SSAHA is a software tool for very fast matching and alignment of DNA

sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.

WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/

PR:		ports/124525
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	gabor (mentor, implicit)

36 files changed, 1362 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 2f591aa84d19..cd0e5740f286 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -81,6 +81,7 @@
     SUBDIR += seaview
     SUBDIR += seqio
     SUBDIR += sim4
+    SUBDIR += ssaha
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tinker
diff --git a/biology/ssaha/Makefile b/biology/ssaha/Makefile
new file mode 100644
index 000000000000..8855ac6ec0fa
--- /dev/null
+++ b/biology/ssaha/Makefile
@@ -0,0 +1,33 @@
+# New ports collection makefile for:	ssaha
+# Date created:				12.Jun.2008
+# Whom:					Fernan Aguero <fernan@iib.unsam.edu.ar>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	ssaha
+PORTVERSION=	3.1c
+CATEGORIES=	biology
+MASTER_SITES=	http://www.sanger.ac.uk/Software/analysis/${PORTNAME:U}/
+DISTNAME=	${PORTNAME}_v${PORTVERSION:S/.//}
+
+MAINTAINER=	fernan@iib.unsam.edu.ar
+COMMENT=	Very fast matching and alignment of DNA sequences
+
+NO_WRKSUBDIR=	yes
+
+USE_GMAKE=	yes
+MAKEFILE=	makefile
+BUILD_WRKSRC=	${WRKDIR}/Binary
+ALL_TARGET=	ssaha
+
+DATA_FILES=	test.fasta test_extract.fasta test_filter.fail \
+		test_filter.fastq test_protein.fasta README
+
+do-install:
+	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/ssaha ${PREFIX}/bin
+	@${MKDIR} ${DATADIR}
+	${INSTALL_SCRIPT} ${BUILD_WRKSRC}/testSSAHA.csh ${DATADIR}/
+	${INSTALL_DATA} ${DATA_FILES:S,^,${WRKSRC}/,} ${DATADIR}/
+
+.include <bsd.port.mk>
diff --git a/biology/ssaha/distinfo b/biology/ssaha/distinfo
new file mode 100644
index 000000000000..1d978ee099cd
--- /dev/null
+++ b/biology/ssaha/distinfo
@@ -0,0 +1,3 @@
+MD5 (ssaha_v31c.tar.gz) = 0260a0cce67c5c465f5b54a45b3f65ae
+SHA256 (ssaha_v31c.tar.gz) = 63fa38ccd2725db6ba10881f8cc94d899afd2eba9c2f6436223d9284c5abfced
+SIZE (ssaha_v31c.tar.gz) = 251510
diff --git a/biology/ssaha/files/patch-GlobalDefinitions.cpp b/biology/ssaha/files/patch-GlobalDefinitions.cpp
new file mode 100644
index 000000000000..dbf6ed8a038f
--- /dev/null
+++ b/biology/ssaha/files/patch-GlobalDefinitions.cpp
@@ -0,0 +1,11 @@
+--- ./Global/GlobalDefinitions.cpp.orig	2004-03-01 13:51:28.000000000 -0300
++++ ./Global/GlobalDefinitions.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -119,7 +119,7 @@
+ MakeIntoWord::MakeIntoWord( int bitsPerSymbol, const char* tt ):
+ bitsPerSymbol_( bitsPerSymbol ), tt_( tt ) 
+ {
+-  for ( unsigned int i(0) ; i < (1<<bitsPerSymbol_) ; ++i )
++  for ( unsigned int i(0) ; i < ( unsigned int )(1<<bitsPerSymbol_) ; ++i )
+   {
+     map_.insert( make_pair( (static_cast<char>(tolower(tt[i]))),i ) );
+     map_.insert( make_pair( (static_cast<char>(toupper(tt[i]))),i ) );
diff --git a/biology/ssaha/files/patch-GlobalDefinitions.h b/biology/ssaha/files/patch-GlobalDefinitions.h
new file mode 100644
index 000000000000..fb7851574cc7
--- /dev/null
+++ b/biology/ssaha/files/patch-GlobalDefinitions.h
@@ -0,0 +1,82 @@
+--- ./Global/GlobalDefinitions.h.orig	2004-03-01 13:51:28.000000000 -0300
++++ ./Global/GlobalDefinitions.h	2008-06-12 15:39:31.000000000 -0300
+@@ -726,8 +726,6 @@
+ template <typename T> class Allocator
+ {
+ public:
+-  typedef T MyType;
+-
+   Allocator( T** ptr, const string& name, ostream& monStream=cerr ) : 
+     ptr_(ptr), name_(name), size_(0), isAllocated_(false), 
+     monStream_( monStream )
+@@ -788,32 +786,34 @@
+  
+   virtual void allocate( unsigned long size )
+   {
+-    size_=size;
+-    (*ptr_)=new T[size_];
+-    isAllocated_=true;
++    Allocator<T>::size_=size;
++    (*Allocator<T>::ptr_)=new T[Allocator<T>::size_];
++    Allocator<T>::isAllocated_=true;
+   }
+ 
+   virtual void allocateAndZero( unsigned long size ) 
+   {
+     const unsigned char zero(0);
+     allocate(size);
+-    memset( (void*)(*ptr_), zero, size_*sizeof(MyType) );
++    memset( (void*)(*Allocator<T>::ptr_), zero, Allocator<T>::size_*sizeof(T) );
+   }
+   virtual void load( unsigned long size )
+   {
+     allocate(size);
+-    loadFromFile( name_, (char*)(*ptr_), size_*sizeof(MyType), monStream_ );
++    loadFromFile( Allocator<T>::name_, (char*)(*Allocator<T>::ptr_),
++        Allocator<T>::size_*sizeof(T), Allocator<T>::monStream_ );
+   }
+   virtual void save()
+   {
+-    saveToFile( name_, (char*)(*ptr_), size_*sizeof(MyType), monStream_ );
++    saveToFile( Allocator<T>::name_, (char*)(*Allocator<T>::ptr_),
++        Allocator<T>::size_*sizeof(T), Allocator<T>::monStream_ );
+   }
+ 
+   virtual void deallocate()
+   {
+-    if (!isAllocated_) return;
+-    delete [] (*ptr_);
+-    isAllocated_=false;
++    if (!Allocator<T>::isAllocated_) return;
++    delete [] (*Allocator<T>::ptr_);
++    Allocator<T>::isAllocated_=false;
+   }
+ protected:
+ };
+@@ -892,7 +892,7 @@
+     if (isAllocated_) return;
+     mode_ = MemoryMapper::createMap;
+     size_ = size;
+-    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(MyType));
++    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(T));
+     isAllocated_ = true;
+   }
+ 
+@@ -908,7 +908,7 @@
+     if (isAllocated_) return;
+     mode_ = MemoryMapper::readMap;
+     size_ = size;
+-    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(MyType));
++    (*ptr_) = (T*) linkToMap(mode_,name_,size_*sizeof(T));
+     isAllocated_ = true;
+   }
+ 
+@@ -921,7 +921,7 @@
+   virtual void deallocate()
+   {
+     if (!isAllocated_) return;
+-    if(munmap((caddr_t)(*ptr_), size_*sizeof(MyType)) < 0)
++    if(munmap((caddr_t)(*ptr_), size_*sizeof(T)) < 0)
+       perror("unmap error"); // don't throw - called from destructor!
