update to gradle-version 6.1.1

lindenb · Feb 6, 2020 · 0d69d16 · 0d69d16
1 parent 583b6f4
commit 0d69d16
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Showing 5 changed files with 72 additions and 31 deletions.
diff --git a/build.gradle b/build.gradle
@@ -4,6 +4,8 @@
 
 
 gradle -Djvarkit.delete.jar=true -Djvarkit.disable.test=true all all2
+gradle -Djvarkit.generate.doc=false all all2
+
 */
 
 //import org.gradle.internal.logging.text.StyledTextOutput 
@@ -267,20 +269,35 @@ libraries.put("arq",new Library().
 
 
 public class CompileJVarkit extends DefaultTask {
+	@Input @Optional
 	String mainClass = ''
+	@Input @Optional
 	String srcDir =''
+	@Input @Optional
 	String testDir =''
+	@Input @Optional
 	String tmpDir = ""
+	@Input @Optional
 	String distDir = ""	
+	@Input @Optional
 	String docDir = ""
+	@Input @Optional
 	String testNgDir=""
+	@Input @Optional
 	String jdkTarget = "8"
+	@Input @Optional
 	String jdkSource = "8"
+	@Input @Optional
 	Library jarLibs = new Library();
-	boolean requireJfx = false;
+	@Input
+	boolean requireJfx = false;	
+	@Input @Optional
 	String deprecatedMsg = null;
-	def xsdFiles =[];
+	@Input @Optional
+	def xsdFiles =[];	
+	@Input @Optional
 	String endMsg = null;
+	@Input
 	boolean with_jni = false;
 
 	CompileJVarkit() {
@@ -448,6 +465,7 @@ public class CompileJVarkit extends DefaultTask {
 
 			}
 		}
+	@Input
 	boolean isJavaFxAvailable() {
 		try {
 		    this.getClass().getClassLoader().loadClass("javafx.embed.swing.JFXPanel");
@@ -457,11 +475,17 @@ public class CompileJVarkit extends DefaultTask {
 		 	return false;
 			}
 		}
-
+	@Input
 	boolean isFatJar() {
 		return java.lang.System.getProperty("jvarkit.fat.jar","true").equals("true");
 		}
 
+	private boolean isGeneratingDoc() {
+		if(!java.lang.System.getProperty("jvarkit.generate.doc","true").equals("true")) return false;
+		return true;
+		}
+
+	@Input
 	String getMainPackage() {
 		String s= this.mainClass;
 		int dollar = s.indexOf('$');
@@ -470,7 +494,8 @@ public class CompileJVarkit extends DefaultTask {
 		if(dot==-1) return "";
 		return s.substring(0,dot);
 		}
-	File getMainJavaTestFile() {
+
+	private File getMainJavaTestFile() {
 		String travis = java.lang.System.getenv("TRAVIS");
 		if(travis!=null && travis.equals("true")) return null;
 		if(java.lang.System.getProperty("jvarkit.disable.test","false").equals("true")) return null;
@@ -482,25 +507,30 @@ public class CompileJVarkit extends DefaultTask {
 		if(!f.exists()) return null;
 		return f;
 		}
+
+	@Input
 	String getMainJavaSource() {
 		String s = this.mainClass;
 		int dollar = s.indexOf('$');
 		if(dollar!=-1) s=s.substring(0,dollar);
 		s = this.srcDir + "/" + s.replace('.','/')+".java";
 		return s;
 		}
+	@Input
 	String getTestNgClass() {
 		String s = this.mainClass;
 		int dollar = s.indexOf('$');
 		if(dollar!=-1) s=s.substring(0,dollar);
 		return s+"Test";
 		}
+	@Input
 	String getAntInclude() {
 		final String s= this.getMainJavaSource();
 		final int slash = s.lastIndexOf('/');
 		String s2 =  "**"+s.substring(slash);
 		return s2;
 		}
+	@Input
 	String getAntTestInclude() {
 		String s= this.getMainJavaSource();
 		int slash = s.lastIndexOf('/');
@@ -510,7 +540,7 @@ public class CompileJVarkit extends DefaultTask {
 		return "**"+s+"Test.java";	
 		}
 	public String toString() {
-		return 	""+this.getName()+" "+this.mainClass;
+		return	""+this.getName()+" "+this.mainClass;
 		}
 
 	private void compileJni() {
@@ -521,11 +551,11 @@ public class CompileJVarkit extends DefaultTask {
 		    }
 		}
 	    catch(Exception err) {
-	    	project.logger.warn("Compiling JNI failed. "+err.getMessage());
-	    	}
+	        project.logger.warn("Compiling JNI failed. "+err.getMessage());
+	        }
 	}
 
