35 files changed, 1361 insertions, 0 deletions

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%%