adjust mmseqs parameters

steineggerlab · Aug 10, 2023 · 3a1fabf · 3a1fabf
1 parent a48a38a
commit 3a1fabf
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/src/process/MMseqsEasySearchProcess.java b/src/process/MMseqsEasySearchProcess.java
@@ -70,7 +70,7 @@ public static MMseqsSearchResultEntity search(String queryPath, String targetPat
 
 		MMseqsWrapper mm = new MMseqsWrapper();
 		mm.setEasySearch(queryPath, targetPath, resultPath, tmpPath);
-		mm.setSearchType(3);
+		mm.setSearchType(0);
 		mm.setThreads(threads);
 		mm.exec();
 
@@ -95,7 +95,7 @@ public static MMseqsSearchResultEntity search(String queryPath, String targetPat
 
 		MMseqsWrapper mm = new MMseqsWrapper();
 		mm.setEasySearch(queryPath, targetPath, resultPath, tmpPath);
-		mm.setSearchType(3);
+		mm.setSearchType(0);
 		mm.setEvalue(evalue);
 		mm.setCoverage(cov);
 		mm.setThreads(threads);

diff --git a/src/wrapper/MMseqsWrapper.java b/src/wrapper/MMseqsWrapper.java
@@ -26,7 +26,7 @@ public void setThreads(int threads) {
 	}
 
 	public void setCoverage(double cov) {
-		super.addArg("--cov-mode", "1");
+		super.addArg("--cov-mode", "0");
 		super.addArg("-c", String.valueOf(cov));
 	}