添加ProtectedCLGATK类，方便调试protect模块中的代码
This commit is contained in:
parent
56e0098a71
commit
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@ -1,6 +1,7 @@
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.idea/
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.idea/
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.queue/
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.queue/
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**/target/
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**/target/
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output/
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/*.bam
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/*.bam
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/*.bai
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/*.bai
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/*.bed
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/*.bed
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@ -0,0 +1,75 @@
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{
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// 使用 IntelliSense 了解相关属性。
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// 悬停以查看现有属性的描述。
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// 欲了解更多信息，请访问: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"type": "java",
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"name": "BaseRecalibrator",
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"request": "launch",
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// "mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
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"mainClass": "org.broadinstitute.gatk.engine.ProtectedCLGATK",
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"projectName": "gatk-tools-protected",
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//"classPaths": [
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// "${workspaceFolder}/target/excutable/GenomeAnalysisTK.jar",
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// "${workspaceFolder}/target/excutable/lib/*"
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//],
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//"classPaths": [
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// "${workspaceFolder}/protected/gatk-tools-protected/target/classes/",
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// "${workspaceFolder}/public/gatk-engine/target/classes/",
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//],
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//"vmArgs": "-verbose:class",
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"args": [
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"-T", "BaseRecalibrator",
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"-R",
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"~/reference/bwa/human_g1k_v37_decoy.fasta",
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"-knownSites",
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"~/data/reference/hg19/vcfs/dbsnp_138.b37.vcf",
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"-knownSites",
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"~/data/reference/hg19/vcfs/1000G_phase1.indels.b37.vcf",
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"-I",
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//"~/data/fastdup-mini-md.bam",
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//"~/data/f1kw.sam",
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//"~/data/ft1kw.sam",
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//"~/data/difft1kw.sam",
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//"~/data/diff.sam",
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//"~/data/diff2kw.sam",
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//"~/data1/x.bam",
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//"~/data1/y.bam",
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"~/data/z.bam",
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//"~/data/z-3.sam",
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//"~/data/z-1.sam",
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"-o",
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// "./output/out-bqsr.table",
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//"./output/x.table",
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//"./output/y.table",
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//"./output/z.table",
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//"./output/z-3.table",
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"./output/f-1.table",
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// "--enable-baq",
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]
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},
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{
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"type": "java",
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"name": "ApplyBQSR",
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"request": "launch",
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"mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
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"projectName": "gatk",
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"args": [
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"ApplyBQSR",
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"-R",
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"~/reference/bwa/human_g1k_v37_decoy.fasta",
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"-I",
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"~/data1/x.bam",
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//"~/data/z.bam",
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//"~/data/ft1kw.sam",
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"-bqsr",
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"./output/f-1.table",
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"-O",
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"./output/f-1.sam",
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]
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}
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]
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}
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{
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"java.compile.nullAnalysis.mode": "automatic",
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"java.configuration.updateBuildConfiguration": "automatic",
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"java.debug.settings.onBuildFailureProceed": true,
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"java.home" : "/usr/lib/jvm/java-8-openjdk-amd64"
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}
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export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
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export PATH=$JAVA_HOME/bin:$PATH
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4
pom.xml
4
pom.xml
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<dependency>
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<dependency>
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<groupId>com.sun</groupId>
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<groupId>com.sun</groupId>
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<artifactId>tools</artifactId>
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<artifactId>tools</artifactId>
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<version>1.8</version>
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<!-- 使用你的JDK版本 -->
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<scope>system</scope>
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<systemPath>/usr/lib/jvm/java-8-openjdk-amd64/lib/tools.jar</systemPath>
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</dependency>
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</dependency>
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</dependencies>
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</dependencies>
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@ -0,0 +1,355 @@
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package org.broadinstitute.gatk.engine;
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import htsjdk.samtools.SAMException;
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import htsjdk.samtools.util.zip.DeflaterFactory;
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import htsjdk.tribble.TribbleException;
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import org.broadinstitute.gatk.utils.commandline.Argument;
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import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
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import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
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import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
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import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager;
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import org.broadinstitute.gatk.engine.walkers.Attribution;
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import org.broadinstitute.gatk.engine.walkers.Walker;
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import org.broadinstitute.gatk.utils.exceptions.UserException;
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import org.broadinstitute.gatk.utils.help.*;
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import org.broadinstitute.gatk.utils.text.TextFormattingUtils;
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import java.net.InetAddress;
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import java.util.*;
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// 添加这个类就是为了能调试gatk-tools-protected里的代码
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public class ProtectedCLGATK extends CommandLineExecutable {
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/**
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* A complete list of tools (sometimes also called walkers because they "walk"
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* through the data to perform analyses)
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* is available in the online documentation.