+     close(fileDesc_);
+     if (mode_.deleteFileOnExit) shm_unlink(name_.c_str());
diff --git a/biology/ssaha/files/patch-HashTable.cpp b/biology/ssaha/files/patch-HashTable.cpp
new file mode 100644
index 000000000000..c57e3745c639
--- /dev/null
+++ b/biology/ssaha/files/patch-HashTable.cpp
@@ -0,0 +1,20 @@
+--- ./HashTable/HashTable.cpp.orig	2004-03-01 13:51:28.000000000 -0300
++++ ./HashTable/HashTable.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -265,7 +265,7 @@
+ void HashTable::countWords( SequenceAdapter& thisSeq )
+ {
+ 
+-   for ( int j(0) ; j < thisSeq.size() ; ++ j )
++   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
+    {
+      // only count words that have not been flagged
+      pWordPositionInHitList_[(thisSeq[j]&(~gCursedWord))]
+@@ -284,7 +284,7 @@
+       // NB We stop at the last but one element of the 
+       // sequence (as the last isn't a full word)
+ 
+-   for ( int j(0) ; j < thisSeq.size() ; ++ j )
++   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
+       {
+ 	thisWord = thisSeq[j];
+ 	// only hash words that have not been flagged
diff --git a/biology/ssaha/files/patch-HashTableGeneric.cpp b/biology/ssaha/files/patch-HashTableGeneric.cpp
new file mode 100644
index 000000000000..0d1ffb441303
--- /dev/null
+++ b/biology/ssaha/files/patch-HashTableGeneric.cpp
@@ -0,0 +1,48 @@
+--- ./HashTable/HashTableGeneric.cpp.orig	2005-06-21 05:48:27.000000000 -0300
++++ ./HashTable/HashTableGeneric.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -63,18 +63,18 @@
+ ( ostream& monitoringStream,
+   const string& name,
+   Allocator<PositionInHitList>& arrayAllocator ) : 
+-  isInitialized_( false ), 
+-  monitoringStream_( monitoringStream ),
+   name_( name ),
+-  bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
++  isInitialized_( false ), 
+   maxNumHits_( defaultMaxNumHits ),
++  bitsPerSymbol_( gBaseBits ), // default: may be overwritten in subclass ctor
+   hitListFormat_( gNotSpecified ),
++  monitoringStream_( monitoringStream ),
+   pArrayAllocator_
+   ( arrayAllocator.clone(&pWordPositionInHitList_,
+ 			 name+(string)".head",
+ 			 monitoringStream_) ),
+-  pSequenceSizes_(NULL),
+-  pNameReader_(NULL)
++  pNameReader_(NULL),
++  pSequenceSizes_(NULL)
+   {
+     monitoringStream_ << "constructing HashTableGeneric\n";
+     if (name_=="")
+@@ -290,7 +290,7 @@
+   WordSequence thisSeq;
+     
+   // NB sequences are numbered 1...n not 0...n-1
+-  for ( unsigned int i(1); i <= numSeqs ; i++ )
++  for ( int i(1); i <= numSeqs ; i++ )
+   {
+     if( sequenceReader.getNextSequence( thisSeq, wordLength_) == -1 ) 
+     {
+@@ -973,10 +973,10 @@
+ 
+ SequenceAdapterWithOverlap::SequenceAdapterWithOverlap
+ ( int bitsPerSymbol, int wordLength, int stepLength ) :
++SequenceAdapter(),
+ bitsPerSymbol_( bitsPerSymbol ), 
+ wordLength_( wordLength ), 
+-stepLength_( stepLength ),
+-SequenceAdapter() 
++stepLength_( stepLength )
+ {
+ 
+   maskLeft_  = new Word[ wordLength_ ];
diff --git a/biology/ssaha/files/patch-HashTablePacked.cpp b/biology/ssaha/files/patch-HashTablePacked.cpp
new file mode 100644
index 000000000000..6efc6d24bd77
--- /dev/null
+++ b/biology/ssaha/files/patch-HashTablePacked.cpp
@@ -0,0 +1,29 @@
+--- ./HashTable/HashTablePacked.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./HashTable/HashTablePacked.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -132,7 +132,7 @@
+ void HashTablePacked::countWords( SequenceAdapter& thisSeq )
+ {
+ 
+-   for ( int j(0) ; j < thisSeq.size() ; ++ j )
++   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
+    {
+      // only count words that have not been flagged
+      pWordPositionInHitList_[(thisSeq[j]&(~gCursedWord))]
+@@ -151,7 +151,7 @@
+   // NB We stop at the last but one element of the 
+   // sequence (as the last isn't a full word)
+ 
+-   for ( int j(0) ; j < thisSeq.size() ; ++ j )
++   for ( WordSequence::size_type j(0) ; j < thisSeq.size() ; ++ j )
+       {
+ 	thisWord = thisSeq[j];
+ 
+@@ -200,7 +200,7 @@
+       for ( WordSequence::const_iterator thisWord(seq.begin());
+             thisWord != last ; ++thisWord )
+       {
+-	int oldSize(packedHits.size()); // %%%%%%
++//	int oldSize(packedHits.size()); // %%%%%%
+ 	matchWordDeluxe( *thisWord, packedHits, baseOffset );
+ 	//	cout << printResidue(*thisWord, wordLength_) << " "
+ 	//  << packedHits.size()-oldSize;
diff --git a/biology/ssaha/files/patch-HashTablePacked.h b/biology/ssaha/files/patch-HashTablePacked.h
new file mode 100644
index 000000000000..c00860d1bbfd
--- /dev/null
+++ b/biology/ssaha/files/patch-HashTablePacked.h
@@ -0,0 +1,16 @@
+--- ./HashTable/HashTablePacked.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./HashTable/HashTablePacked.h	2008-06-12 15:39:31.000000000 -0300
+@@ -236,11 +236,11 @@
+     HashTableView<PositionPacked,HashTablePacked>
+     (monitoringStream, name, hitListAllocator, arrayAllocator),
+     wordNum_(0),
++    numRepeats_(0),
++    substituteThreshold_(0),
+     pMatchSequence_(&HashTablePacked::matchSequenceStandard),
+     pMatchWord_(&HashTablePacked::matchWordStandard),
+     pGenerateSubstitutes_(&generateSubstitutesDNA),
+-    numRepeats_(0),
+-    substituteThreshold_(0),
+     sorter_(4,(sizeof(PositionPacked)*8)/4)
+     {
+       hitListFormat_ = g32BitPacked;
diff --git a/biology/ssaha/files/patch-HashTableTranslated.cpp b/biology/ssaha/files/patch-HashTableTranslated.cpp
new file mode 100644
index 000000000000..e4ab9af82423
--- /dev/null
+++ b/biology/ssaha/files/patch-HashTableTranslated.cpp
@@ -0,0 +1,77 @@
+--- ./HashTable/HashTableTranslated.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./HashTable/HashTableTranslated.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -50,9 +50,9 @@
+  		   Allocator<PositionPacked>& hitListAllocator,
+ 		   Allocator<PositionInHitList>& arrayAllocator 
+ 		   ):
+-  queryFrame_(0),
+   HashTablePacked( monitoringStream, name, 
+-		   hitListAllocator, arrayAllocator  ) 
++		   hitListAllocator, arrayAllocator  ), 
++  queryFrame_(0)
+ {
+   hitListFormat_ = g32BitPackedProtein;
+   bitsPerSymbol_ = gResidueBits;
+@@ -135,12 +135,12 @@
+   Allocator<PositionPacked>& hitListAllocator,
+   Allocator<PositionInHitList>& arrayAllocator 
+   ):
++  HashTablePacked( monitoringStream, name, 
++		     hitListAllocator, arrayAllocator  ),
++  codonEncoder_(5),
+   queryFrame_(0),
+   queryMult_(1),
+-  codonEncoder_(5),
+-  pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein ),
+-  HashTablePacked( monitoringStream, name, 
+-		     hitListAllocator, arrayAllocator  ) 
++  pMatchSequence_( &HashTablePackedProtein::matchSequenceProtein )
+ {
+     hitListFormat_ = g32BitPackedProtein;
+     bitsPerSymbol_ = gResidueBits;
+@@ -249,14 +249,14 @@
+   Allocator<PositionPacked>& hitListAllocator,
+   Allocator<PositionInHitList>& arrayAllocator
+   ) :
++  HashTableGeneric( monitoringStream, name, arrayAllocator ),
+   hashFwd_( monitoringStream, name+(string)"_fwd", 
+ 	    hitListAllocator, arrayAllocator ),
+   hashRev_( monitoringStream, name+(string)"_rev", 
+ 	    hitListAllocator, arrayAllocator ),
+   pHash_(&hashFwd_),
+   codonEncoder_(5),
+-  pMatchSequence_( &HashTableTranslated::matchSequenceProtein ),
+-  HashTableGeneric( monitoringStream, name, arrayAllocator ) 
++  pMatchSequence_( &HashTableTranslated::matchSequenceProtein )
+ {
+   bitsPerSymbol_=gResidueBits;
+   hitListFormat_ = gTranslated;
+@@ -344,8 +344,8 @@
+ 
+     // Change encoding mode
+     SequenceReaderModeFlagReplace mode('X');
