Project updated

pcingola · Sep 13, 2023 · a0f4c06 · a0f4c06
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Showing 3 changed files with 133 additions and 3 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -0,0 +1,127 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "type": "java",
+            "name": "Current File",
+            "request": "launch",
+            "mainClass": "${file}"
+        },
+        {
+            "type": "java",
+            "name": "Fastq2Fastq",
+            "request": "launch",
+            "mainClass": "org.snpeff.Fastq2Fastq",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "PromoterSequences",
+            "request": "launch",
+            "mainClass": "org.snpeff.PromoterSequences",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "Qseq2Fastq",
+            "request": "launch",
+            "mainClass": "org.snpeff.Qseq2Fastq",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "SnpEff",
+            "request": "launch",
+            "mainClass": "org.snpeff.SnpEff",
+            "projectName": "SnpEff",
+            "args": "ann GRCh38.mane.1.0.ensembl tests/integration/zzz/test.splice_region_01.vcf"
+        },
+        {
+            "type": "java",
+            "name": "Zzz",
+            "request": "launch",
+            "mainClass": "org.snpeff.Zzz",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "FastqSplit",
+            "request": "launch",
+            "mainClass": "org.snpeff.fastq.FastqSplit",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "Genotypes",
+            "request": "launch",
+            "mainClass": "org.snpeff.genotypes.Genotypes",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "Hypergeometric",
+            "request": "launch",
+            "mainClass": "org.snpeff.probablility.Hypergeometric",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "RankSumNoReplacementSimulate",
+            "request": "launch",
+            "mainClass": "org.snpeff.probablility.RankSumNoReplacementSimulate",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "RankSumPdf",
+            "request": "launch",
+            "mainClass": "org.snpeff.probablility.RankSumPdf",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "Reactome",
+            "request": "launch",
+            "mainClass": "org.snpeff.reactome.Reactome",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "IntHisto",
+            "request": "launch",
+            "mainClass": "org.snpeff.snpEffect.IntHisto",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "PurityChange",
+            "request": "launch",
+            "mainClass": "org.snpeff.snpEffect.PurityChange",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "SnpEffCmdGenes2Bed",
+            "request": "launch",
+            "mainClass": "org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "CompareToEnsembl",
+            "request": "launch",
+            "mainClass": "org.snpeff.snpEffect.testCases.integration.CompareToEnsembl",
+            "projectName": "SnpEff"
+        },
+        {
+            "type": "java",
+            "name": "CreateSpliceSiteTestCase",
+            "request": "launch",
+            "mainClass": "org.snpeff.snpEffect.testCases.integration.CreateSpliceSiteTestCase",
+            "projectName": "SnpEff"
+        }
+    ]
+}
diff --git a/src/main/java/org/snpeff/SnpEff.java b/src/main/java/org/snpeff/SnpEff.java
@@ -94,10 +94,10 @@ public enum OutputFormat {
 
 	// Version info
 	public static final String SOFTWARE_NAME = "SnpEff";
-	public static final String REVISION = "f";
+	public static final String REVISION = "";
 	public static final String BUILD = Gpr.compileTimeStamp(SnpEff.class);
 	public static final String BUILD_DATE = Gpr.compileDate(SnpEff.class);
-	public static final String VERSION_MAJOR = "5.1";
+	public static final String VERSION_MAJOR = "5.2";
 	public static final String VERSION_SHORT = VERSION_MAJOR + REVISION;
 	public static final String VERSION_BUILD = VERSION_SHORT + " (build " + BUILD + ")";
 	public static final String VERSION_AUTHOR = VERSION_BUILD + ", by " + Pcingola.BY;

diff --git a/src/main/java/org/snpeff/snpEffect/Config.java b/src/main/java/org/snpeff/snpEffect/Config.java
@@ -40,8 +40,11 @@ public class Config implements Serializable, Iterable<String> {
     //     ---------------+-----------
     //                5.1 | 5.0
     //     ---------------+-----------
+    //                5.2 | 5.1, 5.0
+    //     ---------------+-----------
+    public static final String[] COMPATIBLE_WITH_5_2 = {"5.0", "5.1"};
     public static final String[] COMPATIBLE_WITH_5_1 = {"5.0"};
-    public static final Map<String, String[]> DATABASE_COMPATIBLE_VERSIONS = Map.of("5.1", COMPATIBLE_WITH_5_1);
+    public static final Map<String, String[]> DATABASE_COMPATIBLE_VERSIONS = Map.of("5.1", COMPATIBLE_WITH_5_1, "5.2", COMPATIBLE_WITH_5_2);
 
     private static final long serialVersionUID = 877453207407217465L;