stable multithreaded version

vgl-hub · Sep 29, 2024 · 883da12 · 883da12
1 parent b49c3f0
commit 883da12
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Showing 3 changed files with 2 additions and 14 deletions.
diff --git a/gfalibs b/gfalibs
diff --git a/src/input.cpp b/src/input.cpp
@@ -48,10 +48,6 @@ void Input::loadDB() {
         getline(file, line);
         file.close();
         userInput.kLen = stol(line);
-        if (userInput.kLen < userInput.kPrefixLen)
-            userInput.kPrefixLen = userInput.kLen;
-        else
-            userInput.kPrefixLen = std::min((uint32_t)31,userInput.kLen);
     }else if (userInput.kmerDB.size() > 1) {
         fprintf(stderr, "More than one DB provided. Merge them first. Exiting.\n");
         exit(EXIT_FAILURE);
@@ -146,10 +142,6 @@ void Input::read() { // reads the actual input and performing the tasks
             }
 
             userInput.kLen = k;
-            if (userInput.kLen < userInput.kPrefixLen)
-                userInput.kPrefixLen = userInput.kLen;
-            else
-                userInput.kPrefixLen = std::min((uint32_t)31,userInput.kLen);
 
             KDB kcount(userInput); // a new empty kmerdb with the specified kmer length
 

diff --git a/src/main.cpp b/src/main.cpp
@@ -141,12 +141,8 @@ int main(int argc, char **argv) {
                         }
 
                         userInput.kLen = atol(optarg);
-                        if (userInput.kLen < userInput.kPrefixLen)
-                            userInput.kPrefixLen = userInput.kLen;
-                        else
-                            userInput.kPrefixLen = std::min((uint32_t)31,userInput.kLen);
                         break;
-                    case 's': // kmer length
+                    case 's': // smer length
 
                         if (!isNumber(optarg)) {
                             fprintf(stderr, "input '%s' to option -%c must be a number\n", optarg, optopt);
+89 −0		include/MinScan.h
+136 −161		include/kmer.h
+1 −1		include/struct.h
+929 −0		src/MinScan.cpp