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*/
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@Argument(fullName = "analysis_type", shortName = "T", doc = "Name of the tool to run")
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private String analysisName = null;
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// our argument collection, the collection of command line args we accept
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@ArgumentCollection
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private GATKArgumentCollection argCollection = new GATKArgumentCollection();
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/**
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* Get pleasing info about the GATK.
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*
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* @return A list of Strings that contain pleasant info about the GATK.
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*/
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@Override
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protected ApplicationDetails getApplicationDetails() {
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return new ApplicationDetails(createApplicationHeader(),
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getAttribution(),
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ApplicationDetails.createDefaultRunningInstructions(getClass()),
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getAdditionalHelp());
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}
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@Override
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public String getAnalysisName() {
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return analysisName;
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}
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@Override
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protected GATKArgumentCollection getArgumentCollection() {
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return argCollection;
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}
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/**
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* Required main method implementation.
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*/
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public static void main(String[] argv) {
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try {
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ProtectedCLGATK instance = new ProtectedCLGATK();
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start(instance, argv);
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System.exit(CommandLineProgram.result); // todo -- this is a painful hack
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} catch (UserException e) {
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exitSystemWithUserError(e);
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} catch (TribbleException e) {
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// We can generate Tribble Exceptions in weird places when e.g. VCF genotype
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// fields are
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// lazy loaded, so they aren't caught elsewhere and made into User Exceptions
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exitSystemWithUserError(e);
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} catch (SAMException e) {
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checkForMaskedUserErrors(e);
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exitSystemWithSamError(e);
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} catch (OutOfMemoryError e) {
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exitSystemWithUserError(new UserException.NotEnoughMemory());
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} catch (Throwable t) {
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checkForMaskedUserErrors(t);
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exitSystemWithError(t);
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}
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}
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public static final String PICARD_TEXT_SAM_FILE_ERROR_1 = "Cannot use index file with textual SAM file";
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public static final String PICARD_TEXT_SAM_FILE_ERROR_2 = "Cannot retrieve file pointers within SAM text files";
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public static final String NO_SPACE_LEFT_ON_DEVICE_ERROR = "No space left on device";
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public static final String DISK_QUOTA_EXCEEDED_ERROR = "Disk quota exceeded";
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private static void checkForMaskedUserErrors(final Throwable t) {
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// masked out of memory error
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if (t instanceof OutOfMemoryError)
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exitSystemWithUserError(new UserException.NotEnoughMemory());
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// masked user error
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if (t instanceof UserException || t instanceof TribbleException)
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exitSystemWithUserError(new UserException(t.getMessage()));
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// no message means no masked error
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final String message = t.getMessage();
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if (message == null)
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return;
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// too many open files error
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if (message.contains("Too many open files"))
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exitSystemWithUserError(new UserException.TooManyOpenFiles());
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// malformed BAM looks like a SAM file
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if (message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) || message.contains(PICARD_TEXT_SAM_FILE_ERROR_2))
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exitSystemWithSamError(t);
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// can't close tribble index when writing
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if (message.contains("Unable to close index for"))
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exitSystemWithUserError(new UserException(t.getCause() == null ? message : t.getCause().getMessage()));
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// disk is full
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if (message.contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || message.contains(DISK_QUOTA_EXCEEDED_ERROR))
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exitSystemWithUserError(new UserException.NoSpaceOnDevice());
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// masked error wrapped in another one
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if (t.getCause() != null)
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checkForMaskedUserErrors(t.getCause());
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}
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/**
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* Creates the a short blurb about the GATK, copyright info, and where to get
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* documentation.
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*
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* @return The application header.