-	
+
 	private String getExecutablePath(String exe) {
 	    try {
 		def stdout = new ByteArrayOutputStream()
@@ -538,6 +568,7 @@ public class CompileJVarkit extends DefaultTask {
 	    catch(Exception err) { return "";}
 	    }
 
+	@Input
 	public String getGitHash() {
 	    try {
 		def stdout = new ByteArrayOutputStream()
@@ -550,16 +581,17 @@ public class CompileJVarkit extends DefaultTask {
 	    catch(Exception err) { return "undefined";}
 	    }
 
+	/**
 	def getConfiguration() {
-		//System.err.println("SEACHING "+ this.configName);
+		//System.err.println("SEARCHING "+ this.configName);
 		//project.configurations.each{ System.err.println("conf : "+it.name); } 
 		def c= project.configurations.find{it.name == this.configName}
 		//System.err.println("GOT::"+this.configName +" =  "+c);
 		if(c==null) throw new GradleException("Cannot find config "+this.configName+" "+c);
 		
 		return c;	
 		}	
-
+	*/
 
 	 @TaskAction
 	 void doIt() {
@@ -690,7 +722,7 @@ public class CompileJVarkit extends DefaultTask {
 		// done : https://stackoverflow.com/questions/14516693/
 		project.logger.lifecycle("jar file generated :" + distJar)
 
-
+		if( isGeneratingDoc()) {
 		/* generate doc */
 		ant.java(
 			jar :  this.distDir+"/${this.name}.jar" , fork: true
@@ -700,7 +732,7 @@ public class CompileJVarkit extends DefaultTask {
 			arg(value: "--helpFormat")
 			arg(value: "make-doc")
 			}
-
+		}
 
 		/** test */
 

diff --git a/docs/SamFindClippedRegions.md b/docs/SamFindClippedRegions.md
@@ -10,13 +10,20 @@ Fins clipped position in one or more bam.
 ```
 Usage: samfindclippedregions [options] Files
   Options:
+    --bcf-output
+      If this program writes a VCF to a file, The format is first guessed from 
+      the file suffix. Otherwise, force BCF output. The current supported BCF 
+      version is : 2.1 which is not compatible with bcftools/htslib (last 
+      checked 2019-11-15)
+      Default: false
     --generate-vcf-md5
       Generate MD5 checksum for VCF output.
       Default: false
     --gtf
       Optional gtf file. Will be used to set a warning if the junction could 
       be a junction exon-exon of a retrogene. A GTF (General Transfer Format) 
-      file. See https://www.ensembl.org/info/website/upload/gff.html .
+      file. See https://www.ensembl.org/info/website/upload/gff.html . Please 
+      note that CDS are only detected if a start and stop codons are defined.
     -h, --help
       print help and exit
     --helpFormat

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.1.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 
 ##############################################################################
 ##
@@ -28,16 +28,16 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+DEFAULT_JVM_OPTS='"-Xmx64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
 
-warn ( ) {
+warn () {
     echo "$*"
 }
 
-die ( ) {
+die () {
     echo
     echo "$*"
     echo
@@ -154,11 +154,19 @@ if $cygwin ; then
     esac
 fi
 
-# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
-function splitJvmOpts() {
-    JVM_OPTS=("$@")
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
 }
-eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
-JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+APP_ARGS=$(save "$@")
 
-exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
+
+exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
@@ -14,7 +14,7 @@ set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
+set DEFAULT_JVM_OPTS="-Xmx64m"
 
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
@@ -49,7 +49,6 @@ goto fail
 @rem Get command-line arguments, handling Windows variants
 
 if not "%OS%" == "Windows_NT" goto win9xME_args
-if "%@eval[2+2]" == "4" goto 4NT_args
 
 :win9xME_args
 @rem Slurp the command line arguments.
@@ -60,11 +59,6 @@ set _SKIP=2
 if "x%~1" == "x" goto execute
 
 set CMD_LINE_ARGS=%*
-goto execute
-
-:4NT_args
-@rem Get arguments from the 4NT Shell from JP Software
-set CMD_LINE_ARGS=%$
 
 :execute
 @rem Setup the command line