Merge pull request #114 from charite/develop

Release v0.12.
charite · Feb 2, 2015 · 0c00932 · 0c00932
2 parents 05d06fb + 10e7edb
commit 0c00932
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diff --git a/.gitignore b/.gitignore
@@ -18,6 +18,11 @@ cov-int*
 *.jannovar
 *.vcf
 *.vcf.idx
+*.ped
+log.txt
 data
 # built manual
 manual/_build
+# Java Mission Control flight recorder files
+*.jfr
+.attach_pid*
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,50 @@
+**develop**
+
+*jannovar-htsjdk*
+
+* Started bridge module between Jannovar and HTSJDK.
+
+*jannovar-filter*
+
+* Started tool for mode of inheritance--based filters.
+
+*jannovar-cli*
+
+* Splitting out bridge module between jannovar-core and HTSJDK to
+  jannovar-htsjdk.
+* Adding implementation of variant annotation standard 1.0.
+* Adding unit tests for jannovar-cli.
+* Fixing problem with empty `INFO` fields in output.
+* Adding back `--output-dir` to jannovar-cli.
+* Writing output parallel to input file by default.
+* Adding `-v` and `-vv` command line options.
+* Fixing problems with block substitution (delins) case (#87).
+
+*jannovar-core*
+
+* Adding initial support for the transcript support level feature of the new VCF
+  annotation standard (only in very recent ENSEMBL releases, apparently).
+* `TranscriptModel#geneID` is now a `String`
+* Update in various classes, e.g. Annotation.
+* Fixing bug in PED parsing (empty lines are properly skipped now).
+* More tests and fixes for the inheritance compatibility checkers.
+* Updating `Annotation` for the variant annotation standard.
+* `TranscriptPosition` and `TranscriptInterval` use zero-based positions now.
+* Reordering values of `VariantType`.
+* Somewhat renaming `VariantType` method names. 
+* Removing the `VariantType#size` function in favor of a `static public`
+  `final` member.
+* Using log4j/slf4j for I/O in jannovar-core.
+* Adding `PrintStream` as parameter to `JannovarOptions#print`.
+* Compressing serialized file.
+* Changing namespace to `de.charite.compbio.jannovar`.
+* Making `VariantType#priorityLevel` a non-static member.
+* Renaming `TranscriptInfo` to `TranscriptModel`.
+* Moving `HG19RefDictbuilder` from tests to main.
+* Using `ImmutableMap` in `Translator` for small performance improvements.
+* Using `StringBuilder`-based concatenation of strings for generation of HGVS
+  strings etc. since this is much faster than using `String#format`.
+* `GenomePosition` and `GenomeInterval` use zero-based coordinates internally
+  now.
+
+**v0.11**
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 [![Build Status](https://travis-ci.org/charite/jannovar.svg?branch=master)](https://travis-ci.org/charite/jannovar)
-[![Documentation](https://travis-ci.org/charite/jannovar.svg?branch=master)](https://readthedocs.org/projects/pip/badge/?version=master)
+[![Documentation](https://readthedocs.org/projects/jannovar/badge/?version=master)](http://jannovar.readthedocs.org/)
 
 Jannovar
 ========

diff --git a/jannovar-cli/examples/delins.vcf b/jannovar-cli/examples/delins.vcf
@@ -0,0 +1,3 @@
+##fileformat=VCFv4.1
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+X	103041654	.	AGGTGATC	AA	.	.	.
diff --git a/jannovar-cli/pom.xml b/jannovar-cli/pom.xml
@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>de.charite.compbio</groupId>
 		<artifactId>Jannovar</artifactId>
-		<version>0.11</version>
+		<version>0.12</version>
 	</parent>
 
 	<properties>
@@ -51,6 +51,33 @@
 			<artifactId>jannovar-core</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>de.charite.compbio</groupId>
+			<artifactId>jannovar-htsjdk</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<!--Logging framework -->
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-api</artifactId>
+			<version>1.7.7</version>
+		</dependency>
+		<!-- Logging -->
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-api</artifactId>
+			<version>${log4j.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-core</artifactId>
+			<version>${log4j.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-slf4j-impl</artifactId>
+			<version>${log4j.version}</version>
+		</dependency>
 	</dependencies>
 
 	<build>
@@ -76,28 +103,32 @@
 							<!-- set useUniqueVersions=false in order that the classpath has the 
 								SNAPSHOT instead of the build number prefixed to the dependency -->
 							<useUniqueVersions>false</useUniqueVersions>
-							<mainClass>jannovar.Jannovar</mainClass>
+							<mainClass>de.charite.compbio.jannovar.Jannovar</mainClass>
 						</manifest>
 					</archive>
+					<compilerArgument>-Xlint:all</compilerArgument>
+					<showWarnings>true</showWarnings>
+					<showDeprecation>true</showDeprecation>
 				</configuration>
 			</plugin>
-			<!-- Specify the dependencies to copy -->
+			<!-- More JAR building -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-dependency-plugin</artifactId>
-				<version>2.8</version>
+				<artifactId>maven-shade-plugin</artifactId>
+				<version>2.2</version>
 				<executions>
 					<execution>
-						<id>copy-dependencies</id>
 						<phase>package</phase>
 						<goals>
-							<goal>copy-dependencies</goal>
+							<goal>shade</goal>
 						</goals>
 						<configuration>
-							<outputDirectory>${project.build.directory}/lib</outputDirectory>
-							<overWriteReleases>false</overWriteReleases>
-							<overWriteSnapshots>false</overWriteSnapshots>
-							<overWriteIfNewer>true</overWriteIfNewer>
+							<transformers>
+								<transformer
+									implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+									<mainClass>de.charite.compbio.jannovar.Jannovar</mainClass>
+								</transformer>
+							</transformers>
 						</configuration>
 					</execution>
 				</executions>