+-    assert(ttCodon['X']==ttProtein['X']);
+-    assert(ttCodon['X']!=nv);
++    assert(ttCodon[(int)'X']==ttProtein[(int)'X']);
++    assert(ttCodon[(int)'X']!=nv);
+     codonEncoder_.changeMode( &mode );
+ 
+ 
+@@ -418,7 +418,7 @@
+   seq->link( translatedSeq );
+ 
+   // NB sequences are numbered 1...n not 0...n-1
+-  for ( unsigned int i(1); i <= numSeqs ; i++ )
++  for ( int i(1); i <= numSeqs ; i++ )
+   {
+     //    cout << "hashing sequence " << i << endl;
+     if( sequenceReader.getNextSequence( thisSeq, eDNAWordSizeForHashing) == -1 ) 
+@@ -520,7 +520,7 @@
+ int HashTableTranslated::getHitTypeSize( void ) const 
+ {
+   assert(1==0);
+-  return NULL;
++  return 0;
+ }
+ void HashTableTranslated::allocateHitList( unsigned long size ) 
+ {
diff --git a/biology/ssaha/files/patch-MatchAligner.cpp b/biology/ssaha/files/patch-MatchAligner.cpp
new file mode 100644
index 000000000000..e7420b1ddec4
--- /dev/null
+++ b/biology/ssaha/files/patch-MatchAligner.cpp
@@ -0,0 +1,94 @@
+--- ./QueryManager/MatchAligner.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/MatchAligner.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -53,13 +53,13 @@
+   bool reverseQueryCoords,
+   bool doAlignment,
+   ostream& outputStream ):
++  pAlign_(pAlign),
++  outputStream_(outputStream),
+   querySource_(querySource), 
+   subjectSource_(subjectSource),
+-  pAlign_(pAlign),
+   //  numCols_(numCols),
+   reverseQueryCoords_(reverseQueryCoords),
+-  doAlignment_(doAlignment),
+-  outputStream_(outputStream)
++  doAlignment_(doAlignment)
+ {
+ } // ~MatchTaskAlign::MatchTaskAlign
+ 
+@@ -194,10 +194,10 @@
+   int bandExtension,
+   ScoreTable* pTable,
+   ostream& outputStream ) :
++  outputStream_(outputStream),
+   numCols_(numCols),
+   bandExtension_(bandExtension),
+-  pTable_(pTable),
+-  outputStream_(outputStream)
++  pTable_(pTable)
+ {
+   pBufSeq1_= new char [numCols+1];
+   pBufSeq2_= new char [numCols+1];
+@@ -563,17 +563,17 @@
+       //  cout << int ( ttDNA[ *(pChar++ ] << 4
+       //     | (ttDNA[ *(pChar++) ] << 2)
+       //     | ttDNA[ *(pChar++) ] ) << endl; 
+-      if (    (ttDNA[ *(pChar)   ]==nv)
+-           || (ttDNA[ *(pChar+1) ]==nv)
+-           || (ttDNA[ *(pChar+2) ]==nv) )
++      if (    (ttDNA[ (int) *(pChar)   ]==nv)
++           || (ttDNA[ (int) *(pChar+1) ]==nv)
++           || (ttDNA[ (int) *(pChar+2) ]==nv) )
+       {	
+ 	*i='X';
+       } // ~if   
+       else
+       {
+-	*i= gResidueNames[ ttCodon[ ttDNA[ *(pChar) ] << 4
+-				  | ttDNA[ *(pChar+1) ] << 2
+-				  | ttDNA[ *(pChar+2) ] ] ];
++	*i= gResidueNames[ ttCodon[ ttDNA[ (int) *(pChar) ] << 4
++				  | ttDNA[ (int) *(pChar+1) ] << 2
++				  | ttDNA[ (int) *(pChar+2) ] ] ];
+       } // ~else
+ 
+     } // ~for i
+@@ -983,7 +983,7 @@
+ 
+ void print( PathMatrix<PathType>& p )
+ {
+-  for (int i(0); i< p.front().size(); i++)
++  for (size_t i(0); i< p.front().size(); i++)
+   {
+     for (vector<vector<PathType> >::iterator j(p.begin());
+ 	 j!=p.end();++j)
+@@ -1249,16 +1249,16 @@
+   bandWidth_(p2Size-p1Size+1),
+   bandLength_(p1Size+1),
+   colSize_(p2Size-p1Size+1+(2*bandExtension_)),
+-  fillCell_(),
+   finalFrame1_(p1FinalFrame),
+   finalFrame2_(p2FinalFrame),
+   numFrames1_((p1Trans[1]==NULL)?1:gNumReadingFrames),
+   numFrames2_((p2Trans[1]==NULL)?1:gNumReadingFrames),
++  fillCell_(),
++  getScore_(scoreTable),
+   v1_(colSize_, veryBadScore3D ), 
+   v2_(colSize_, veryBadScore3D ),
+   pLast_(&v1_),
+-  pCurrent_(&v2_),
+-  getScore_(scoreTable)
++  pCurrent_(&v2_)
+ {
+   
+   p1_[0] = p1Trans[0];
+@@ -1287,7 +1287,7 @@
+ {
+ 
+   //  ScoreType lastScore, prevFrameScore1, prevFrameScore2;
+-  int i,j,k,l;
++  int i,j;
+ 
+   matrix.resize(bandLength_, vector<PathType3D>(colSize_) );
+ 
diff --git a/biology/ssaha/files/patch-MatchAligner.h b/biology/ssaha/files/patch-MatchAligner.h
new file mode 100644
index 000000000000..1eafad595c91
--- /dev/null
+++ b/biology/ssaha/files/patch-MatchAligner.h
@@ -0,0 +1,33 @@
+--- ./QueryManager/MatchAligner.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/MatchAligner.h	2008-06-12 15:39:31.000000000 -0300
+@@ -315,13 +315,13 @@
+ 
+   static char getCodon( const char* pChar )
+   {
+-    return (  (    (ttDNA[ *pChar ] ==nv)
+-		   || (ttDNA[ *(pChar+1) ] ==nv)
+-		   || (ttDNA[ *(pChar+2) ] ==nv) )
++    return (  (    (ttDNA[ (int) *pChar ] ==nv)
++		   || (ttDNA[ (int) *(pChar+1) ] ==nv)
++		   || (ttDNA[ (int) *(pChar+2) ] ==nv) )
+ 	      ? 'X'
+-	      : gResidueNames[ ttCodon[ ttDNA[ *(pChar) ] << 4
+-				      | ttDNA[ *(pChar+1) ] << 2
+-				      | ttDNA[ *(pChar+2) ] ] ] );
++	      : gResidueNames[ ttCodon[ ttDNA[ (int) *(pChar) ] << 4
++				      | ttDNA[ (int) *(pChar+1) ] << 2
++				      | ttDNA[ (int) *(pChar+2) ] ] ] );
+   } // ~getCodon
+ 
+ 
+@@ -519,8 +519,8 @@
+   : public vector<vector<PATH_TYPE> >
+ {
+ public:
+-  typedef pair<vector<vector<PATH_TYPE> >::iterator,
+-    vector<PATH_TYPE>::iterator> CellIterator;
++  typedef pair<typename vector<vector<PATH_TYPE> >::iterator,
++    typename vector<PATH_TYPE>::iterator> CellIterator;
+ 
+   template<class MATRIX_FILLER> ScoreType fillIn( MATRIX_FILLER& doMatrix )
+   {
diff --git a/biology/ssaha/files/patch-MatchStore.h b/biology/ssaha/files/patch-MatchStore.h
new file mode 100644
index 000000000000..076639489869
--- /dev/null
+++ b/biology/ssaha/files/patch-MatchStore.h
@@ -0,0 +1,54 @@
+--- ./QueryManager/MatchStore.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/MatchStore.h	2008-06-12 15:39:31.000000000 -0300
+@@ -93,20 +93,20 @@
+   virtual SequenceNumber getSubjectNum( void ) const 
+     { return subjectNum_; }
+   //  virtual inline string  getSubjectName( void ) const;
+-  virtual inline const char*  getSubjectName( void ) const;
++  virtual const char*  getSubjectName( void ) const;
+   virtual SequenceOffset getSubjectStart( void ) const 
+     { return subjectStart_; }
+   virtual SequenceOffset getSubjectEnd( void ) const 
+     { return subjectEnd_; }
+ 
+-  virtual inline SequenceNumber getQueryNum( void ) const;
+-  virtual inline string         getQueryName( void ) const;
++  virtual SequenceNumber getQueryNum( void ) const;
++  virtual string         getQueryName( void ) const;
+   virtual SequenceOffset getQueryStart( void ) const 
+     { return queryStart_; }
+   virtual SequenceOffset getQueryEnd( void ) const 
+     { return queryEnd_; }
+   
+-  virtual inline int  getQuerySize( void ) const; 
++  virtual int  getQuerySize( void ) const; 
+   virtual int  getNumBases(void ) const 
+     { return numBases_; }
+   virtual bool isQueryForward( void ) const 
+@@ -127,7 +127,6 @@
+              SequenceOffset subjectEnd,
+              bool isQueryForward,
+              bool isSubjectForward ):
+-    myStore_( myStore ),
+     subjectNum_( subjectNum ),  
+     numBases_( numBases ),  
+     queryStart_( queryStart ),
+@@ -135,7 +134,8 @@
+     subjectStart_( subjectStart ),
+     subjectEnd_( subjectEnd ),
+     isQueryForward_( isQueryForward ),
+-    isSubjectForward_( isSubjectForward ){}
++    isSubjectForward_( isSubjectForward ),
++    myStore_( myStore )   {}
+ 
+   SequenceNumber subjectNum_;
+   SequenceOffset numBases_;
+@@ -444,7 +444,7 @@
+   ( 
+     unsigned int maxToSort = 1<<30,
+     double partialThreshold = 0.0
+-  ) : sorter_(), maxToSort_(maxToSort), partialThreshold_(partialThreshold) {}
++  ) : maxToSort_(maxToSort), partialThreshold_(partialThreshold), sorter_()  {}
+   // TBD should be virtual???
