Fixes...

pfeiferd · Feb 25, 2025 · 88d2db0 · 88d2db0
1 parent 8c115ba
commit 88d2db0
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Showing 3 changed files with 15 additions and 2 deletions.
diff --git a/src/main/java/org/metagene/genestrip/GSMaker.java b/src/main/java/org/metagene/genestrip/GSMaker.java
@@ -407,9 +407,20 @@ protected void doMakeThis() {
 		registerGoal(krakenResCountGoal);
 	}
 
+	public MatchingResult cleanMatch(boolean lr, String key, String... pathsOrURLs) {
+		return match(lr, true, key, pathsOrURLs);
+	}
+
 	public MatchingResult match(boolean lr, String key, String... pathsOrURLs) {
+		return match(lr, false, key, pathsOrURLs);
+	}
+
+	public MatchingResult match(boolean lr, boolean clean, String key, String... pathsOrURLs) {
 		MatchGoal matchGoal = createGoalChainForMatch(lr, key, pathsOrURLs);
 
+		if (clean) {
+			matchGoal.cleanThis();
+		}
 		matchGoal.make();
 		return matchGoal.getMatchResults().get(key);
 	}

diff --git a/src/test/java/org/metagene/genestrip/goals/DB2FastqGoalTest.java b/src/test/java/org/metagene/genestrip/goals/DB2FastqGoalTest.java
@@ -73,9 +73,11 @@ public void testDB2FastqGoal() throws IOException {
 		goal.cleanThis();
 		goal.make();
 
+
+
 		for (int i = 0; i < taxids.length; i++) {
 			File file = goal.getOutputFile(taxids[i]);
-			MatchingResult result = maker.match(false, taxids[i], file.toString());
+			MatchingResult result = maker.cleanMatch(false, taxids[i], file.toString());
 			Map<String, CountsPerTaxid> map = result.getTaxid2Stats();
 
 			assertEquals(kmers[i], map.get(taxids[i]).getKMers());

diff --git a/src/test/java/org/metagene/genestrip/match/FastqKMerMatcherTest.java b/src/test/java/org/metagene/genestrip/match/FastqKMerMatcherTest.java
@@ -126,7 +126,7 @@ protected void testMatchReadHelp(boolean bitMap) {
 					maxContigLen[previousPos] = contigLen;
 				}
 			}
-			matcher.matchRead(entry, i, false);
+			matcher.matchRead(entry, 0, false);
 
 			ByteArrayUtil.print(entry.read, System.out);
 			System.out.println();