1 files changed, 75 insertions, 0 deletions
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) ) );