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package org.broadinstitute.gatk.tools.walkers.bqsr;
import com.google.java.contract.Requires;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Input;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.RodWalker;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
import org.broadinstitute.gatk.utils.help.HelpConstants;
import org.broadinstitute.gatk.utils.recalibration.RecalUtils;
import org.broadinstitute.gatk.utils.recalibration.RecalibrationReport;
import org.broadinstitute.gatk.utils.recalibration.BaseRecalibration;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* Tool to analyze and evaluate base recalibration tables.
* <p/>
* It generates plots to assess the quality of a recalibration run.
*
* <h3>Input</h3>
*
* The tool can take up to three different sets of recalibration tables.
* The resulting plots will be overlaid on top of each other to make
* comparisons easy.
*
* <table style="text-align: left">
* <thead>
* <tr><th>Set</th><th>Argument</th><th>Label</th><th>Color</th><th>Description</th></tr>
* </thead>
* <tbody>
* <tr><td>Original</td><td>-before</td><td>BEFORE</td><td style="color: #ff34b3">Maroon1</td>
* <td>First pass recalibration
* tables obtained from applying {@link BaseRecalibration}
* on the original alignment.</td></tr>
* <tr><td>Recalibrated</td><td>-after</td><td>AFTER</td><td style="color: #0000ff">Blue</td>
* <td>Second pass recalibration tables
* results from the application of {@link BaseRecalibration}
* on the alignment recalibrated using the first pass tables</td></tr>
* <tr><td>Input</td><td>-BQSR</td><td>BQSR</td><td style="color: #000000">Black</td>
* <td>Any recalibration table without a specific role</td></tr>
* </tbody>
* </table>
* <br/>
*
* You need to specify one set at least. Multiple sets need to have the same values for the following parameters:
* <br/></br>
* <i>covariate (order is not important), no_standard_covs, run_without_dbsnp, solid_recal_mode,
* solid_nocall_strategy, mismatches_context_size, mismatches_default_quality, deletions_default_quality,
* insertions_default_quality, maximum_cycle_value, low_quality_tail, default_platform, force_platform,
* quantizing_levels</i> and <i>binary_tag_name</i>
* <h3>Output</h3>
*
* Currently this tool generates two outputs:
*
* <dl>
* <dt style="font-weight: normal">-plots <i>my-report.pdf</i></dt>
* <dd>A pdf document that encloses plots to assess the quality of the recalibration.</dd>
* <dt style="font-weight: normal">-csv <i>my-report.csv</i></dt>
* <dd>A csv file that contains a table with all the data required to generate those plots.</dd>
* </dl>
*
* You need to specify at least one of them.
*
* <h3>Other Arguments</h3>
*
* <h4>-ignoreLMT, --ignoreLastModificationTimes</h4>
*
* when set, no warning message will be displayed in the -before recalibration table file is older than the -after one.
*
* <h3>Examples</h3>
*
*
* <h4>Plot a single recalibration table</h4>
* <pre>
* java -jar GenomeAnalysisTK.jar \
* -T AnalyzeCovariates \
* -R myrefernce.fasta \
* -BQSR myrecal.table \
* -plots BQSR.pdf
* </pre>
*
* <h4>Plot before (first pass) and after (second pass) recalibration table to compare them</h4>
*
* <pre>
* java -jar GenomeAnalysisTK.jar \
* -T AnalyzeCovariates \
* -R myrefernce.fasta \
* -before recal2.table \
* -after recal3.table \
* -plots recalQC.pdf
* </pre>
*
* <h4>Plot up to three recalibration tables for comparison</h4>
*
* <pre>
*
* # You can ignore the before/after semantics completely if you like (if you do add -ignoreLMT
* # to avoid a possible warning), but all tables should have been generated using the same parameters.
*
* java -jar GenomeAnalysisTK.jar \
* -T AnalyzeCovariates \
* -R myrefernce.fasta \
* -ignoreLMT \
* -BQSR recal1.table \ # you can discard any two
* -before recal2.table \
* -after recal3.table \
* -plots myrecals.pdf
* </pre>
*
* <h4>Full BQSR quality assessment pipeline</h4>
*
* <pre>
* # Generate the first pass recalibration table file.