+   void operator()(MatchStore& store )
+   {
diff --git a/biology/ssaha/files/patch-MatchStoreGapped.h b/biology/ssaha/files/patch-MatchStoreGapped.h
new file mode 100644
index 000000000000..7252f06a6ad8
--- /dev/null
+++ b/biology/ssaha/files/patch-MatchStoreGapped.h
@@ -0,0 +1,25 @@
+--- ./QueryManager/MatchStoreGapped.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/MatchStoreGapped.h	2008-06-12 15:39:31.000000000 -0300
+@@ -57,7 +57,8 @@
+ {
+  public:
+   MatchAlgorithm( int numRepeats ) : 
+-    numRepeats_( numRepeats ), sortNeeded_(true) {}
++    sortNeeded_(true), numRepeats_( numRepeats )  {}
++  virtual ~MatchAlgorithm() {};
+   void operator()  
+     ( WordSequence& querySeq, 
+       MatchAdder& addMatch, 
+@@ -82,10 +83,10 @@
+  public:
+   MatchAlgorithmGapped
+     ( int maxGap, int maxInsert, int minToProcess, int numRepeats ):
++    MatchAlgorithm( numRepeats ),
+     maxGap_( maxGap ),
+     maxInsert_( maxInsert ), 
+-    minToProcess_( minToProcess ),
+-    MatchAlgorithm( numRepeats )
++    minToProcess_( minToProcess )
+     {}
+ 
+   virtual void generateMatches
diff --git a/biology/ssaha/files/patch-MatchStoreUngapped.h b/biology/ssaha/files/patch-MatchStoreUngapped.h
new file mode 100644
index 000000000000..f71815fa673c
--- /dev/null
+++ b/biology/ssaha/files/patch-MatchStoreUngapped.h
@@ -0,0 +1,13 @@
+--- ./QueryManager/MatchStoreUngapped.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/MatchStoreUngapped.h	2008-06-12 15:39:31.000000000 -0300
+@@ -60,8 +60,8 @@
+  public:
+   MatchAlgorithmUngapped
+     ( int minToProcess, int numRepeats ):
+-    minToProcess_( minToProcess ),
+-    MatchAlgorithm( numRepeats )
++    MatchAlgorithm( numRepeats ),
++    minToProcess_( minToProcess )
+     {}
+ 
+   virtual void generateMatches
diff --git a/biology/ssaha/files/patch-QueryManager.cpp b/biology/ssaha/files/patch-QueryManager.cpp
new file mode 100644
index 000000000000..bb80ea676c1d
--- /dev/null
+++ b/biology/ssaha/files/patch-QueryManager.cpp
@@ -0,0 +1,54 @@
+--- ./QueryManager/QueryManager.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/QueryManager.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -164,8 +164,8 @@
+ // MatchPolicy member function definitions
+ 
+ MatchPolicy::MatchPolicy( HashTableGeneric& subjectTable ) :
+-  subjectTable_( subjectTable ), 
+-  queryWordLength_( subjectTable.getWordLength() ) 
++  queryWordLength_( subjectTable.getWordLength() ),
++  subjectTable_( subjectTable )
+ {}
+ 
+ 
+@@ -203,8 +203,8 @@
+ 
+ MatchPolicyProteinProtein::MatchPolicyProteinProtein
+ ( HashTablePackedProtein& subjectTable ) :
+-subjectTable_( subjectTable ),
+-MatchPolicy( subjectTable )
++MatchPolicy( subjectTable ),
++subjectTable_( subjectTable )
+ {
+ 
+   subjectTable_.setQueryProtein();
+@@ -386,9 +386,9 @@
+   QueryManager::QueryManager
+   ( SequenceReader& querySeqs,  
+     HashTableGeneric& subjectSeqs, ostream& monitoringStream ) :
+-   queryReader_( querySeqs ), 
+    subjectTable_(  subjectSeqs ), 
+-   monitoringStream_( monitoringStream )
++   monitoringStream_( monitoringStream ),
++   queryReader_( querySeqs ) 
+    {
+      monitoringStream_ << "constructing QueryManager\n";
+ 
+@@ -518,7 +518,7 @@
+ 
+       task( store );
+ 
+-      if ( queryReader_.getLastSequenceNumber() == queryEnd ) break;
++      if ( (int)queryReader_.getLastSequenceNumber() == queryEnd ) break;
+ 
+       // clear the query sequence ready to read in next query
+       querySeqFwd.clear();
+@@ -530,7 +530,7 @@
+     } // ~while
+     while ( numBasesInLast != -1 );
+ 
+-    if (    ( queryReader_.getLastSequenceNumber() < queryEnd  )
++    if (    ( (int)queryReader_.getLastSequenceNumber() < queryEnd  )
+          && ( queryEnd != - 1 ) )
+     {
+       monitoringStream_ << "Info: requested final sequence (" << queryEnd
diff --git a/biology/ssaha/files/patch-QueryManager.h b/biology/ssaha/files/patch-QueryManager.h
new file mode 100644
index 000000000000..fef80e7b3865
--- /dev/null
+++ b/biology/ssaha/files/patch-QueryManager.h
@@ -0,0 +1,19 @@
+--- ./QueryManager/QueryManager.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/QueryManager.h	2008-06-12 15:39:31.000000000 -0300
+@@ -145,6 +145,7 @@
+     //    readFrame_(0), 
+     pStore_(NULL), 
+     subjectTable_( subjectTable ) {}
++  virtual ~MatchAdder() {};
+   virtual void operator()(  SequenceNumber subjectNum,
+ 			    SequenceOffset numBases,
+ 			    SequenceOffset queryStart,
+@@ -172,7 +173,7 @@
+ {
+ public:
+   MatchAdderImp( HashTableGeneric& subjectTable ) : 
+-    lastSubjectNum_(0), name_(), MatchAdder( subjectTable ) {}
++    MatchAdder( subjectTable ), name_(), lastSubjectNum_(0)  {}
+     virtual void operator()(  SequenceNumber subjectNum,
+ 				     SequenceOffset numBases,
+ 				     SequenceOffset queryStart,
diff --git a/biology/ssaha/files/patch-README b/biology/ssaha/files/patch-README
new file mode 100644
index 000000000000..e1a8461090b7
--- /dev/null
+++ b/biology/ssaha/files/patch-README
@@ -0,0 +1,13 @@
+--- ./Binary/README.orig	2004-08-25 11:35:58.000000000 -0300
++++ ./Binary/README	2008-06-12 15:39:31.000000000 -0300
+@@ -34,6 +34,10 @@
+ 
+ Patched for linux/g++3.2.2 25/8/4 AWS.
+ 
++This version was patched for Linux/GCC 4.0.2 and Mac OS X/GCC 4.0.1 by
++Conrad Halling on 26 January 2006. See http://www.bifx.org/SSAHA/index.html
++for more information.
++
+ 1. To compile the main ssaha executable
+ 
+ make ssaha
diff --git a/biology/ssaha/files/patch-SSAHAMain.cpp b/biology/ssaha/files/patch-SSAHAMain.cpp
new file mode 100644
index 000000000000..c65c50796f9f
--- /dev/null
+++ b/biology/ssaha/files/patch-SSAHAMain.cpp
@@ -0,0 +1,48 @@
+--- ./Global/SSAHAMain.cpp.orig	2004-03-01 14:12:38.000000000 -0300
++++ ./Global/SSAHAMain.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -86,7 +86,8 @@
+ Copyright (C) 2004 by Genome Research Limited\n\
+ This software is released under the terms of version 2 of the GNU General\n\
+ Public Licence, as published by the Free Software Foundation.\n\
+-This is SSAHA Version 3.2, released 1st March 2004.\n\n";
++This is SSAHA Version 3.2, released 1st March 2004,\n\
++patched 26 January 2006.\n\n";
+ 
+   Timer timeStamp;
+ 
+@@ -623,7 +624,7 @@
+     {
+       pHashTable = new HashTablePacked( cerr, queryParams.saveName );
+       if (    ( queryParams.wordLength <= 0 )
+-	      || ( queryParams.wordLength*gBaseBits > ( 8*sizeof(Word)) -1 ) )
++	      || ( (size_t) queryParams.wordLength*gBaseBits > ( 8*sizeof(Word)) -1 ) )
+       {
+ 	cerr << "Warning: word length (" << queryParams.wordLength 
+ 	     << ") outside valid range (0 to " 
+@@ -656,7 +657,7 @@
+       } // ~if
+ 
+       if (    ( queryParams.wordLength <= 0 )
+-	      || ( queryParams.wordLength*gResidueBits > ( 8*sizeof(Word)) -1 ) )
++	      || ( (size_t) queryParams.wordLength*gResidueBits > ( 8*sizeof(Word)) -1 ) )
+       {
+ 	cerr << "Warning: word length (" << queryParams.wordLength 
+ 	     << ") outside valid range (0 to " 
+@@ -782,7 +783,7 @@
+   cerr << "Info: would expect " << expectedNumHits 
+          << " hits per word for a random database of this size." << endl;
+ 
+-  queryParams.maxStore=1+(int)(expectedNumHits*queryParams.maxStore);
++  queryParams.maxStore=(int)(expectedNumHits*queryParams.maxStore);
+ 
+   cerr << "Info: will ignore hits on words that occur more than " 
+        << queryParams.maxStore << " times in the database." << endl;
+@@ -1151,7 +1152,7 @@
+     } // ~if
+     dirent* dirEntry;
+     string entryName;
+-    while( dirEntry = readdir(pDir) )
++    while( 0 != ( dirEntry = readdir(pDir) ) )
+     {
+       entryName = (string) dirEntry->d_name;
+       if ((entryName == ".")||(entryName=="..")) continue;
diff --git a/biology/ssaha/files/patch-SSAHAMain.h b/biology/ssaha/files/patch-SSAHAMain.h
new file mode 100644
index 000000000000..ee646b476fc1
--- /dev/null
+++ b/biology/ssaha/files/patch-SSAHAMain.h
@@ -0,0 +1,19 @@
+--- ./Global/SSAHAMain.h.orig	2004-03-01 13:51:28.000000000 -0300
++++ ./Global/SSAHAMain.h	2008-06-12 15:39:31.000000000 -0300
+@@ -131,7 +131,7 @@
+   -1,        // int    queryEnd; 
+   -1,        // int    wordLength;
+   -1,        // int    stepLength;
+-  100000,    // int    maxToStore; 
++  10000,     // int    maxToStore; 
+   1,         // int    minToPrint;
+   -1,        // int    maxGap;
+   0,         // int    maxInsert;
+@@ -174,6 +174,7 @@
+ 
+   CommandLineArg( const string& nameLong, const string& nameShort ) :
+     nameLong_( nameLong ), nameShort_( nameShort ) {}
++  virtual ~CommandLineArg() {};  // base class with virtual functions requires virtual constructor
+   // Is the current argument equal to 'my' argument name?
