1 files changed, 29 insertions, 0 deletions
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;