diff --git a/...-cli/src/main/java/jannovar/Jannovar.java → ...de/charite/compbio/jannovar/Jannovar.java b/...-cli/src/main/java/jannovar/Jannovar.java → ...de/charite/compbio/jannovar/Jannovar.java
@@ -1,14 +1,16 @@
-package jannovar;
+package de.charite.compbio.jannovar;
 
 /** Command line functions from apache */
-import jannovar.cmd.CommandLineParsingException;
-import jannovar.cmd.HelpRequestedException;
-import jannovar.cmd.JannovarCommand;
-import jannovar.cmd.annotate_pos.AnnotatePositionCommand;
-import jannovar.cmd.annotate_vcf.AnnotateVCFCommand;
-import jannovar.cmd.db_list.DatabaseListCommand;
-import jannovar.cmd.download.DownloadCommand;
-import jannovar.reference.TranscriptInfo;
+import de.charite.compbio.jannovar.JannovarException;
+import de.charite.compbio.jannovar.JannovarOptions;
+import de.charite.compbio.jannovar.cmd.CommandLineParsingException;
+import de.charite.compbio.jannovar.cmd.HelpRequestedException;
+import de.charite.compbio.jannovar.cmd.JannovarCommand;
+import de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand;
+import de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand;
+import de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand;
+import de.charite.compbio.jannovar.cmd.download.DownloadCommand;
+import de.charite.compbio.jannovar.reference.TranscriptModel;
 
 /**
  * This is the driver class for a program called Jannovar. It has two purposes
@@ -25,7 +27,7 @@
  * <P>
  * {@code java -Xms1G -Xmx1G -jar Jannovar.jar -V xyz.vcf -D $SERIAL}
  * <P>
- * This will annotate a VCF file. The results of jannovar annotation are shown in the form
+ * This will annotate a VCF file. The results of de.charite.compbio.jannovar annotation are shown in the form
  *
  * <PRE>
  * Annotation {original VCF line}
@@ -109,21 +111,21 @@ else if (argv[0].equals("annotate-pos"))
 	 * Print top level help (without any command).
 	 */
 	private static void printTopLevelHelp() {
-		System.err.println("Program: jannovar (functional annotation of VCF files)");
+		System.err.println("Program: de.charite.compbio.jannovar (functional annotation of VCF files)");
 		System.err.println("Version: 0.10");
 		System.err.println("Contact: Peter N Robinson <[email protected]>");
 		System.err.println("");
-		System.err.println("Usage: java -jar jannovar.jar <command> [options]");
+		System.err.println("Usage: java -jar de.charite.compbio.jannovar.jar <command> [options]");
 		System.err.println("");
 		System.err.println("Command: download      download transcript database");
 		System.err.println("         db-list       list downloadable databases");
 		System.err.println("         annotate      functional annotation of VCF files");
 		System.err.println("         annotate-pos  functional annotation of genomic change");
 		System.err.println("");
-		System.err.println("Example: java -jar jannovar.jar download hg19/ucsc");
-		System.err.println("         java -jar jannovar.jar db-list");
-		System.err.println("         java -jar jannovar.jar annotate data/hg19_ucsc.ser variants.vcf");
-		System.err.println("         java -jar jannovar.jar annotate-pos data/hg19_ucsc.ser 'chr1:12345C>A'");
+		System.err.println("Example: java -jar de.charite.compbio.jannovar.jar download hg19/ucsc");
+		System.err.println("         java -jar de.charite.compbio.jannovar.jar db-list");
+		System.err.println("         java -jar de.charite.compbio.jannovar.jar annotate data/hg19_ucsc.ser variants.vcf");
+		System.err.println("         java -jar de.charite.compbio.jannovar.jar annotate-pos data/hg19_ucsc.ser 'chr1:12345C>A'");
 		System.err.println("");
 	}
 

diff --git a/...ovar/cmd/CommandLineParsingException.java → ...ovar/cmd/CommandLineParsingException.java b/...ovar/cmd/CommandLineParsingException.java → ...ovar/cmd/CommandLineParsingException.java
@@ -1,6 +1,6 @@
-package jannovar.cmd;
+package de.charite.compbio.jannovar.cmd;
 
-import jannovar.JannovarException;
+import de.charite.compbio.jannovar.JannovarException;
 
 /**
  * Exception thrown on problems with the command line.