+   virtual bool isThisMe( const string& argName )
+   { 
diff --git a/biology/ssaha/files/patch-SequenceEncoder.cpp b/biology/ssaha/files/patch-SequenceEncoder.cpp
new file mode 100644
index 000000000000..5832a96a40bb
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceEncoder.cpp
@@ -0,0 +1,75 @@
+--- ./SequenceReader/SequenceEncoder.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./SequenceReader/SequenceEncoder.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -54,10 +54,10 @@
+     ostream& monitoringStream):
+     monitoringStream_( monitoringStream ),
+     tt_(tt), sourceData_( sourceData ), bitsPerSymbol_(bitsPerSymbol),
++    symbolMask_((1<<bitsPerSymbol)-1),
+     pState_( new SequenceReaderModeIgnore( monitoringStream ) ),
+     wordFlag_(0),
+-    doubleBitShift_(bitsPerSymbol<<1),
+-    symbolMask_((1<<bitsPerSymbol)-1)
++    doubleBitShift_(bitsPerSymbol<<1)
+   //    numSymbolPairs_(wordLength>>1),
+   //   oddNumSymbols_(wordLength%1==1),
+   { 
+@@ -71,13 +71,13 @@
+   ett_( rhs.ett_ ),
+   sourceData_( rhs.sourceData_ ),
+   bitsPerSymbol_( rhs.bitsPerSymbol_ ),
++  symbolMask_(rhs.symbolMask_),
+   wordLength_( rhs.wordLength_ ),
+     //  pSeq_( rhs.pSeq_ ),// don't want 2 encoders linking to same seq
+   pState_( rhs.pState_->clone() ),
+   wordFlag_(0),
+   //  numSymbolPairs_(rhs.numSymbolPairs_),
+   //  oddNumSymbols_(rhs.oddNumSymbols_),
+-  symbolMask_(rhs.symbolMask_),
+   doubleBitShift_(rhs.doubleBitShift_)
+   {
+     monitoringStream_ << "copy constructing SequenceEncoder" << endl;
+@@ -218,7 +218,7 @@
+   {
+     pTemp = (uchar*)p;
+     //    cout << basesInLast << " doing odd char at end " << *pTemp << endl;
+-    encodeChar( *p, thisWord, wordFlag_, basesInLast );
++    encodeChar( *pTemp, thisWord, wordFlag_, basesInLast );
+   }
+ 
+   pSeq_->setNumBasesInLast(basesInLast);
+@@ -453,7 +453,7 @@
+ 
+     for( ; i!=lastWord ; ++i )
+     {
+-      if (toCarry!=~0)
++      if (toCarry!=(Word)~0)
+       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
+ 	? flaggedChar
+ 	: ( toCarry | (((*i) >> (4*gCodonBits + 2*gBaseBits))&maskBase ));
+@@ -488,7 +488,7 @@
+ 
+     for( ; i!=lastWord ; ++i )
+     {
+-      if (toCarry!=~0)
++      if (toCarry!=(Word)~0)
+       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
+ 	? flaggedChar
+ 	: ( toCarry | (((*i) >> (4*gCodonBits + gBaseBits))&mask2Bases ));
+@@ -610,7 +610,7 @@
+     do
+     {
+       i--;
+-      if (toCarry!=~0)
++      if (toCarry!=(Word)~0)
+       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
+ 	? flaggedChar
+ 	: ( toCarry | ( ((*i) & mask2Bases ) << gBaseBits ) );
+@@ -650,7 +650,7 @@
+     do
+     {
+       i--;
+-      if (toCarry!=~0)
++      if (toCarry!=(Word)~0)
+       (*pCodon++) = ( ((*i)&gCursedWord)|lastWordFlag )
+ 	? flaggedChar
+ 	: ( toCarry | ( ((*i) & maskBase ) << (2*gBaseBits) ) );
diff --git a/biology/ssaha/files/patch-SequenceReader.cpp b/biology/ssaha/files/patch-SequenceReader.cpp
new file mode 100644
index 000000000000..356c6e8363d9
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReader.cpp
@@ -0,0 +1,20 @@
+--- ./SequenceReader/SequenceReader.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./SequenceReader/SequenceReader.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -179,7 +179,7 @@
+ 
+   for ( ; i != reverseBuffer_.end() ; i++, j-- )
+   {
+-    *i= reverseChar[ *j ];
++    *i= reverseChar[ (int) *j ];
+     //    cout << "char: " << (int)*j << *j << " - " << (int)*i << *i << endl;
+   }
+ 
+@@ -356,7 +356,7 @@
+       throw SSAHAException
+ 	("Requested seq start exceeds requested seq end in SourceReaderIndex::extractSource");
+   } // ~if
+-  else if (seqEnd>lastSourceSeq_.size() )
++  else if (seqEnd>(int)lastSourceSeq_.size() )
+   {
+     cout << seqEnd << " " << lastSourceSeq_.size() << endl;
+       throw SSAHAException
diff --git a/biology/ssaha/files/patch-SequenceReader.h b/biology/ssaha/files/patch-SequenceReader.h
new file mode 100644
index 000000000000..c230fa08cbd8
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReader.h
@@ -0,0 +1,11 @@
+--- ./SequenceReader/SequenceReader.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./SequenceReader/SequenceReader.h	2008-06-12 15:39:31.000000000 -0300
+@@ -264,6 +264,8 @@
+     pReader_( rhs.pReader_ ),
+     seqNum_( rhs.seqNum_ ) {}
+ 
++    // A virtual destructor is required because this is a base class.
