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添加ProtectedCLGATK类，方便调试protect模块中的代码

This commit is contained in:
zzh 2026-01-07 18:21:50 +08:00
parent 56e0098a71
commit 266936ed73
7 changed files with 458 additions and 1 deletions
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1
.gitignore vendored
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@ -1,6 +1,7 @@
.idea/
.queue/
**/target/
output/
/*.bam
/*.bai
/*.bed

75
.vscode/launch.json vendored 100644
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@ -0,0 +1,75 @@
{
// 使用 IntelliSense 了解相关属性。
// 悬停以查看现有属性的描述。
// 欲了解更多信息，请访问: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [
{
"type": "java",
"name": "BaseRecalibrator",
"request": "launch",
// "mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
"mainClass": "org.broadinstitute.gatk.engine.ProtectedCLGATK",
"projectName": "gatk-tools-protected",
//"classPaths": [
// "${workspaceFolder}/target/excutable/GenomeAnalysisTK.jar",
// "${workspaceFolder}/target/excutable/lib/*"
//],
//"classPaths": [
// "${workspaceFolder}/protected/gatk-tools-protected/target/classes/",
// "${workspaceFolder}/public/gatk-engine/target/classes/",
//],
//"vmArgs": "-verbose:class",
"args": [
"-T", "BaseRecalibrator",
"-R",
"~/reference/bwa/human_g1k_v37_decoy.fasta",
"-knownSites",
"~/data/reference/hg19/vcfs/dbsnp_138.b37.vcf",
"-knownSites",
"~/data/reference/hg19/vcfs/1000G_phase1.indels.b37.vcf",
"-I",
//"~/data/fastdup-mini-md.bam",
//"~/data/f1kw.sam",
//"~/data/ft1kw.sam",
//"~/data/difft1kw.sam",
//"~/data/diff.sam",
//"~/data/diff2kw.sam",
//"~/data1/x.bam",
//"~/data1/y.bam",
"~/data/z.bam",
//"~/data/z-3.sam",
//"~/data/z-1.sam",
"-o",
// "./output/out-bqsr.table",
//"./output/x.table",
//"./output/y.table",
//"./output/z.table",
//"./output/z-3.table",
"./output/f-1.table",
// "--enable-baq",
]
},
{
"type": "java",
"name": "ApplyBQSR",
"request": "launch",
"mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
"projectName": "gatk",
"args": [
"ApplyBQSR",
"-R",
"~/reference/bwa/human_g1k_v37_decoy.fasta",
"-I",
"~/data1/x.bam",
//"~/data/z.bam",
//"~/data/ft1kw.sam",
"-bqsr",
"./output/f-1.table",
"-O",
"./output/f-1.sam",
]
}
]
}

6
.vscode/settings.json vendored 100644
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@ -0,0 +1,6 @@
{
"java.compile.nullAnalysis.mode": "automatic",
"java.configuration.updateBuildConfiguration": "automatic",
"java.debug.settings.onBuildFailureProceed": true,
"java.home" : "/usr/lib/jvm/java-8-openjdk-amd64"
}

2
java.sh 100755
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@ -0,0 +1,2 @@
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64
export PATH=$JAVA_HOME/bin:$PATH

4
pom.xml
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@ -86,6 +86,10 @@
<dependency>
<groupId>com.sun</groupId>
<artifactId>tools</artifactId>
<version>1.8</version>
<!-- 使用你的JDK版本 -->
<scope>system</scope>
<systemPath>/usr/lib/jvm/java-8-openjdk-amd64/lib/tools.jar</systemPath>
</dependency>
</dependencies>

