Merge pull request #563 from pcingola/wgs_annotate

Wgs annotate
pcingola · Sep 28, 2024 · 17cc55e · 17cc55e
2 parents 93588ed + 4d8c9fe
commit 17cc55e
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Showing 38 changed files with 135,051 additions and 956 deletions.
diff --git a/.classpath b/.classpath
@@ -24,7 +24,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-21">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
@@ -36,18 +36,18 @@
 			<attribute name="optional" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
+	<classpathentry kind="src" path="target/generated-sources/annotations">
 		<attributes>
 			<attribute name="optional" value="true"/>
-			<attribute name="test" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 			<attribute name="ignore_optional_problems" value="true"/>
 			<attribute name="m2e-apt" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" path="target/generated-sources/annotations">
+	<classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
 		<attributes>
 			<attribute name="optional" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>

diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -10,7 +10,7 @@
             "request": "launch",
             "mainClass": "org.snpeff.SnpEff",
             "projectName": "SnpEff",
-            "args": "build -v hg19"
+            "args": "-v -noOut testHg3882Chr22 /Users/kqrw311/snpEff/z.vcf"
         },
     ]
 }