++    virtual ~SequenceReaderPrinter() {};
+ 
+     SequenceReaderPrinter& operator()( SequenceNumber inSeqNum )
+     { 
diff --git a/biology/ssaha/files/patch-SequenceReaderFasta.cpp b/biology/ssaha/files/patch-SequenceReaderFasta.cpp
new file mode 100644
index 000000000000..eaf3a2a5477f
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReaderFasta.cpp
@@ -0,0 +1,32 @@
+--- ./SequenceReader/SequenceReaderFasta.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./SequenceReader/SequenceReaderFasta.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -135,9 +135,9 @@
+     seqStopChar_( rhs.seqStopChar_ ),
+     pInputFileStream_( new ifstream( rhs.fileName_.c_str() ) ),
+     fileName_( rhs.fileName_.c_str() ),
+-    seqPositions_( rhs.seqPositions_ ),
+     //   lastSourceSeqNum_(0),
+-    pEncoder_( rhs.pEncoder_->clone() )
++    pEncoder_( rhs.pEncoder_->clone() ),
++    seqPositions_( rhs.seqPositions_ )
+   {
+     monitoringStream_ << "copy constructing SequenceReaderFile" << this 
+ 		      << endl;
+@@ -603,7 +603,7 @@
+       throw SSAHAException
+ 	("Requested seq start exceeds requested seq end in SequenceReaderFile::extractSource");
+   } // ~if
+-  else if (seqEnd>lastSourceSeq_.size() )
++  else if (seqEnd>(SequenceOffset)lastSourceSeq_.size() )
+   {
+       throw SSAHAException
+ 	("Requested last byte exceeds end of seq in SequenceReaderFile::extractSource");
+@@ -628,7 +628,7 @@
+   computeNumSequencesInFile(); // ensure have scanned to end of file
+   fileFile << fileName_ << endl;
+   SeqIndexInfo* pIndex = new SeqIndexInfo[seqPositions_.size()];
+-  for (int i(0) ; i < seqPositions_.size() ; i++)
++  for (unsigned int i(0) ; i < seqPositions_.size() ; i++)
+   {
+     pIndex[i].fileNum=fileNumber;
+     pIndex[i].seqPos=seqPositions_[i];
diff --git a/biology/ssaha/files/patch-SequenceReaderFasta.h b/biology/ssaha/files/patch-SequenceReaderFasta.h
new file mode 100644
index 000000000000..a2988fbb91d8
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReaderFasta.h
@@ -0,0 +1,11 @@
+--- ./SequenceReader/SequenceReaderFasta.h.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./SequenceReader/SequenceReaderFasta.h	2008-06-12 15:39:31.000000000 -0300
+@@ -55,7 +55,7 @@
+ {
+  public:
+   SequenceReaderFileState( SequenceNumber lsn, std::streampos fp ) :
+-  filePos_(fp),  SequenceReaderState(lsn) {}
++  SequenceReaderState(lsn), filePos_(fp)  {}
+   // no point in making this private as it's const
+   const std::streampos filePos_;
+ };
diff --git a/biology/ssaha/files/patch-SequenceReaderFilter.h b/biology/ssaha/files/patch-SequenceReaderFilter.h
new file mode 100644
index 000000000000..38c65183fb7a
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReaderFilter.h
@@ -0,0 +1,20 @@
+--- ./SequenceReader/SequenceReaderFilter.h.orig	2004-03-01 13:51:30.000000000 -0300
++++ ./SequenceReader/SequenceReaderFilter.h	2008-06-12 15:39:31.000000000 -0300
+@@ -80,7 +80,7 @@
+ 
+   size_t max( void ) const 
+   { 
+-    int max(0);
++    size_t max(0);
+     for (vector<vector<string*> >::const_iterator i(bins_.begin()); i!= bins_.end(); i++ )
+       if (i->size()>max) max=i->size();
+     return max;
+@@ -109,7 +109,7 @@
+  public:
+   SequenceReaderFilterState
+     ( SequenceNumber lsn, SequenceReader* ps ) :
+-    pState_(ps->saveState()), SequenceReaderState(lsn) {}
++    SequenceReaderState(lsn), pState_(ps->saveState())  {}
+   virtual ~SequenceReaderFilterState() {} //delete pState_;
+   // no point in making this private as it's const
+   // this is state info for *ps, whatever it is
diff --git a/biology/ssaha/files/patch-SequenceReaderLocal.cpp b/biology/ssaha/files/patch-SequenceReaderLocal.cpp
new file mode 100644
index 000000000000..f8629b6ffafe
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReaderLocal.cpp
@@ -0,0 +1,28 @@
+--- ./SequenceReader/SequenceReaderLocal.cpp.orig	2004-03-01 13:51:30.000000000 -0300
++++ ./SequenceReader/SequenceReaderLocal.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -46,10 +46,10 @@
+   // and seqNames_
+ SequenceReaderLocal::SequenceReaderLocal
+ ( SequenceReader& seqFile, int wordLength, ostream& monitoringStream ) :
+-sourceData_( seqFile.getSourceDataType() ),
++SequenceReader( monitoringStream ),
+ wordLength_( wordLength ),
+ bitsPerSymbol_( seqFile.getBitsPerSymbol() ),
+-SequenceReader( monitoringStream )
++sourceData_( seqFile.getSourceDataType() )
+ {
+   monitoringStream_ 
+     << "constructing SequenceReaderLocal from SequenceReader" << endl;
+@@ -72,10 +72,10 @@
+ 
+ SequenceReaderLocal::SequenceReaderLocal
+ ( int wordLength, int bitsPerSymbol, ostream& monitoringStream ) :
+-sourceData_( gUnknownData ),
++SequenceReader( monitoringStream ),
+ wordLength_( wordLength ),
+ bitsPerSymbol_( bitsPerSymbol ),
+-SequenceReader( monitoringStream )
++sourceData_( gUnknownData )
+ {
+   monitoringStream_ 
+     << "constructing empty SequenceReaderLocal" << endl;
diff --git a/biology/ssaha/files/patch-SequenceReaderMulti.cpp b/biology/ssaha/files/patch-SequenceReaderMulti.cpp
new file mode 100644
index 000000000000..1e160249d180
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReaderMulti.cpp
@@ -0,0 +1,30 @@
+--- ./SequenceReader/SequenceReaderMulti.cpp.orig	2004-03-01 13:51:30.000000000 -0300
++++ ./SequenceReader/SequenceReaderMulti.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -166,7 +166,7 @@
+   {
+     if (thisReader_->allSeqsRead_)
+     {
+-      if ( currentSeqNum_ <= thisReader_->size_ )
++      if ( currentSeqNum_ <= (SequenceNumber)thisReader_->size_ )
+       {
+ 	//	assert( thisReader_->ptr_->findSequence( currentSeqNum_ ) == true );
+ 	lastSequenceNumber_ = --seqNum; // last read = 1 behind current
+@@ -240,7 +240,7 @@
+     for ( vector<SeqReaderInfo>::iterator i = allReaders_.begin(); 
+           i != allReaders_.end(); i++ )
+     {
+-      if ( seqNum <= i->size_ ) { thisReader_ = i; break; } // %%%%%
++      if ( seqNum <= (SequenceNumber)i->size_ ) { thisReader_ = i; break; } // %%%%%
+       seqNum -= i->size_;
+     } // ~for i
+ 
+@@ -276,7 +276,8 @@
+   {
+     DEBUG_L2( "SequenceReaderMulti::getNextSequence" );
+ 
+-    int numInLast;
++    int numInLast = -1;  // Initialized to avoid -Wall possibly used before initialized warning.
++                         // The algorithm should be checked carefully.
+ 
+     while 
+       (    ( thisReader_ 
diff --git a/biology/ssaha/files/patch-SequenceReaderMulti.h b/biology/ssaha/files/patch-SequenceReaderMulti.h
new file mode 100644
index 000000000000..72f079f97add
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReaderMulti.h
@@ -0,0 +1,13 @@
+--- ./SequenceReader/SequenceReaderMulti.h.orig	2004-03-01 13:51:30.000000000 -0300
++++ ./SequenceReader/SequenceReaderMulti.h	2008-06-12 15:39:31.000000000 -0300
+@@ -81,8 +81,9 @@
+     ( SequenceNumber lsn, 
+       vector<SeqReaderInfo>::iterator tr,
+       SequenceReaderState* ps ) :
++  SequenceReaderState(lsn),
+   thisReader_(tr),  
+-    pState_(ps), SequenceReaderState(lsn) {}
++  pState_(ps)  {}
+   virtual ~SequenceReaderMultiState() {} //delete pState_;
+   // no point in making this private as it's const
+   const vector<SeqReaderInfo>::iterator thisReader_;
diff --git a/biology/ssaha/files/patch-SequenceReaderString.h b/biology/ssaha/files/patch-SequenceReaderString.h
new file mode 100644
index 000000000000..a35c0b7cfc01
--- /dev/null
+++ b/biology/ssaha/files/patch-SequenceReaderString.h
@@ -0,0 +1,26 @@
+--- ./SequenceReader/SequenceReaderString.h.orig	2004-03-01 13:51:30.000000000 -0300
++++ ./SequenceReader/SequenceReaderString.h	2008-06-12 15:39:31.000000000 -0300
+@@ -65,9 +65,9 @@
+   // NB SequenceReaderStringBase takes ownership of *pEncoder
+   SequenceEncoder* pEncoder,
+   ostream& monitoringStream = cerr ) :
++  SequenceReader( monitoringStream ),
+   sequenceString_( sequenceString ), 
+-  pEncoder_( pEncoder ),
+-  SequenceReader( monitoringStream )
++  pEncoder_( pEncoder )
+ {
+   monitoringStream_ << "constructing SequenceReaderStringBase" << endl;
+ } // constructor
+@@ -78,9 +78,9 @@
+   // TYPE  NAME  IN/OUT COMMENT
+   // Returns: TYPE COMMENT
+ SequenceReaderStringBase( const SequenceReaderStringBase& rhs ) :
++SequenceReader( rhs.monitoringStream_ ),
+ sequenceString_( rhs.sequenceString_ ), 
+-pEncoder_( rhs.pEncoder_->clone() ),
+-SequenceReader( rhs.monitoringStream_ )
++pEncoder_( rhs.pEncoder_->clone() )
+ {
+   monitoringStream_ << "copy constructing SequenceReaderStringBase" << endl;
+ } // copy constructor
diff --git a/biology/ssaha/files/patch-makefile b/biology/ssaha/files/patch-makefile
new file mode 100644
index 000000000000..0154077a92ce
--- /dev/null
+++ b/biology/ssaha/files/patch-makefile
@@ -0,0 +1,15 @@
+--- ./Binary/makefile.orig	2008-06-12 16:00:19.000000000 -0300
++++ ./Binary/makefile	2008-06-12 16:00:43.000000000 -0300
+@@ -11,10 +11,10 @@
+ # copy of the SSAHA directory structure you should be able to make files
+ # straight away.
