(TIndexOffU cmp,
-						TIndexOffU i,
+	                      TIndexOffU i,
 	                      int64_t& j,
 	                      int64_t& k,
 	                      bool& kSoft,
@@ -320,8 +320,8 @@ void KarkkainenBlockwiseSA<TStr>::qsort(String<TIndexOffU>& bucket) {
 	typedef typename Value<TStr>::Type TAlphabet;
 	const TStr& t = this->text();
 	TIndexOffU *s = begin(bucket);
-	uint32_t slen = seqan::length(bucket);
-	TIndexOffU len = seqan::length(t);
+	TIndexOffU slen = (TIndexOffU)seqan::length(bucket);
+	TIndexOffU len = (TIndexOffU)seqan::length(t);
 	if(_dc != NULL) {
 		// Use the difference cover as a tie-breaker if we have it
 		VMSG_NL("  (Using difference cover)");
@@ -350,8 +350,8 @@ template<>
 void KarkkainenBlockwiseSA<String<Dna, Packed<> > >::qsort(String<TIndexOffU>& bucket) {
 	const String<Dna, Packed<> >& t = this->text();
 	TIndexOffU *s = begin(bucket);
-	uint32_t slen = (uint32_t)seqan::length(bucket);
-	TIndexOffU len = seqan::length(t);
+	TIndexOffU slen = (TIndexOffU)seqan::length(bucket);
+	TIndexOffU len = (TIndexOffU)seqan::length(t);
 	if(_dc != NULL) {
 		// Use the difference cover as a tie-breaker if we have it
 		VMSG_NL("  (Using difference cover)");
@@ -555,7 +555,7 @@ void KarkkainenBlockwiseSA<TStr>::buildSamples() {
 //		VMSG_NL("Iterated too many times; trying again...");
 //		buildSamples();
 //	}
-	VMSG_NL("Avg bucket size: " << ((float)(len-length(_sampleSuffs)) / (length(_sampleSuffs)+1)) << " (target: " << bsz << ")");
+	VMSG_NL("Avg bucket size: " << ((double)(len-length(_sampleSuffs)) / (length(_sampleSuffs)+1)) << " (target: " << bsz << ")");
 }
 
 /**
@@ -579,8 +579,8 @@ static TIndexOffU suffixLcp(const T& t, TIndexOffU aOff, TIndexOffU bOff) {
  */
 template<typename TStr> inline
 bool KarkkainenBlockwiseSA<TStr>::tieBreakingLcp(TIndexOffU aOff,
-												TIndexOffU bOff,
-												TIndexOffU& lcp,
+                                                 TIndexOffU bOff,
+                                                 TIndexOffU& lcp,
                                                  bool& lcpIsSoft)
 {
 	const TStr& t = this->text();
@@ -619,10 +619,11 @@ bool KarkkainenBlockwiseSA<TStr>::tieBreakingLcp(TIndexOffU aOff,
  * filled in then calculate it from scratch.
  */
 template<typename T>
-static TIndexOffU lookupSuffixZ(const T& t,
-								TIndexOffU zOff,
-								TIndexOffU off,
-                              const String<TIndexOffU>& z)
+static TIndexOffU lookupSuffixZ(
+	const T& t,
+	TIndexOffU zOff,
+	TIndexOffU off,
+	const String<TIndexOffU>& z)
 {
 	if(zOff < length(z)) {
 		TIndexOffU ret = z[zOff];
@@ -638,12 +639,13 @@ static TIndexOffU lookupSuffixZ(const T& t,
  * false -> i > cmp
  */
 template<typename TStr> inline
-bool KarkkainenBlockwiseSA<TStr>::suffixCmp(TIndexOffU cmp,
-											TIndexOffU i,
-                                            int64_t& j,
-                                            int64_t& k,
-                                            bool& kSoft,
-                                            const String<TIndexOffU>& z)
+bool KarkkainenBlockwiseSA<TStr>::suffixCmp(
+	TIndexOffU cmp,
+	TIndexOffU i,
+	int64_t& j,
+	int64_t& k,
+	bool& kSoft,
+	const String<TIndexOffU>& z)
 {
 	const TStr& t = this->text();
 	TIndexOffU len = TIndexOffU(length(t));

bowtie_build_main.cpp

@@ -43,7 +43,7 @@ int main(int argc, const char **argv) {
 				myargs[i] = args[i].c_str();
 			}
 			if(args.size() == 1) continue;
-			lastret = bowtie_build(args.size(), myargs);
+			lastret = bowtie_build((int)args.size(), myargs);
 			free(myargs);
 		}
 		if(lastret == -1) {

bowtie_inspect.cpp

@@ -397,7 +397,7 @@ void print_index_summary(
 	cout << "FTab-Chars" << '\t' << ebwt.eh().ftabChars() << endl;
 	for(size_t i = 0; i < ebwt.nPat(); i++) {
 		cout << "Sequence-" << (i+1)
-		     << '\t' << p_refnames[refs.expandIdx(i)]
+		     << '\t' << p_refnames[refs.expandIdx((uint32_t)i)]
 		     << '\t' << (ebwt.plen()[i] + (color ? 1 : 0))
 		     << endl;
 	}

bowtie_main.cpp

@@ -43,7 +43,7 @@ int main(int argc, const char **argv) {
 				myargs[i] = args[i].c_str();
 			}
 			if(args.size() == 1) continue;
-			lastret = bowtie(args.size(), myargs);
+			lastret = bowtie((int)args.size(), myargs);
 			free(myargs);
 		}
 		if(lastret == -1) {

color_dec.cpp

@@ -190,7 +190,7 @@ void decodeHit(
 		assert_geq(readc, 0);
 		omin = INT_MAX;
 		// t <- index of column in dynamic programming table
-		t = c - readi + 1;
+		t = (int)(c - readi + 1);
 		const int refc = ref[refi + t];
 		int from[] = { table[0][4][t-1], table[1][4][t-1],
 		               table[2][4][t-1], table[3][4][t-1] };