355
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/ProtectedCLGATK.java 100644
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@ -0,0 +1,355 @@
package org.broadinstitute.gatk.engine;
import htsjdk.samtools.SAMException;
import htsjdk.samtools.util.zip.DeflaterFactory;
import htsjdk.tribble.TribbleException;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
import org.broadinstitute.gatk.utils.refdata.tracks.FeatureManager;
import org.broadinstitute.gatk.engine.walkers.Attribution;
import org.broadinstitute.gatk.engine.walkers.Walker;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.*;
import org.broadinstitute.gatk.utils.text.TextFormattingUtils;
import java.net.InetAddress;
import java.util.*;
// 添加这个类就是为了能调试gatk-tools-protected里的代码
public class ProtectedCLGATK extends CommandLineExecutable {
/**
* A complete list of tools (sometimes also called walkers because they "walk"
* through the data to perform analyses)
* is available in the online documentation.
*/
@Argument(fullName = "analysis_type", shortName = "T", doc = "Name of the tool to run")
private String analysisName = null;
// our argument collection, the collection of command line args we accept
@ArgumentCollection
private GATKArgumentCollection argCollection = new GATKArgumentCollection();
/**
* Get pleasing info about the GATK.
*
* @return A list of Strings that contain pleasant info about the GATK.
*/
@Override
protected ApplicationDetails getApplicationDetails() {
return new ApplicationDetails(createApplicationHeader(),
getAttribution(),
ApplicationDetails.createDefaultRunningInstructions(getClass()),
getAdditionalHelp());
}
@Override
public String getAnalysisName() {
return analysisName;
}
@Override
protected GATKArgumentCollection getArgumentCollection() {
return argCollection;
}
/**
* Required main method implementation.
*/
public static void main(String[] argv) {
try {
ProtectedCLGATK instance = new ProtectedCLGATK();
start(instance, argv);
System.exit(CommandLineProgram.result); // todo -- this is a painful hack
} catch (UserException e) {
exitSystemWithUserError(e);
} catch (TribbleException e) {
// We can generate Tribble Exceptions in weird places when e.g. VCF genotype
// fields are
// lazy loaded, so they aren't caught elsewhere and made into User Exceptions
exitSystemWithUserError(e);
} catch (SAMException e) {
checkForMaskedUserErrors(e);
exitSystemWithSamError(e);
} catch (OutOfMemoryError e) {
exitSystemWithUserError(new UserException.NotEnoughMemory());
} catch (Throwable t) {
checkForMaskedUserErrors(t);
exitSystemWithError(t);
}
}
public static final String PICARD_TEXT_SAM_FILE_ERROR_1 = "Cannot use index file with textual SAM file";
public static final String PICARD_TEXT_SAM_FILE_ERROR_2 = "Cannot retrieve file pointers within SAM text files";
public static final String NO_SPACE_LEFT_ON_DEVICE_ERROR = "No space left on device";
public static final String DISK_QUOTA_EXCEEDED_ERROR = "Disk quota exceeded";
private static void checkForMaskedUserErrors(final Throwable t) {
// masked out of memory error
if (t instanceof OutOfMemoryError)
exitSystemWithUserError(new UserException.NotEnoughMemory());
// masked user error
if (t instanceof UserException || t instanceof TribbleException)
exitSystemWithUserError(new UserException(t.getMessage()));
// no message means no masked error
final String message = t.getMessage();
if (message == null)
return;
// too many open files error
if (message.contains("Too many open files"))
exitSystemWithUserError(new UserException.TooManyOpenFiles());
// malformed BAM looks like a SAM file
if (message.contains(PICARD_TEXT_SAM_FILE_ERROR_1) || message.contains(PICARD_TEXT_SAM_FILE_ERROR_2))
exitSystemWithSamError(t);
// can't close tribble index when writing
if (message.contains("Unable to close index for"))
exitSystemWithUserError(new UserException(t.getCause() == null ? message : t.getCause().getMessage()));
// disk is full
if (message.contains(NO_SPACE_LEFT_ON_DEVICE_ERROR) || message.contains(DISK_QUOTA_EXCEEDED_ERROR))
exitSystemWithUserError(new UserException.NoSpaceOnDevice());
// masked error wrapped in another one
if (t.getCause() != null)
checkForMaskedUserErrors(t.getCause());
}
/**
* Creates the a short blurb about the GATK, copyright info, and where to get
* documentation.
*
* @return The application header.
*/
public static List<String> createApplicationHeader() {
List<String> header = new ArrayList<String>();
header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s", getVersionNumber(),
getBuildTime()));
header.add("Copyright (c) 2010-2016 The Broad Institute");
header.add("For support and documentation go to " + HelpConstants.BASE_GATK_URL);
try {
header.add("[" + new Date() + "] Executing on " +
System.getProperty("os.name") + " " + System.getProperty("os.version") +
" " + System.getProperty("os.arch"));
header.add(System.getProperty("java.vm.name") +
" " + System.getProperty("java.runtime.version"));
} catch (Exception e) {
