Created
December 4, 2017 18:39
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| --- A/src/hhprefilter.C 2017-08-28 14:44:32.000000000 +0200 | |
| +++ B/src/hhprefilter.C 2013-02-18 14:44:26.000000000 +0100 | |
| @@ -49,7 +49,7 @@ | |
| #define SHORT_BIAS 32768 | |
| const int NUMCOLSTATES = cs::AS219::kSize; | |
| int num_dbs = 0; // number of sequences in prefilter database file | |
| Hash<char>* doubled; | |
| @@ -808,7 +808,7 @@ | |
| void init_prefilter() | |
| { | |
| // Get Prefilter Pvalue (Evalue / Par.Dbsize) | |
| - LDB = CountSeqsInFile(db, par.dbsize); // Get DBsize but not number of chars | |
| + size_t LDB = CountSeqsInFile(db, par.dbsize); // Get DBsize but not number of chars | |
| if (par.dbsize == 0 || LDB == 0) | |
| {cerr<<endl<<"Error! Could not determine DB-size of prefilter db ("<<db<<")\n"; exit(4);} | |
| @@ -824,7 +824,7 @@ | |
| // Read in database | |
| num_dbs = 0; | |
| int len = 0; | |
| - int pos = 0; | |
| + size_t pos = 0; | |
| char word[NAMELEN]; | |
| FILE* dbf = NULL; | |
| dbf = fopen(db,"rb"); | |
| --- A/src/hhutil.C 2017-08-28 14:16:18.000000000 +0200 | |
| +++ B/src/hhutil.C 2013-02-18 14:44:26.000000000 +0100 | |
| @@ -508,11 +508,11 @@ | |
| ///////////////////////////////////////////////////////////////////////////////////// | |
| // Count the number of sequences "^>" in <file> | |
| ///////////////////////////////////////////////////////////////////////////////////// | |
| -int CountSeqsInFile(char* file, int& numseqs) | |
| +size_t CountSeqsInFile(char* file, int& numseqs) | |
| { | |
| char line[LINELEN]=""; // input line | |
| char tmp_file[NAMELEN]; | |
| - int LDB=0; | |
| + size_t LDB=0; | |
| numseqs=0; | |
| strcpy(tmp_file, file); | |
| strcat(tmp_file, ".sizes"); | |
| @@ -520,9 +520,8 @@ | |
| if (fin) | |
| { | |
| char* ptr=fgets(line, LINELEN, fin); | |
| - numseqs = strint(ptr); | |
| - LDB = strint(ptr); | |
| + char * pEnd; | |
| + numseqs = strtoull(ptr, &pEnd, 10); | |
| + LDB = strtoull(pEnd, &pEnd, 10); | |
| fclose(fin); | |
| } | |
| else |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| --- A/src/hhprefilter.C 2017-08-28 14:44:32.000000000 +0200 | |
| +++ B/src/hhprefilter.C 2013-02-18 14:44:26.000000000 +0100 | |
| @@ -49,7 +49,7 @@ | |
| #define SHORT_BIAS 32768 | |
| const int NUMCOLSTATES = cs::AS219::kSize; | |
| int num_dbs = 0; // number of sequences in prefilter database file | |
| Hash<char>* doubled; | |
| @@ -808,7 +808,7 @@ | |
| void init_prefilter() | |
| { | |
| // Get Prefilter Pvalue (Evalue / Par.Dbsize) | |
| - LDB = CountSeqsInFile(db, par.dbsize); // Get DBsize but not number of chars | |
| + size_t LDB = CountSeqsInFile(db, par.dbsize); // Get DBsize but not number of chars | |
| if (par.dbsize == 0 || LDB == 0) | |
| {cerr<<endl<<"Error! Could not determine DB-size of prefilter db ("<<db<<")\n"; exit(4);} | |
| @@ -824,7 +824,7 @@ | |
| // Read in database | |
| num_dbs = 0; | |
| int len = 0; | |
| - int pos = 0; | |
| + size_t pos = 0; | |
| char word[NAMELEN]; | |
| FILE* dbf = NULL; | |
| dbf = fopen(db,"rb"); | |
| --- A/src/hhutil.C 2017-08-28 14:16:18.000000000 +0200 | |
| +++ B/src/hhutil.C 2013-02-18 14:44:26.000000000 +0100 | |
| @@ -508,11 +508,11 @@ | |
| ///////////////////////////////////////////////////////////////////////////////////// | |
| // Count the number of sequences "^>" in <file> | |
| ///////////////////////////////////////////////////////////////////////////////////// | |
| -int CountSeqsInFile(char* file, int& numseqs) | |
| +size_t CountSeqsInFile(char* file, int& numseqs) | |
| { | |
| char line[LINELEN]=""; // input line | |
| char tmp_file[NAMELEN]; | |
| - int LDB=0; | |
| + size_t LDB=0; | |
| numseqs=0; | |
| strcpy(tmp_file, file); | |
| strcat(tmp_file, ".sizes"); | |
| @@ -520,9 +520,8 @@ | |
| if (fin) | |
| { | |
| char* ptr=fgets(line, LINELEN, fin); | |
| - numseqs = strint(ptr); | |
| - LDB = strint(ptr); | |
| + char * pEnd; | |
| + numseqs = strtoull(ptr, &pEnd, 10); | |
| + LDB = strtoull(pEnd, &pEnd, 10); | |
| fclose(fin); | |
| } | |
| else |
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