+ # 
+-# SSAHA_TOP_DIR=$(SSAHA_DIR?$(SSAHA_DIR):$(PWD)/../)
++SSAHA_TOP_DIR=$(PWD)/../
+ # Above is a nice idea, but syntax doesn't work for all versions of make
+ # so must define CURRENT_SSAHA_VERSION, eg in your .cshrc file - TC 14.3.01
+-SSAHA_TOP_DIR=$(CURRENT_SSAHA_VERSION)
++# SSAHA_TOP_DIR=$(CURRENT_SSAHA_VERSION)
+ 
+ GLOBAL_DIR=${SSAHA_TOP_DIR}/Global
+ SEQ_DIR=${SSAHA_TOP_DIR}/SequenceReader
diff --git a/biology/ssaha/files/patch-testHashTableNoOverlap.cpp b/biology/ssaha/files/patch-testHashTableNoOverlap.cpp
new file mode 100644
index 000000000000..721e03ae9134
--- /dev/null
+++ b/biology/ssaha/files/patch-testHashTableNoOverlap.cpp
@@ -0,0 +1,178 @@
+--- ./HashTable/testHashTableNoOverlap.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./HashTable/testHashTableNoOverlap.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -70,10 +70,10 @@
+   cout << "     Test of class HashTable" << endl << endl;
+   cout << "*******************************************" << endl << endl;
+ 
+-  int numSeqs = 10;
+-  int seqSize = 100;
+-  int wordLength = 10;
+-  int maxHits = 50;
++  unsigned int numSeqs = 10;
++  unsigned int seqSize = 100;
++  unsigned int wordLength = 10;
++  unsigned int maxHits = 50;
+ 
+   // Generate a random sequence of (numSeqs*seqSize) base pairs ...
+   // 1128 is the seed value for the random number generator
+@@ -116,7 +116,7 @@
+   // so we are checking that all sequence data 'finds itself' in the hash
+   // table in the correct position
+ 
+-  for ( int i(1) ; i <= numSeqs ; i++ )
++  for ( unsigned int i(1) ; i <= numSeqs ; i++ )
+   { // for each sequence in testReader ...
+     testReader.getNextSequence(seq,wordLength);
+ 
+@@ -131,7 +131,7 @@
+     cout << seq.getNumBasesInLast() << "!!\n";
+     // ... go through the Words in the sequence one by one and look
+     //    for matches in the hash table
+-    for ( int j(0) ; j < (seqSize/wordLength) ; j++ )
++    for ( unsigned int j(0) ; j < (seqSize/wordLength) ; j++ )
+     {
+        cout << j << " " << printBase(seq[j],wordLength) << endl; 
+       
+@@ -146,7 +146,7 @@
+        // ... and that the sequence number and offset for the hit are OK
+ 
+        assert(hits[0].subjectNum == i );
+-       assert(hits[0].diff == j*wordLength );
++       assert((unsigned int)hits[0].diff == j*wordLength );
+        assert(hits[0].queryPos == 1);
+  
+        hits.clear();
+@@ -157,12 +157,12 @@
+     testHash.matchWord(seq,hits); 
+     cout << hits.size() << "!!!!!\n";
+     assert( hits.size() == (seqSize/wordLength) );
+-    for ( int j(0) ; j < hits.size() ; j ++ )
++    for ( unsigned int j(0) ; j < hits.size() ; j ++ )
+     {
+ 
+       assert(hits[j].subjectNum == i);
+       assert(hits[j].diff   == 0);
+-      assert(hits[j].queryPos == 1 + ( j * wordLength ) );
++      assert((unsigned int)hits[j].queryPos == 1 + ( j * wordLength ) );
+      
+     } // ~for j
+ 
+@@ -194,7 +194,7 @@
+   assert( testLoad.isInitialized() == true );
+   
+   // and that word length matches original
+-  assert( testLoad.getWordLength() == wordLength );
++  assert( (unsigned int)testLoad.getWordLength() == wordLength );
+ 
+   testLoad.setMaxNumHits( testHash.getMaxNumHits() );
+ 
+@@ -208,7 +208,7 @@
+   // and new hash tables, storing the resulting hits in hitsOrig and
+   // hitsCopy respectively.
+ 
+-  for ( int i(0) ; i < numSeqs ; i++ )
++  for ( unsigned int i(0) ; i < numSeqs ; i++ )
+   {
+ 
+     // ... check that the name strings match 
+@@ -258,7 +258,7 @@
+   HashTable   shiftHash(cout);
+   creator.createHashTable(shiftHash,shiftReader,wordLength,maxHits);
+ 
+-  for ( int i(0) ; i < wordLength ; i++ )
++  for ( unsigned int i(0) ; i < wordLength ; i++ )
+   {
+     testSeq = testSeq.substr(1); // delete first character
+     { // braces ensure a new instance is created each time round loop
+@@ -460,7 +460,7 @@
+     SequenceEncoderCodon encoder;
+     encoder.setWordLength(wordLength);
+ 
+-    for ( int i(1) ; i < hashTrans.getNumSequences() ; i++ )
++    for ( unsigned int i(1) ; i < hashTrans.getNumSequences() ; i++ )
+     {
+ 
+       hashTrans.getSequenceName( s1, i );
+@@ -477,7 +477,7 @@
+       assert(hashTrans.getSequenceSize(i)==hashTrans2.getSequenceSize(i));
+ 
+       assert( (((w1.size()-1) * gMaxBasesPerWord ) + w1.getNumBasesInLast())
+-	      == hashTrans.getSequenceSize(i));
++	      == (unsigned int)hashTrans.getSequenceSize(i));
+ 
+ 
+       // Sequence should produce same (nonzero) num hits in fwd direction
+@@ -573,19 +573,19 @@
+     string s, s1;
+     Word w;
+     vector<Word> subs;
+-    int wl=15;
++    unsigned int wl=15;
+ 
+     // test substitution for DNA
+     // 
+ 
+-    for (int i(0); i<wl; i++) s+="A";
++    for ( unsigned int i(0); i<wl; i++) s+="A";
+ 
+     w = makeBase(s);
+ 
+     generateSubstitutesDNA( w, subs, wl );
+     assert(subs.size()==wl);
+     
+-    for (int i(0); i<wl ; i++)
++    for (unsigned int i(0); i<wl ; i++)
+     {
+       cout << printWord(subs[i],wl) << endl;
+       s1=s;
+@@ -596,14 +596,14 @@
+     //
+     s=""; subs.clear();
+ 
+-    for (int i(0); i<wl; i++) s+="C";
++    for (unsigned int i(0); i<wl; i++) s+="C";
+ 
+     w = makeBase(s);
+ 
+     generateSubstitutesDNA( w, subs, wl );
+     assert(subs.size()==wl);
+     
+-    for (int i(0); i<wl ; i++)
++    for (unsigned int i(0); i<wl ; i++)
+     {
+       cout << printWord(subs[i],wl) << endl;
+       s1=s;
+@@ -614,14 +614,14 @@
+     //
+     s=""; subs.clear();
+ 
+-    for (int i(0); i<wl; i++) s+="G";
++    for (unsigned int i(0); i<wl; i++) s+="G";
+ 
+     w = makeBase(s);
+ 
+     generateSubstitutesDNA( w, subs, wl );
+     assert(subs.size()==wl);
+     
+-    for (int i(0); i<wl ; i++)
++    for (unsigned int i(0); i<wl ; i++)
+     {
+       cout << printWord(subs[i],wl) << endl;
+       s1=s;
+@@ -632,14 +632,14 @@
+     //
+     s=""; subs.clear();
+ 
+-    for (int i(0); i<wl; i++) s+="T";
++    for (unsigned int i(0); i<wl; i++) s+="T";
+ 
+     w = makeBase(s);
+ 
+     generateSubstitutesDNA( w, subs, wl );
+     assert(subs.size()==wl);
+     
+-    for (int i(0); i<wl ; i++)
++    for (unsigned int i(0); i<wl ; i++)
+     {
+       cout << printWord(subs[i],wl) << endl;
+       s1=s;
diff --git a/biology/ssaha/files/patch-testQueryManager.cpp b/biology/ssaha/files/patch-testQueryManager.cpp
new file mode 100644
index 000000000000..19f1ec879fd5
--- /dev/null
+++ b/biology/ssaha/files/patch-testQueryManager.cpp
@@ -0,0 +1,20 @@
+--- ./QueryManager/testQueryManager.cpp.orig	2004-03-01 13:51:29.000000000 -0300
++++ ./QueryManager/testQueryManager.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -53,7 +53,7 @@
+ void reverseString( string& seq )
+ {
+   string rc;
+-  for ( int i(0) ; i < seq.size() ; i++ )
++  for ( unsigned int i(0) ; i < seq.size() ; i++ )
+   {
+     if  ( ( seq[i] == 'A' ) || (seq[i] == 'a') ) rc = 'T' + rc; 
+     else if ( ( seq[i] == 'T' ) || (seq[i] == 't') ) rc = 'A' + rc; 
+@@ -165,7 +165,7 @@
+   int numSeqs = 3;
+   int seqSize = 1000;
+   int wordLength = 7;
+-  int maxHits = 50;
++//  int maxHits = 50;
+ 
+   // Generate a random sequence of (numSeqs*seqSize) base pairs ...