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*/
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public static List<String> createApplicationHeader() {
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List<String> header = new ArrayList<String>();
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header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s", getVersionNumber(),
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getBuildTime()));
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header.add("Copyright (c) 2010-2016 The Broad Institute");
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header.add("For support and documentation go to " + HelpConstants.BASE_GATK_URL);
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try {
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header.add("[" + new Date() + "] Executing on " +
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System.getProperty("os.name") + " " + System.getProperty("os.version") +
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" " + System.getProperty("os.arch"));
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header.add(System.getProperty("java.vm.name") +
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" " + System.getProperty("java.runtime.version"));
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} catch (Exception e) {
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/* Unpossible! */ }
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return header;
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}
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/**
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* If the user supplied any additional attribution, return it here.
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*
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* @return Additional attribution if supplied by the user. Empty (non-null) list
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* otherwise.
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*/
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private List<String> getAttribution() {
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List<String> attributionLines = new ArrayList<String>();
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// If no analysis name is present, fill in extra help on the walkers.
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WalkerManager walkerManager = engine.getWalkerManager();
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String analysisName = getAnalysisName();
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if (analysisName != null && walkerManager.exists(analysisName)) {
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Class<? extends Walker> walkerType = walkerManager.getWalkerClassByName(analysisName);
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if (walkerType.isAnnotationPresent(Attribution.class))
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attributionLines.addAll(Arrays.asList(walkerType.getAnnotation(Attribution.class).value()));
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}
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return attributionLines;
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}
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/**
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* Retrieves additional information about GATK walkers.
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* the code in HelpFormatter and supply it as a helper to this method.
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*
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* @return A string summarizing the walkers available in this distribution.
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*/
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private String getAdditionalHelp() {
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String additionalHelp;
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// If no analysis name is present, fill in extra help on the walkers.
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WalkerManager walkerManager = engine.getWalkerManager();
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if (analysisName != null && walkerManager.exists(analysisName))
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additionalHelp = getWalkerHelp(walkerManager.getWalkerClassByName(analysisName));
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else
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additionalHelp = getAllWalkerHelp();
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return additionalHelp;
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}
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private static final int PACKAGE_INDENT = 1;
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private static final int WALKER_INDENT = 3;
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private static final String FIELD_SEPARATOR = " ";
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private String getWalkerHelp(Class<? extends Walker> walkerType) {
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// Construct a help string to output details on this walker.
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StringBuilder additionalHelp = new StringBuilder();
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Formatter formatter = new Formatter(additionalHelp);
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formatter.format("Available Reference Ordered Data types:%n");
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formatter.format(new FeatureManager().userFriendlyListOfAvailableFeatures());
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formatter.format("%n");
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formatter.format("For a full description of this walker, see its GATKdocs at:%n");
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formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
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return additionalHelp.toString();
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}
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/**
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* Load in additional help information about all available walkers.
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*
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* @return A string representation of the additional help.
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*/
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private String getAllWalkerHelp() {
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// Construct a help string to output available walkers.
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StringBuilder additionalHelp = new StringBuilder();
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Formatter formatter = new Formatter(additionalHelp);
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// Get the list of walker names from the walker manager.
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WalkerManager walkerManager = engine.getWalkerManager();
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// Build a list sorted by walker display name. As this information is collected,
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// keep track of the longest
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// package / walker name for later formatting.
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SortedSet<HelpEntry> helpText = new TreeSet<HelpEntry>(new HelpEntryComparator());
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int longestPackageName = 0;
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int longestWalkerName = 0;
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for (Map.Entry<String, Collection<Class<? extends Walker>>> walkersByPackage : walkerManager
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.getWalkerNamesByPackage(true).entrySet()) {
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// Get the display name.
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String packageName = walkersByPackage.getKey();
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String packageDisplayName = walkerManager.getPackageDisplayName(walkersByPackage.getKey());
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String packageHelpText = walkerManager.getPackageSummaryText(packageName);
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// Compute statistics about which names is longest.
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longestPackageName = Math.max(longestPackageName, packageDisplayName.length());
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SortedSet<HelpEntry> walkersInPackage = new TreeSet<HelpEntry>(new HelpEntryComparator());
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for (Class<? extends Walker> walkerType : walkersByPackage.getValue()) {
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String walkerName = walkerType.getName();
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String walkerDisplayName = walkerManager.getName(walkerType);
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String walkerHelpText = walkerManager.getWalkerSummaryText(walkerType);
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longestWalkerName = Math.max(longestWalkerName, walkerManager.getName(walkerType).length());
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walkersInPackage.add(new HelpEntry(walkerName, walkerDisplayName, walkerHelpText));
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}
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// Dump the walkers into the sorted set.