* java -jar GenomeAnalysisTK.jar \
* -T BaseRecalibrator \
* -R myreference.fasta \
* -I myinput.bam \
* -knownSites bundle/my-trusted-snps.vcf \ # optional but recommendable
* -knownSites bundle/my-trusted-indels.vcf \ # optional but recommendable
* ... other options
* -o firstpass.table
*
* # Generate the second pass recalibration table file.
* java -jar GenomeAnalysisTK.jar \
* -T BaseRecalibrator \
* -BQSR firstpass.table \
* -R myreference.fasta \
* -I myinput.bam \
* -knownSites bundle/my-trusted-snps.vcf \
* -knownSites bundle/my-trusted-indels.vcf \
* ... other options \
* -o secondpass.table
*
* # Finally generate the plots and also keep a copy of the csv (optional).
* java -jar GenomeAnalysisTK.jar \
* -T AnalyzeCovariates \
* -R myrefernce.fasta \
* -before firstpass.table \
* -after secondpass.table \
* -csv BQSR.csv \ # optional
* -plots BQSR.pdf
* </pre>
*
* @author Valentin Ruano-Rubio <valentin@broadinstitute.org>
* @version 6/16/2013
* @since 2.6
*/
@DocumentedGATKFeature(groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class})
public final class AnalyzeCovariates extends RodWalker<AnalyzeCovariates.None,AnalyzeCovariates.None> {
// Constants on option short names that are used in some error/warning messages:
static final String CSV_ARG_SHORT_NAME = "csv";
static final String PDF_ARG_SHORT_NAME = "plots";
static final String BEFORE_ARG_SHORT_NAME = "before";
static final String AFTER_ARG_SHORT_NAME = "after";
/**
* File containing the recalibration tables from the first pass.
*/
@Input(shortName=BEFORE_ARG_SHORT_NAME,fullName="beforeReportFile", doc = "file containing the BQSR first-pass report file",required = false)
protected File beforeFile = null;
/**
* File containing the recalibration tables from the second pass.
*/
@Input(shortName=AFTER_ARG_SHORT_NAME, fullName="afterReportFile", doc = "file containing the BQSR second-pass report file",required = false)
protected File afterFile = null;
/**
* If true, it won't show a warning if the last-modification time of the before and after input files suggest that they have been reversed.
*/
@Argument(shortName="ignoreLMT", fullName="ignoreLastModificationTimes", doc= "do not emit warning messages related to suspicious last modification time order of inputs", required = false)
protected boolean ignoreLastModificationTime = false;
/**
* Output report file name.
*/
@Output(shortName=PDF_ARG_SHORT_NAME, fullName="plotsReportFile" ,doc = "location of the output report", required = false)
protected File pdfFile = null;
/**
* Output csv file name.
*/
@Output(shortName=CSV_ARG_SHORT_NAME,fullName="intermediateCsvFile" ,doc = "location of the csv intermediate file", required = false)
protected File csvFile = null;
/**
* Convenience reference to the RECAL_BQSR_FILE argument value.
* <p/>
* This field value is resolved by {@link #initialize()}.
*/
protected File bqsrFile = null;
/**
* Checks inputs and argument values.
* <p/>
* Notice that this routine will not validate the content of files. It may have some minor side effects as
* the output of warning messages back to the user.
*
* @throw IllegalStateException there is some required argument value that has not been loaded yet.
* @throw UserException if there is some error caused by or under the end user's control.
*/
private void checkArgumentsValues() {
checkInputReportFile("BQSR",bqsrFile);
checkInputReportFile("before",beforeFile);
checkInputReportFile("after",afterFile);
if (bqsrFile == null && beforeFile == null && afterFile == null) {
throw new UserException("you must provide at least one recalibration report file "
+ "(arguments -BQSR, -" + BEFORE_ARG_SHORT_NAME + " or -" + AFTER_ARG_SHORT_NAME);
}
checkOutputFile(PDF_ARG_SHORT_NAME,pdfFile);
checkOutputFile(CSV_ARG_SHORT_NAME, csvFile);
checkInputReportFileLMT(beforeFile,afterFile);
checkOutputRequested();
}
/**
* Checks whether the last-modification-time of the inputs is consistent with their relative roles.
*
* This routine does not thrown an exception but may output a warning message if inconsistencies are spotted.
*
* @param beforeFile the before report file.
* @param afterFile the after report file.