+   // 1128 is the seed value for the random number generator
diff --git a/biology/ssaha/files/patch-testSequenceReaderFasta.cpp b/biology/ssaha/files/patch-testSequenceReaderFasta.cpp
new file mode 100644
index 000000000000..3bc005bff32b
--- /dev/null
+++ b/biology/ssaha/files/patch-testSequenceReaderFasta.cpp
@@ -0,0 +1,171 @@
+--- ./SequenceReader/testSequenceReaderFasta.cpp.orig	2004-08-25 11:31:17.000000000 -0300
++++ ./SequenceReader/testSequenceReaderFasta.cpp	2008-06-12 15:39:31.000000000 -0300
+@@ -49,12 +49,12 @@
+ // ### Function Definitions ###
+ void capitalise( string& s )
+ {
+-  for ( int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]);
++  for ( unsigned int i(0) ; i < s.size() ; ++i ) s[i] = toupper(s[i]);
+ }
+ void reverseString( string& seq )
+ {
+   string rc;
+-  for ( int i(0) ; i < seq.size() ; i++ )
++  for ( unsigned int i(0) ; i < seq.size() ; i++ )
+   {
+     if  ( ( seq[i] == 'A' ) || (seq[i] == 'a') ) rc = 'T' + rc; 
+     else if ( ( seq[i] == 'T' ) || (seq[i] == 't') ) rc = 'A' + rc; 
+@@ -91,7 +91,7 @@
+   cout << "Test " << ++numTests <<": test of function getNextSequence" 
+        << endl << endl;
+ 
+-  int numSeqs = 10;
++  unsigned int numSeqs = 10;
+   int seqSize = 57;
+ 
+   // Generate a random sequence of (numSeqs*seqSize) base pairs ...
+@@ -118,7 +118,7 @@
+ 
+ 
+ 
+-  for ( int i(0) ; i < numSeqs ; i++ )
++  for ( unsigned int i(0) ; i < numSeqs ; i++ )
+   {
+   
+     testReader.getNextSequence(w,wordLength);
+@@ -188,7 +188,7 @@
+   cout << "Test " << ++numTests <<": test of getSequence" 
+        << endl << endl;
+ 
+-    int toRead = 5;
++    unsigned int toRead = 5;
+ 
+     w.clear();
+     testReader.getSequence(w,toRead,wordLength);
+@@ -242,7 +242,7 @@
+     cout << "Test " << ++numTests <<": test of random access output functions" 
+        << endl << endl;
+ 
+-    for ( int i(1) ; i <= numSeqs; i++ )
++    for ( unsigned int i(1) ; i <= numSeqs; i++ )
+     {
+       cout << testReader.getName(i) << endl;
+       cout << testReader.getSideInfo(i) << endl;
+@@ -275,7 +275,7 @@
+   // add on the end of the expected sequence string for it to match actual.
+   //  const string spareBases( wordLength - ( seqSize % wordLength ), 'A');
+ 
+-  for ( int i(0) ; i < numSeqs ; i++ )
++  for ( unsigned int i(0) ; i < numSeqs ; i++ )
+   {
+   
+     testReaderFastq.getNextSequence(w,wordLength);
+@@ -403,7 +403,7 @@
+     cout << "Test " << ++numTests <<": test of random access output functions" 
+        << endl << endl;
+ 
+-    for ( int i(1) ; i <= numSeqs; i++ )
++    for ( unsigned int i(1) ; i <= numSeqs; i++ )
+     {
+       cout << testReaderFastq.getName(i) << endl;
+       cout << testReaderFastq.getSideInfo(i) << endl;
+@@ -466,7 +466,7 @@
+     {
+ 
+       testReader.rewind();
+-      for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
++      for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
+       {
+ 		cout << i << " " << j << endl;
+         wSingle.clear(); wMulti.clear(); 
+@@ -772,7 +772,7 @@
+       
+       for (int wordLength(9); wordLength <= 12; wordLength++)
+       {
+-	for (int i(0) ; i < fiftyAs.size(); i++)
++	for (unsigned int i(0) ; i < fiftyAs.size(); i++)
+ 	{
+ 	  thisString=fiftyAs;
+ 	  thisString[i]='X';
+@@ -793,7 +793,7 @@
+ 	  stringReader.changeMode(&ignore);
+ 	  w.clear();
+ 	  numInLast = stringReader.getNextSequence(w,wordLength);
+-	  assert(numInLast==(fiftyAs.size()-1)%wordLength);
++	  assert(numInLast==(int)(fiftyAs.size()-1)%wordLength);
+ 	  assert((w.size()-1)*wordLength+numInLast==fiftyAs.size()-1);
+ 
+ 	  for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
+@@ -810,7 +810,7 @@
+ 	  numInLast = stringReader.getNextSequence(w,wordLength);
+ 	  cout << "blegh " << wordLength << " " << i  << " " << fiftyAs.size() << " " << numInLast << " " << w.size() << endl;
+ 	  
+-	  assert(numInLast==fiftyAs.size()%wordLength);
++	  assert(numInLast==(int)fiftyAs.size()%wordLength);
+ 	  assert((w.size()-1)*wordLength+numInLast==fiftyAs.size());
+ 
+ 	  for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
+@@ -828,7 +828,7 @@
+ 	  stringReader.changeMode(&tag);
+ 	  w.clear();
+ 	  numInLast = stringReader.getNextSequence(w,wordLength);
+-	  assert(numInLast==fiftyAs.size()%wordLength);
++	  assert(numInLast==(int)fiftyAs.size()%wordLength);
+ 	  assert((w.size()-1)*wordLength+numInLast==fiftyAs.size());
+ 
+ 	  for (WordSequence::iterator j(w.begin()); j!=w.end();j++)
+@@ -915,7 +915,7 @@
+       cout << "actual:   " << printResidue(W,wordLength) << endl;
+       
+ 
+-      for ( int i(0),j(0);  i < protString.size() ; i+=wordLength,j++ )
++      for ( unsigned int i(0),j(0);  i < protString.size() ; i+=wordLength,j++ )
+ 	{
+ 	  wordString = protString.substr(i, wordLength);
+ 	  cout << wordString << " " << printResidue(W[j],wordLength) << endl;
+@@ -1163,7 +1163,7 @@
+           assert (    localReader.getNumSequencesInFile()
+                ==  testReader.getNumSequencesInFile() );
+ 
+-            for ( int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
++            for ( unsigned int j(0) ; j < testReader.getNumSequencesInFile() ; j ++ ) 
+         {
+           wSingle.clear(); wMulti.clear(); 
+ 
+@@ -1244,7 +1244,7 @@
+      WordSequence seq;
+      string name;
+ 
+-     for ( int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ )
++     for ( unsigned int i(1) ; i <= filterer.getNumSequencesInFile() ; i++ )
+      {
+        filterer.getSequence(seq, i, 16);
+        filterer.getLastSequenceName(name);
+@@ -1330,12 +1330,12 @@
+        //       assert(v1==v1i);
+        //     assert(v2==v2i);
+ 
+-       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]);
+-       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]);
+-       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]);
+-       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]);
+-       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]);
+-       for ( int (i(j)) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]);
++       for ( int i(j) ; i <=seqSize ; i++ ) assert(v1[i-j]==data[i-1]);
++       for ( int i(j) ; i <=seqSize ; i++ ) assert(v2[i-j]==data[i-1]);
++       for ( int i(j) ; i <=seqSize ; i++ ) assert(v1m[i-j]==data[i-1]);
++       for ( int i(j) ; i <=seqSize ; i++ ) assert(v2m[i-j]==data[i-1]);
++       for ( int i(j) ; i <=seqSize ; i++ ) assert(v1i[i-j]==data[i-1]);
++       for ( int i(j) ; i <=seqSize ; i++ ) assert(v2i[i-j]==data[i-1]);
+ 
+      }
+      cout << "got through  first bit" << endl;
+@@ -1402,7 +1402,7 @@
+ 
+      string n1,n2;
+ 
+-     for (int i(0);i<numSeqs; i++)
++     for (unsigned int i(0);i<(unsigned int)numSeqs; i++)
+      {
+        cout << "i: " << i << endl;
+        w1.clear(); w2.clear();
diff --git a/biology/ssaha/pkg-descr b/biology/ssaha/pkg-descr
new file mode 100644
index 000000000000..97d3b05a3d8d
--- /dev/null
+++ b/biology/ssaha/pkg-descr
@@ -0,0 +1,11 @@
+SSAHA is a software tool for very fast matching and alignment of DNA
+sequences. It stands for Sequence Search and Alignment by Hashing
+Algorithm. It achieves its fast search speed by converting sequence
+information into a `hash table' data structure, which can then be
+searched very rapidly for matches.
+
+SSAHA: a fast search method for large DNA databases (2001).
+Ning Z, Cox AJ, Mullikin JC. Genome Res. 11: 1725-9. 
+PMID: 11591649
+
+WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/
diff --git a/biology/ssaha/pkg-plist b/biology/ssaha/pkg-plist
new file mode 100644
index 000000000000..c1b49b17ae24
--- /dev/null
+++ b/biology/ssaha/pkg-plist
@@ -0,0 +1,9 @@
+bin/ssaha
+%%DATADIR%%/testSSAHA.csh
+%%DATADIR%%/test.fasta
+%%DATADIR%%/test_extract.fasta
+%%DATADIR%%/test_filter.fail
+%%DATADIR%%/test_filter.fastq
+%%DATADIR%%/test_protein.fasta
+%%DATADIR%%/README
+@dirrmtry %%DATADIR%%