1 files changed, 0 insertions, 57 deletions
diff --git a/biology/ssaha/files/patch-SSAHAMain.cpp b/biology/ssaha/files/patch-SSAHAMain.cpp
deleted file mode 100644
index e0e078386263..000000000000
--- a/biology/ssaha/files/patch-SSAHAMain.cpp
+++ /dev/null
@@ -1,57 +0,0 @@
---- ./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;
-@@ -964,7 +965,7 @@ delete pQueryMode;
- 
-     } // ~else
- 
--    assert( pAligner!=false);
-+    assert(pAligner!=NULL);
- 
-     // ownership of *pAligner passes to *pPrintTask
-     pPrintTask = new MatchTaskAlign( *pQuery, *pSubjectSource, pAligner,
-@@ -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;