Merge branch 'develop'

.travis.yml

@@ -1,6 +1,6 @@
 language: java
 
 jdk:
-  - openjdk6
   - openjdk7
   - oraclejdk7
+  - oraclejdk8

CHANGELOG.md

@@ -1,14 +1,102 @@
-**v0.13**
+# Jannovar Changelog
 
-*jannovar-htsjdk*
+## develop
+
+### jannovar-cli
+
+* Moving `JannovarOptions` into jannovar-cli.
+* Displaying online help on unknown Jannovar command.
+* Fixing `NullPointerException` bug for local paths.
+* Switching to official HTSJDK release and version 0.128.
+* Writing out annotation about Jannovar call and version into the VCF file.
+* Added option `--no-3-prime-shifting` to disable shifting towards the
+  3' end of the transcripts.
+* Added option `--no-escape-ann-field` to disable escaping of the `ANN`
+  `INFO` field.
+* Variants in `ANN` field are now annotated with proper Sequence Ontology
+  terms.
+
+### jannovar-htsjdk
+
+* Modified `VariantContextWriterConstructionHelper` to allow explicit
+  disabling of index creation.
+* Modified `VariantContextAnnotator` for adjustment to the new Exomiser.
+* Switching to official HTSJDK release and version 0.128.
+* Changing `VariantContextWriterConstructionHelper` to allow writing out
+  of additional header lines.
+* Added option to `VariantContextAnnotator#Options` for disabling
+  3' shifting.
+* Modified `VariantContextAnnotator` allowing to disable escaping of the
+  `ANN` `INFO` field.
+
+### jannovar-core
+
+* Moving `JannovarOptions` into jannovar-cli.
+* Renaming `ACompatibilityChecker` and `ICompatibilityChecker`.
+* Adding `GenomePosition.differenceTo(GenomeInterval)`.
+* Renaming package `de.charite.compbio.jannovar.io` to `de.charite.compbio.jannovar.data`
+* Renaming `AnnotationLocation.toHGVSString` to `.toHGVSChunk`.
+* Adding `Pedigree.subsetOfMembers`
+* Renaming `GenomeChange` to `GenomeVariant`, same with types having the same
+  prefix.
+* Introducing `DatasourceOptions` for configuring data download.
+* Removing support for using `"-"` as REF or ALT value.
+* Making previous `public final` members `private final` (or
+ `protected final`) and adding getters for read-only access to them.
+* Removing position type member of `CDSInterval`.
+* Using type `Strand` instead of `'+'` and `'-'`, requires database rebuild.
+* Adding enum `Strand` with `PLUS` and `MINUS` values.
+* Adding `VariantEffect.isOffExome` and updating
+  `VariantEffect.isOffTranscript`.
+* Removing `genomeRegion` member from `GenotypeList`. Also, adjusting the
+  pedigree compatibility checkers for this, the check for being on the X
+  chromosome has to be performed outside the checker now.
+* `VariantList.getHighestImpactEffect` now returns
+  `VariantEffect#SEQUENCE_VARIANT` if no annotation can be found.
+* `VariantList` implements the `List<Annotation>` interface now and the
+  `entries` member has become private.
+* Adding `VariantEffect#SEQUENCE_VARIANT` for variants with unknown
+  effects.
+* `GenomeChange.toString()` now always converts to forward strand.
+* Fixing bug in `Annotation` and enforcing forward strand `GenomeChange`
+  instances.
+* Updates to the manual.
+* `JannovarData` now also stores a mapping from transcript accession to
+  `TranscriptModel` and from gene symbol to `TranscriptModel`.
+* Adding functionality for conversion from CDS to transcript and genome
+  position and tests.
+* Adding `AnnotationBuilderOption` object that allows disabling of 3'
+  shifting towards the transcript.
+* Adding `JannovarOptions#escapeAnnField`.
+* Renaming `VariantType` to `VariantEffect`
+* Changing `VariantType` to use proper Sequence Ontology terms. Legacy
+  names can be obtained through `VariantType#getLegacyName`.
+* Spliting `CompatibilityCheckerXRecessive` into `CompatibilityCheckerXRecessiveCompoundHet` and `CompatibilityCheckerXRecessiveHomozygous`. Now all inheritance checkers ar ready to use (AR,XR,AD,XD)
+* move all pedigree compatibility checkers from `de.charite.compbio.jannovar.pedigree` to `de.charite.compbio.jannovar.pedigree.compatibilitychecker` and divide it into ar,xr,ad,xd.
+* generate interface `ICompatibilityChecker` for pedigree compatibility checkers.
+* Combine compatibility fields and methods in an abstract class`ACompatibilityChecker` to unify methods, builders, and fields.
+
+### jannovar-filter
+
+* Splitting into `jped-cli` and `jannovar-filter`
+* Changing public final members to accessors. 
+* `jannovar-filter` now has the Jannovar DB as the mandatory first argument.
+
+### jannovar-htsjdk
+
+* Changing public final members to accessors. 
+
+## v0.12
+
+### jannovar-htsjdk
 
 * Started bridge module between Jannovar and HTSJDK.
 
-*jannovar-filter*
+### jannovar-filter
 
 * Started tool for mode of inheritance--based filters.
 
-*jannovar-cli*
+### jannovar-cli
 
 * Splitting out bridge module between jannovar-core and HTSJDK to
   jannovar-htsjdk.
@@ -20,7 +108,7 @@
 * Adding `-v` and `-vv` command line options.
 * Fixing problems with block substitution (delins) case (#87).
 
-*jannovar-core*
+### jannovar-core
 
 * Adding initial support for the transcript support level feature of the new VCF
   annotation standard (only in very recent ENSEMBL releases, apparently).
@@ -47,4 +135,4 @@
 * `GenomePosition` and `GenomeInterval` use zero-based coordinates internally
   now.
 
-**v0.11**
+## v0.11

README.md

@@ -13,6 +13,8 @@ Jannovar is licenced under the BSD2 license.
 More information is available in the [Jannovar
 manual](http://jannovar.readthedocs.org/).
 
+Jannovar is compatible with Java 7 and higher.
+
 Quickstart
 ----------
 
@@ -24,21 +26,21 @@ After extracting the ZIP file, you can call Jannovar as follows.
 Download the UCSC transcripts for hg19:
 
 ```
-# java -jar jannovar-cli-0.11.jar download hg19/ucsc
+# java -jar jannovar-cli-0.13.jar download hg19/ucsc
 [...]
 ```
 
 Annotate the example file `small.vcf`:
 
 ```
-# java -jar jannovar-cli-0.11.jar annotate data/hg19_ucsc.ser examples/small.vcf
+# java -jar jannovar-cli-0.13.jar annotate data/hg19_ucsc.ser examples/small.vcf
 [...]
 ```
 
 Inspect the resulting annotated file:
 
 ```
-# less small.jv.vcf
+# less examples/small.jv.vcf
 ```
 
 Also see the

jannovar-cli/pom.xml

@@ -5,13 +5,14 @@
 	<artifactId>jannovar-cli</artifactId>
 	<packaging>jar</packaging>
 
-	<name>jannovar-cli</name>
-	<url>http://maven.apache.org</url>
+	<name>${project.groupId}:${project.artifactId}</name>
+	<description>jannovar-cli is the command line interface for Jannovar</description>
+	<url>http://charite.github.io/jannovar/</url>
 
 	<parent>
 		<groupId>de.charite.compbio</groupId>
 		<artifactId>Jannovar</artifactId>
-		<version>0.12</version>
+		<version>0.13-SNAPSHOT</version>
 	</parent>
 
 	<properties>
@@ -32,9 +33,9 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.seqdoop</groupId>
+			<groupId>com.github.samtools</groupId>
 			<artifactId>htsjdk</artifactId>
-			<version>1.118</version>
+			<version>1.128</version>
 		</dependency>
 		<dependency>
 			<groupId>com.google.guava</groupId>

jannovar-cli/src/main/java/de/charite/compbio/jannovar/Jannovar.java

@@ -1,16 +1,13 @@
 package de.charite.compbio.jannovar;
 