diff --git a/.../jannovar/cmd/HelpRequestedException.java → .../jannovar/cmd/HelpRequestedException.java b/.../jannovar/cmd/HelpRequestedException.java → .../jannovar/cmd/HelpRequestedException.java
@@ -1,6 +1,6 @@
-package jannovar.cmd;
+package de.charite.compbio.jannovar.cmd;
 
-import jannovar.JannovarException;
+import de.charite.compbio.jannovar.JannovarException;
 
 /**
  * Thrown when the user requests help.

diff --git a/...nnovar/cmd/JannovarAnnotationCommand.java → ...nnovar/cmd/JannovarAnnotationCommand.java b/...nnovar/cmd/JannovarAnnotationCommand.java → ...nnovar/cmd/JannovarAnnotationCommand.java
@@ -1,13 +1,13 @@
-package jannovar.cmd;
-
-import jannovar.JannovarException;
-import jannovar.io.Chromosome;
-import jannovar.io.JannovarData;
-import jannovar.io.JannovarDataSerializer;
-import jannovar.io.ReferenceDictionary;
+package de.charite.compbio.jannovar.cmd;
 
 import com.google.common.collect.ImmutableMap;
 
+import de.charite.compbio.jannovar.JannovarException;
+import de.charite.compbio.jannovar.io.Chromosome;
+import de.charite.compbio.jannovar.io.JannovarData;
+import de.charite.compbio.jannovar.io.JannovarDataSerializer;
+import de.charite.compbio.jannovar.io.ReferenceDictionary;
+
 /**
  * Base class for commands needing annotation data.
  *
@@ -39,12 +39,9 @@ public JannovarAnnotationCommand(String[] argv) throws CommandLineParsingExcepti
 	 *             when the user requested the help page
 	 */
 	protected void deserializeTranscriptDefinitionFile() throws JannovarException, HelpRequestedException {
-		final long startTime = System.nanoTime();
 		JannovarData data = new JannovarDataSerializer(this.options.dataFile).load();
 		this.refDict = data.refDict;
 		this.chromosomeMap = data.chromosomes;
-		final long endTime = System.nanoTime();
-		System.err.println(String.format("Deserialization took %.2f sec.",
-				(endTime - startTime) / 1000.0 / 1000.0 / 1000.0));
 	}
-}
+
+}
diff --git a/.../JannovarAnnotationCommandLineParser.java → .../JannovarAnnotationCommandLineParser.java b/.../JannovarAnnotationCommandLineParser.java → .../JannovarAnnotationCommandLineParser.java
@@ -1,13 +1,13 @@
-package jannovar.cmd;
-
-import jannovar.JannovarOptions;
+package de.charite.compbio.jannovar.cmd;
 
 import org.apache.commons.cli.GnuParser;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.Parser;
 
+import de.charite.compbio.jannovar.JannovarOptions;
+
 /**
  * Base class for the command line parser for the annotation commands.
  *

diff --git a/...in/java/jannovar/cmd/JannovarCommand.java → ...compbio/jannovar/cmd/JannovarCommand.java b/...in/java/jannovar/cmd/JannovarCommand.java → ...compbio/jannovar/cmd/JannovarCommand.java
@@ -1,7 +1,12 @@
-package jannovar.cmd;
+package de.charite.compbio.jannovar.cmd;
 
-import jannovar.JannovarException;
-import jannovar.JannovarOptions;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.core.LoggerContext;
+import org.apache.logging.log4j.core.config.Configuration;
+
+import de.charite.compbio.jannovar.JannovarException;
+import de.charite.compbio.jannovar.JannovarOptions;
 
 /**
  * Super class for all commands, i.e. the classes implementing one Jannovar execution step.
@@ -12,6 +17,8 @@ public abstract class JannovarCommand {
 
 	/** Configuration to use for the command execution. */
 	protected JannovarOptions options;
+	/** Verbosity level: (0) quiet, (1) normal, (2) verbose, (3) very verbose */
+	protected int verbosity = 1;
 
 	/**
 	 * Initialize the JannovarCommand.
@@ -25,6 +32,25 @@ public abstract class JannovarCommand {
 	 */
 	public JannovarCommand(String[] argv) throws CommandLineParsingException, HelpRequestedException {
 		this.options = parseCommandLine(argv);
+		this.verbosity = options.verbosity;
+		setLogLevel();
+	}
+
+	/**
+	 * Set log level, depending on this.verbosity.
+	 */
+	private void setLogLevel() {
+		LoggerContext ctx = (LoggerContext) LogManager.getContext(false);
+		Configuration conf = ctx.getConfiguration();
+
+		if (verbosity <= 1)
+			conf.getLoggerConfig(LogManager.ROOT_LOGGER_NAME).setLevel(Level.INFO);
+		else if (verbosity <= 2)
+			conf.getLoggerConfig(LogManager.ROOT_LOGGER_NAME).setLevel(Level.DEBUG);
+		else
+			conf.getLoggerConfig(LogManager.ROOT_LOGGER_NAME).setLevel(Level.TRACE);
+
+		ctx.updateLoggers(conf);
 	}
 
 	/**