*/
private void checkInputReportFileLMT(final File beforeFile, final File afterFile) {
if (ignoreLastModificationTime || beforeFile == null || afterFile == null) {
return; // nothing to do here
} else if (beforeFile.lastModified() > afterFile.lastModified()) {
Utils.warnUser("Last modification timestamp for 'Before' and 'After'"
+ "recalibration reports are in the wrong order. Perhaps, have they been swapped?");
}
}
/**
* Checks that at least one output was requested.
*
* @throw UserException if no output was requested.
*/
private void checkOutputRequested() {
if (pdfFile == null && csvFile == null) {
throw new UserException("you need to request at least one output:"
+ " the intermediate csv file (-" + CSV_ARG_SHORT_NAME + " FILE)"
+ " or the final plot file (-" + PDF_ARG_SHORT_NAME + " FILE).");
}
}
/**
* Checks the value provided to input file arguments.
*
* @throw UserException if there is any problem cause by or under the end user's control
*
* @param name command line argument short name.
* @param value the argument value.
*/
private void checkInputReportFile(final String name,final File value) {
if (value == null) {
return;
} else if (!value.exists()) {
throw new UserException.BadArgumentValue(name, "input report '" +
value + "' does not exist or is unreachable");
} else if (!value.isFile()) {
throw new UserException.BadArgumentValue(name, "input report '" +
value + "' is not a regular file");
} else if (!value.canRead()) {
throw new UserException.BadArgumentValue(name, "input report '" +
value + "' cannot be read");
}
}
/**
* Checks the value provided for output arguments.
*
* @throw UserException if there is any problem cause by or under the end user's control
*
* @param name command line argument short name.
* @param value the argument value.
*/
private void checkOutputFile(final String name, final File value) {
if (value == null) {
return;
}
if (value.exists() && !value.isFile()) {
throw new UserException.BadArgumentValue(name, "the output file location '"
+ value + "' exists as not a file");
}
final File parent = value.getParentFile();
if (parent == null) {
return;
}
if (!parent.exists()) {
throw new UserException.BadArgumentValue(name, "the output file parent directory '"
+ parent + "' does not exists or is unreachable");
} else if (!parent.isDirectory()) {
throw new UserException.BadArgumentValue(name, "the output file parent directory '"
+ parent + "' is not a directory");
} else if (!parent.canWrite()) {
throw new UserException.BadArgumentValue(name, "the output file parent directory '"
+ parent + "' cannot be written");
}
}
/**
* Generates the plots using the external R script.
*
* <p/>
* If <code>plotsFile</code> is <code>null</code>, it does not perform any plotting.
*
* @param csvFile the intermediary csv file.
* @param plotsFile the output plot location.
*/
private void generatePlots(final File csvFile, final Map<String,File> reportFiles, final File plotsFile) {
if (plotsFile == null) {
return;
}
logger.info("Generating plots file '" + plotsFile + "'");
final File exampleReportFile = reportFiles.values().iterator().next();
RecalUtils.generatePlots(csvFile,exampleReportFile,plotsFile);
}
@Override
public void initialize() {
super.initialize();
bqsrFile = getToolkit().getArguments().BQSR_RECAL_FILE;
checkArgumentsValues();
final Map<String, File> reportFiles = buildReportFileMap();
final Map<String, RecalibrationReport> reports = buildReportMap(reportFiles);
checkReportConsistency(reports);
final File csvFile = resolveCsvFile();
generateCsvFile(csvFile,reports);
final File plotFile = resolvePlotFile();
generatePlots(csvFile, reportFiles, plotFile);
}
/**
* Returns the plot output file
* @return might be <code>null</code> if the user has not indicated and output file.
*/
private File resolvePlotFile() {
return pdfFile;
}
/**
* Generates the intermediary Csv file.
*
* @param csvFile where to write the file.
* @param reports the reports to be included.
*/
private void generateCsvFile(final File csvFile, final Map<String, RecalibrationReport> reports) {
try {
logger.info("Generating csv file '" + csvFile + "'");
RecalUtils.generateCsv(csvFile, reports);
} catch (FileNotFoundException e) {
throw new UserException(
String.format("There is a problem creating the intermediary Csv file '%s': %s",
csvFile,e.getMessage()),e);
}
}
/**
* Checks whether multiple input recalibration report files argument values are consistent (equal).
*
* @param reports map with report to verify.
*
* @throw UserException if there is any inconsistency.
