mercy k-mer simple test through

rhinempi · Nov 27, 2024 · 5dcd4d5 · 5dcd4d5
1 parent a3b6ca9
commit 5dcd4d5
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Showing 4 changed files with 750 additions and 58 deletions.
diff --git a/src/main/java/uni/bielefeld/cmg/reflexiv/pipeline/Pipelines.java b/src/main/java/uni/bielefeld/cmg/reflexiv/pipeline/Pipelines.java
@@ -554,7 +554,7 @@ private int checkStepsForDynamicAssemblyPipe() throws IOException {
             info.readParagraphedMessages("An assembly already exist: \nUse a new output directory or delete the existing one at:\n\t"+ param.outputPath + "/Assembly");
             info.screenDump();
             return 10; // 10 as kill
-        } else if (checkOutputFile(param.outputPath + "/09ExtendAgain") ){
+        } else if (checkOutputFile(param.outputPath + "/Assembly_intermediate/09ExtendAgain") ){
             info.readParagraphedMessages("09ExtendAgain succeed, will use existing results:\n"+ param.outputPath + "/Assembly_intermediate/03FixingAgain");
             info.screenDump();
 
@@ -584,7 +584,7 @@ private int checkStepsForDynamicAssemblyPipe() throws IOException {
 
             return 9;
 
-        } else if (checkOutputFile(param.outputPath + "/08Extend")){
+        } else if (checkOutputFile(param.outputPath + "/Assembly_intermediate/08Extend")){
             info.readParagraphedMessages("08Extend succeed, will use existing results:\n"+ param.outputPath + "/Assembly_intermediate/03FixingAgain");
             info.screenDump();