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702ce22305
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)
49 lines
2.0 KiB
C++
49 lines
2.0 KiB
C++
--- ./Global/SSAHAMain.cpp.orig 2004-03-01 14:12:38.000000000 -0300
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+++ ./Global/SSAHAMain.cpp 2008-06-12 15:39:31.000000000 -0300
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@@ -86,7 +86,8 @@
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Copyright (C) 2004 by Genome Research Limited\n\
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This software is released under the terms of version 2 of the GNU General\n\
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Public Licence, as published by the Free Software Foundation.\n\
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-This is SSAHA Version 3.2, released 1st March 2004.\n\n";
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+This is SSAHA Version 3.2, released 1st March 2004,\n\
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+patched 26 January 2006.\n\n";
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Timer timeStamp;
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@@ -623,7 +624,7 @@
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{
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pHashTable = new HashTablePacked( cerr, queryParams.saveName );
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if ( ( queryParams.wordLength <= 0 )
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- || ( queryParams.wordLength*gBaseBits > ( 8*sizeof(Word)) -1 ) )
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+ || ( (size_t) queryParams.wordLength*gBaseBits > ( 8*sizeof(Word)) -1 ) )
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{
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cerr << "Warning: word length (" << queryParams.wordLength
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<< ") outside valid range (0 to "
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@@ -656,7 +657,7 @@
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} // ~if
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if ( ( queryParams.wordLength <= 0 )
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- || ( queryParams.wordLength*gResidueBits > ( 8*sizeof(Word)) -1 ) )
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+ || ( (size_t) queryParams.wordLength*gResidueBits > ( 8*sizeof(Word)) -1 ) )
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{
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cerr << "Warning: word length (" << queryParams.wordLength
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<< ") outside valid range (0 to "
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@@ -782,7 +783,7 @@
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cerr << "Info: would expect " << expectedNumHits
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<< " hits per word for a random database of this size." << endl;
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- queryParams.maxStore=1+(int)(expectedNumHits*queryParams.maxStore);
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+ queryParams.maxStore=(int)(expectedNumHits*queryParams.maxStore);
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cerr << "Info: will ignore hits on words that occur more than "
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<< queryParams.maxStore << " times in the database." << endl;
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@@ -1151,7 +1152,7 @@
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} // ~if
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dirent* dirEntry;
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string entryName;
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- while( dirEntry = readdir(pDir) )
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+ while( 0 != ( dirEntry = readdir(pDir) ) )
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{
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entryName = (string) dirEntry->d_name;
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if ((entryName == ".")||(entryName=="..")) continue;
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