/* Unpossible! */ }
return header;
}
/**
* If the user supplied any additional attribution, return it here.
*
* @return Additional attribution if supplied by the user. Empty (non-null) list
* otherwise.
*/
private List<String> getAttribution() {
List<String> attributionLines = new ArrayList<String>();
// If no analysis name is present, fill in extra help on the walkers.
WalkerManager walkerManager = engine.getWalkerManager();
String analysisName = getAnalysisName();
if (analysisName != null && walkerManager.exists(analysisName)) {
Class<? extends Walker> walkerType = walkerManager.getWalkerClassByName(analysisName);
if (walkerType.isAnnotationPresent(Attribution.class))
attributionLines.addAll(Arrays.asList(walkerType.getAnnotation(Attribution.class).value()));
}
return attributionLines;
}
/**
* Retrieves additional information about GATK walkers.
* the code in HelpFormatter and supply it as a helper to this method.
*
* @return A string summarizing the walkers available in this distribution.
*/
private String getAdditionalHelp() {
String additionalHelp;
// If no analysis name is present, fill in extra help on the walkers.
WalkerManager walkerManager = engine.getWalkerManager();
if (analysisName != null && walkerManager.exists(analysisName))
additionalHelp = getWalkerHelp(walkerManager.getWalkerClassByName(analysisName));
else
additionalHelp = getAllWalkerHelp();
return additionalHelp;
}
private static final int PACKAGE_INDENT = 1;
private static final int WALKER_INDENT = 3;
private static final String FIELD_SEPARATOR = " ";
private String getWalkerHelp(Class<? extends Walker> walkerType) {
// Construct a help string to output details on this walker.
StringBuilder additionalHelp = new StringBuilder();
Formatter formatter = new Formatter(additionalHelp);
formatter.format("Available Reference Ordered Data types:%n");
formatter.format(new FeatureManager().userFriendlyListOfAvailableFeatures());
formatter.format("%n");
formatter.format("For a full description of this walker, see its GATKdocs at:%n");
formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
return additionalHelp.toString();
}
/**
* Load in additional help information about all available walkers.
*
* @return A string representation of the additional help.
*/
private String getAllWalkerHelp() {
// Construct a help string to output available walkers.
StringBuilder additionalHelp = new StringBuilder();
Formatter formatter = new Formatter(additionalHelp);
// Get the list of walker names from the walker manager.
WalkerManager walkerManager = engine.getWalkerManager();
// Build a list sorted by walker display name. As this information is collected,
// keep track of the longest
// package / walker name for later formatting.
SortedSet<HelpEntry> helpText = new TreeSet<HelpEntry>(new HelpEntryComparator());
int longestPackageName = 0;
int longestWalkerName = 0;
for (Map.Entry<String, Collection<Class<? extends Walker>>> walkersByPackage : walkerManager
.getWalkerNamesByPackage(true).entrySet()) {
// Get the display name.
String packageName = walkersByPackage.getKey();
String packageDisplayName = walkerManager.getPackageDisplayName(walkersByPackage.getKey());
String packageHelpText = walkerManager.getPackageSummaryText(packageName);
// Compute statistics about which names is longest.
longestPackageName = Math.max(longestPackageName, packageDisplayName.length());
SortedSet<HelpEntry> walkersInPackage = new TreeSet<HelpEntry>(new HelpEntryComparator());
for (Class<? extends Walker> walkerType : walkersByPackage.getValue()) {
String walkerName = walkerType.getName();
String walkerDisplayName = walkerManager.getName(walkerType);
String walkerHelpText = walkerManager.getWalkerSummaryText(walkerType);
longestWalkerName = Math.max(longestWalkerName, walkerManager.getName(walkerType).length());
walkersInPackage.add(new HelpEntry(walkerName, walkerDisplayName, walkerHelpText));
}
// Dump the walkers into the sorted set.
helpText.add(new HelpEntry(packageName, packageDisplayName, packageHelpText,
Collections.unmodifiableSortedSet(walkersInPackage)));
}
final int headerWidth = Math.max(longestPackageName + PACKAGE_INDENT, longestWalkerName + WALKER_INDENT);
for (HelpEntry packageHelp : helpText) {
printDescriptorLine(formatter, PACKAGE_INDENT, packageHelp.displayName, headerWidth, FIELD_SEPARATOR,
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);
}
}

16
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java
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@ -74,6 +74,12 @@ public class PluginManager<PluginType> {
if (!url.equals(cwd))
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()
.setUrls(classPathUrls)
.setScanners(new SubTypesScanner()));
@ -148,10 +154,18 @@ public class PluginManager<PluginType> {
.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.
@SuppressWarnings("unchecked")
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.
if(JVMUtils.isAnonymous(type))
continue;