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helpText.add(new HelpEntry(packageName, packageDisplayName, packageHelpText,
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Collections.unmodifiableSortedSet(walkersInPackage)));
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}
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final int headerWidth = Math.max(longestPackageName + PACKAGE_INDENT, longestWalkerName + WALKER_INDENT);
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for (HelpEntry packageHelp : helpText) {
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printDescriptorLine(formatter, PACKAGE_INDENT, packageHelp.displayName, headerWidth, FIELD_SEPARATOR,
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packageHelp.summary, TextFormattingUtils.DEFAULT_LINE_WIDTH);
|
||||||
|
|
||||||
|
for (HelpEntry walkerHelp : packageHelp.children)
|
||||||
|
printDescriptorLine(formatter, WALKER_INDENT, walkerHelp.displayName, headerWidth, FIELD_SEPARATOR,
|
||||||
|
walkerHelp.summary, TextFormattingUtils.DEFAULT_LINE_WIDTH);
|
||||||
|
|
||||||
|
// Print a blank line between sets of walkers.
|
||||||
|
printDescriptorLine(formatter, 0, "", headerWidth, FIELD_SEPARATOR, "",
|
||||||
|
TextFormattingUtils.DEFAULT_LINE_WIDTH);
|
||||||
|
}
|
||||||
|
|
||||||
|
return additionalHelp.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
private void printDescriptorLine(Formatter formatter,
|
||||||
|
int headerIndentWidth,
|
||||||
|
String header,
|
||||||
|
int headerWidth,
|
||||||
|
String fieldSeparator,
|
||||||
|
String description,
|
||||||
|
int lineWidth) {
|
||||||
|
final int headerPaddingWidth = headerWidth - header.length() - headerIndentWidth;
|
||||||
|
final int descriptionWidth = lineWidth - fieldSeparator.length() - headerWidth;
|
||||||
|
List<String> wordWrappedText = TextFormattingUtils.wordWrap(description, descriptionWidth);
|
||||||
|
|
||||||
|
String headerIndentFormatString = headerIndentWidth > 0 ? "%" + headerIndentWidth + "s" : "%s";
|
||||||
|
String headerPaddingFormatString = headerPaddingWidth > 0 ? "%" + headerPaddingWidth + "s" : "%s";
|
||||||
|
String headerWidthFormatString = headerWidth > 0 ? "%" + headerWidth + "s" : "%s";
|
||||||
|
|
||||||
|
// Output description line.
|
||||||
|
formatter.format(headerIndentFormatString + "%s" + headerPaddingFormatString + "%s%s%n",
|
||||||
|
"", header, "", fieldSeparator, wordWrappedText.size() > 0 ? wordWrappedText.get(0) : "");
|
||||||
|
for (int i = 1; i < wordWrappedText.size(); i++)
|
||||||
|
formatter.format(headerWidthFormatString + "%s%s%n", "", fieldSeparator, wordWrappedText.get(i));
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Represents a given help entry; contains a display name, a summary and
|
||||||
|
* optionally some children.
|
||||||
|
*/
|
||||||
|
class HelpEntry {
|
||||||
|
public final String uid;
|
||||||
|
public final String displayName;
|
||||||
|
public final String summary;
|
||||||
|
public final SortedSet<HelpEntry> children;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Create a new help entry with the given display name, summary and children.
|
||||||
|
*
|
||||||
|
* @param uid a unique identifier. Usually, the java package.
|
||||||
|
* @param displayName display name for this help entry.
|
||||||
|
* @param summary summary for this help entry.
|
||||||
|
* @param children children for this help entry.
|
||||||
|
*/
|
||||||
|
public HelpEntry(String uid, String displayName, String summary, SortedSet<HelpEntry> children) {
|
||||||
|
this.uid = uid;
|
||||||
|
this.displayName = displayName;
|
||||||
|
this.summary = summary;
|
||||||
|
this.children = children;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Create a new help entry with the given display name, summary and children.