 /** Command line functions from apache */
-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
@@ -78,18 +75,22 @@ public static void main(String argv[]) {
 		// Create the corresponding command.
 		JannovarCommand cmd = null;
 		try {
-			if (argv[0].equals("download"))
+			if (argv[0].equals("download")) {
 				cmd = new DownloadCommand(argv);
-			else if (argv[0].equals("db-list"))
+			} else if (argv[0].equals("db-list")) {
 				cmd = new DatabaseListCommand(argv);
-			else if (argv[0].equals("annotate"))
+			} else if (argv[0].equals("annotate")) {
 				cmd = new AnnotateVCFCommand(argv);
-			else if (argv[0].equals("annotate-pos"))
+			} else if (argv[0].equals("annotate-pos")) {
 				cmd = new AnnotatePositionCommand(argv);
-			else
+			} else {
 				System.err.println("unrecognized command " + argv[0]);
+				printTopLevelHelp();
+			}
 		} catch (CommandLineParsingException e) {
-			System.err.println("problem with parsing command line options: " + e.getMessage());
+			System.err.println("ERROR: problem with parsing command line options: " + e.getMessage());
+			System.err.println("");
+			System.err.println("Use --help for obtaining usage instructions.");
 		} catch (HelpRequestedException e) {
 			return; // no error, user wanted help
 		}
@@ -112,7 +113,7 @@ else if (argv[0].equals("annotate-pos"))
 	 */
 	private static void printTopLevelHelp() {
 		System.err.println("Program: de.charite.compbio.jannovar (functional annotation of VCF files)");
-		System.err.println("Version: 0.10");
+		System.err.println("Version: " + JannovarOptions.JANNOVAR_VERSION);
 		System.err.println("Contact: Peter N Robinson <[email protected]>");
 		System.err.println("");
 		System.err.println("Usage: java -jar de.charite.compbio.jannovar.jar <command> [options]");
@@ -124,8 +125,10 @@ private static void printTopLevelHelp() {
 		System.err.println("");
 		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("         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("");
 	}
 

jannovar-core/src/main/java/de/charite/compbio/jannovar/JannovarOptions.java → jannovar-cli/src/main/java/de/charite/compbio/jannovar/JannovarOptions.java

@@ -16,6 +16,9 @@
  * @author Peter N Robinson <[email protected]>
  */
 public final class JannovarOptions {
+	/** the version of the program */
+	public static final String JANNOVAR_VERSION = "0.13";
+
 	/** the selected command */
 	public Command command = null;
 
@@ -67,6 +70,12 @@ public final class JannovarOptions {
 	/** whether or not to write out the VCF annotation standard fields */
 	public boolean writeVCFAnnotationStandardInfoFields = true;
 
+	/** whether or not to escape characters like <code>'='</code> in the <code>ANN</code> VCF field. */
+	public boolean escapeAnnField = true;
+
+	/** whether or not to shift variants towards the 3' end of the transcript */
+	public boolean nt3PrimeShifting = true;
+
 	// TODO(holtgrem): enable and use this!
 	/** path to output VCF file path (overrides generation of file name from input file name) */
 	public String outVCFFile = null;
@@ -83,13 +92,6 @@ public enum Command {
 		DOWNLOAD, ANNOTATE_VCF, ANNOTATE_POSITION, DB_LIST
 	}
 
-	/**
-	 * Enumeration of the supported data sources.
-	 */
-	public enum DataSource {
-		ENSEMBL, REFSEQ, REFSEQ_CURATED, UCSC
-	}
-
 	/**
 	 * Print option values to stderr.
 	 */

jannovar-cli/src/main/java/de/charite/compbio/jannovar/cmd/CommandLineParsingException.java

@@ -9,10 +9,18 @@
  */
 public class CommandLineParsingException extends JannovarException {
 
+	public CommandLineParsingException() {
+		super();
+	}
+
 	public CommandLineParsingException(String msg) {
 		super(msg);
 	}
 
+	public CommandLineParsingException(String msg, Throwable cause) {
+		super(msg, cause);
+	}
+
 	private static final long serialVersionUID = 1L;
 
 }

jannovar-cli/src/main/java/de/charite/compbio/jannovar/cmd/HelpRequestedException.java

@@ -12,10 +12,15 @@ public class HelpRequestedException extends JannovarException {
 	private static final long serialVersionUID = 1L;
 
 	public HelpRequestedException() {
+		super();
 	}
 
 	public HelpRequestedException(String msg) {
 		super(msg);
 	}
 
+	public HelpRequestedException(String msg, Throwable cause) {
+		super(msg, cause);
+	}
+
 }