*/
private void checkReportConsistency(final Map<String, RecalibrationReport> reports) {
final Map.Entry<String,RecalibrationReport>[] reportEntries =
reports.entrySet().toArray((Map.Entry<String,RecalibrationReport>[]) new Map.Entry[reports.size()]);
final Map.Entry<String,RecalibrationReport> exampleEntry = reportEntries[0];
for (int i = 1; i < reportEntries.length; i++) {
final Map<String,? extends CharSequence> diffs = exampleEntry.getValue().getRAC().compareReportArguments(
reportEntries[i].getValue().getRAC(),exampleEntry.getKey(),reportEntries[i].getKey());
if (diffs.size() != 0) {
throw new UserException.IncompatibleRecalibrationTableParameters("There are differences in relevant arguments of"
+ " two or more input recalibration reports. Please make sure"
+ " they have been created using the same recalibration parameters."
+ " " + Utils.join("// ", reportDifferencesStringArray(diffs)));
}
}
}
/**
* Creates a map with all input recalibration files indexed by their "role".
* <p/>
* The key is the role and the value the corresponding report file.
* <p/>
* Roles: "Before" (recalibration), "After" (recalibration), "BQSR" (the tool standard argument recalibration file)
*
* @return never <code>null</code>
*/
private Map<String, File> buildReportFileMap() {
final Map<String,File> reports = new LinkedHashMap<>(3);
if (bqsrFile != null) {
reports.put("BQSR",bqsrFile);
}
if (beforeFile != null) {
reports.put("Before",beforeFile);
}
if (afterFile != null) {
reports.put("After",afterFile);
}
return reports;
}
/**
* Transforms a recalibration file map into a report object map.
*
* @param reportFileMap the file map to transforms.
* @return never <code>null</code>, a new map with the same size as
* <code>reportFileMap</code> and the same key set.
*/
@Requires("reportFileMap != null")
private Map<String, RecalibrationReport> buildReportMap(final Map<String, File> reportFileMap) {
final Map<String,RecalibrationReport> reports = new LinkedHashMap<>(reportFileMap.size());
for (final Map.Entry<String,File> e : reportFileMap.entrySet()) {
reports.put(e.getKey(),new RecalibrationReport(e.getValue()));
}
return reports;
}
/**
* Generates a flatter String array representation of recalibration argument differences.
* @param diffs the differences to represent.
*
* @return never <code>null</code>, an array of the same length as the size of the input <code>diffs</code>.
*/
@Requires("diffs != null")
private String[] reportDifferencesStringArray(final Map<String, ? extends CharSequence> diffs) {
final String[] result = new String[diffs.size()];
int i = 0;
for (final Map.Entry<String, ? extends CharSequence> e : diffs.entrySet()) {
result[i++] = capitalize(e.getKey()) + ": " + e.getValue();
}
return result;
}
/**
* Returns the input string capitalizing the first letter.
*
* @param str the string to capitalize
* @return never <code>null</code>.
*/
@Requires("str != null")
private String capitalize(final String str) {
if (str.isEmpty()) {
return str;
} else {
return Character.toUpperCase(str.charAt(0)) + str.substring(1);
}
}
/**
* Returns the csv file to use.
* <p/>
* This is the the one specified by the user if any or a temporary file
* that will be deleted as soon as the VM exists by default.
*
* @return never <code>null</code>.
*/
private File resolveCsvFile() {
if (csvFile != null) {
return csvFile;
} else {
try {
final File result = File.createTempFile("AnalyzeCovariates", ".csv");
result.deleteOnExit();
return result;
} catch (IOException e) {
throw new UserException("Could not create temporary Csv file",e);
}
}
}
/**
* Always return true, forcing the immediate termination of the travesal.
* @return
*/
@Override
public boolean isDone() {
return true;
}
/**
* {@inheritDoc}
*/
@Override
public None reduceInit() {
return new None();
}
/**
* Is not supposed to ever be called, thus it always results in an exception.
*
* @throws IllegalStateException always.
*/
@Override
public None reduce(None value, None sum) {
throw new IllegalStateException("AnalyzeCovariates reduce method is not supposed to be invoked ever");
}
/**
* Is not supposed to ever be called, thus it always results in an exception.
*
* @throws IllegalStateException always.
*/
@Override
public None map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
throw new IllegalStateException("AnalyzeCovariates map method is not supposed to be invoked ever");
}
/**
* Dummy map and reduce types for the {@link AnalyzeCovariates} tool that in fact does not do any traversal.
*/
protected static class None {
private None() {
}
}
}