|
||||||
|
*
|
||||||
|
* @param uid a unique identifier. Usually, the java package.
|
||||||
|
* @param displayName display name for this help entry.
|
||||||
|
* @param summary summary for this help entry.
|
||||||
|
*/
|
||||||
|
public HelpEntry(String uid, String displayName, String summary) {
|
||||||
|
this(uid, displayName, summary, null);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Compare two help entries by display name.
|
||||||
|
*/
|
||||||
|
class HelpEntryComparator implements Comparator<HelpEntry> {
|
||||||
|
private static TextFormattingUtils.CaseInsensitiveComparator textComparator = new TextFormattingUtils.CaseInsensitiveComparator();
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Compares the order of lhs to rhs, not taking case into account.
|
||||||
|
*
|
||||||
|
* @param lhs First object to compare.
|
||||||
|
* @param rhs Second object to compare.
|
||||||
|
* @return 0 if objects are identical; -1 if lhs is before rhs, 1 if rhs is
|
||||||
|
* before lhs. Nulls are treated as after everything else.
|
||||||
|
*/
|
||||||
|
public int compare(HelpEntry lhs, HelpEntry rhs) {
|
||||||
|
if (lhs == null && rhs == null)
|
||||||
|
return 0;
|
||||||
|
if (lhs == null || lhs.displayName.equals(""))
|
||||||
|
return 1;
|
||||||
|
if (rhs == null || rhs.displayName.equals(""))
|
||||||
|
return -1;
|
||||||
|
return lhs.displayName.equals(rhs.displayName) ? textComparator.compare(lhs.uid, rhs.uid)
|
||||||
|
: textComparator.compare(lhs.displayName, rhs.displayName);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -74,6 +74,12 @@ public class PluginManager<PluginType> {
|
||||||
if (!url.equals(cwd))
|
if (!url.equals(cwd))
|
||||||
classPathUrls.add(url);
|
classPathUrls.add(url);
|
||||||
|
|
||||||
|
//try {
|
||||||
|
// // classPathUrls.add(new URL("file:/home/zzh/work/ngs/gatk3.8/gatk-protected/protected/gatk-tools-protected/target/classes/"));
|
||||||
|
// classPathUrls.add(new URL("file:/home/zzh/work/ngs/gatk3.8/gatk-protected/protected/gatk-tools-protected/target/gatk-tools-protected-3.8-1.jar"));
|
||||||
|
//} catch (Exception e) {
|
||||||
|
//}
|
||||||
|
|
||||||
defaultReflections = new Reflections( new ConfigurationBuilder()
|
defaultReflections = new Reflections( new ConfigurationBuilder()
|
||||||
.setUrls(classPathUrls)
|
.setUrls(classPathUrls)
|
||||||
.setScanners(new SubTypesScanner()));
|
.setScanners(new SubTypesScanner()));
|
||||||
|
|
@ -148,10 +154,18 @@ public class PluginManager<PluginType> {
|
||||||
.setScanners(new SubTypesScanner()));
|
.setScanners(new SubTypesScanner()));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// if (classpath != null)
|
||||||
|
// for (URL cp : classpath)
|
||||||
|
// System.out.println("zzh: " + cp.toString());
|
||||||
|
// else
|
||||||
|
// System.out.println("zzh: classpath is null");
|
||||||
|
|
||||||
// Load all classes types filtering them by concrete.
|
// Load all classes types filtering them by concrete.
|
||||||
@SuppressWarnings("unchecked")
|
@SuppressWarnings("unchecked")
|
||||||
Set<Class<? extends PluginType>> allTypes = reflections.getSubTypesOf(pluginType);
|
Set<Class<? extends PluginType>> allTypes = reflections.getSubTypesOf(pluginType);
|
||||||
|
|
||||||
for (Class<? extends PluginType> type : allTypes) {
|
for (Class<? extends PluginType> type : allTypes) {
|
||||||
|
// System.out.println("zzh: " + type.getName());
|
||||||
// The plugin manager does not support anonymous classes; to be a plugin, a class must have a name.
|
// The plugin manager does not support anonymous classes; to be a plugin, a class must have a name.
|
||||||
if(JVMUtils.isAnonymous(type))
|
if(JVMUtils.isAnonymous(type))
|
||||||
continue;
|
continue;
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue