[options] Input files - $ Options: - $ * -o, --output Output file - -Mandatory arguments are denoted with a (*). - -Other tools require more input: - - $ > ./toolRunner.sh ngs.Autocorrelation - $ Usage:

[options] - $ Options: - $ * -i, --input Input file - $ * -l, --loci Genomic loci (Bed format) - $ -m, --max Autocorrelation limit (bp) - $ Default: 200 - $ * -o, --output Output file - -=== Log transform a Wig file with base 2 - - $ > ./toolRunner.sh wigmath.LogTransform --input input.wig --base 2 --output output.log2.wig - -== Java Genomics IO - -Those wishing to write their own scripts may be interested in https://github.com/timpalpant/java-genomics-io, the toolkit upon which these applications are built. \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba build.properties diff -r e16016635b2a -r 4b610dc8f6ba build.xml --- a/build.xml Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,112 +0,0 @@ - - - - build the toolkit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r e16016635b2a -r 4b610dc8f6ba galaxy-conf/BaseAlignCounts.xml --- a/galaxy-conf/BaseAlignCounts.xml Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ - - of sequencing reads - galaxyToolRunner.sh -i $input -g $dbkey -x $X -p 4 -o $output - - - - - - - - - - .. class:: warningmark - - This tool requires sequencing reads in SAM/BAM/Bed/BedGraph format. - - .. class:: warningmark - - This tool was contributed by Timothy Palpant. - - diff -r e16016635b2a -r 4b610dc8f6ba galaxy-conf/galaxyToolRunner.sh --- a/galaxy-conf/galaxyToolRunner.sh Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#!/usr/bin/env bash - -if [ $# -eq 0 ] -then - echo "USAGE: galaxyToolRunner.sh APPNAME [ARGS]"; - exit; -fi - -if [ "$1" = "list" ] -then - find src/edu/unc/genomics/**/*.java -exec basename -s .java {} \; -fi - -java -Dlog4j.configuration=log4j.properties -cp .:../build:../lib/* edu.unc.genomics."$@" \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba galaxyToolConf.xml --- a/galaxyToolConf.xml Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - -

- - -

- - - - - -

- - - - - - - -

- - - - - - - - - - - -

- - - - -

\ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/AssemblyManager.java --- a/gui/edu/unc/genomics/AssemblyManager.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -package edu.unc.genomics; - -import java.io.IOException; -import java.nio.file.DirectoryStream; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.List; -import java.util.zip.DataFormatException; - -import org.apache.log4j.Logger; - -/** - * Suite of static methods for managing the built-in assemblies in the resources dir - * as well as keeping track of the last used assembly - * - * @author timpalpant - * - */ -public class AssemblyManager { - - private static final Logger log = Logger.getLogger(AssemblyManager.class); - - /** - * The last used Assembly - */ - private static Assembly lastUsed; - - /** - * Returns all available assemblies in the resources directory - * @return the assemblies available in the resources directory - */ - public static List getAvailableAssemblies() { - List assemblies = new ArrayList<>(); - - try (DirectoryStream stream = Files.newDirectoryStream(ResourceManager.getAssembliesDirectory(), "*.{len}")) { - for (Path entry : stream) { - log.debug("Loading assembly: " + entry); - try { - Assembly a = new Assembly(entry); - assemblies.add(a); - } catch (IOException | DataFormatException e1) { - log.warn("Error loading assembly: " + entry); - } - } - } catch (IOException e) { - log.error("Error listing assemblies"); - e.printStackTrace(); - } - - return assemblies; - } - - public static void deleteAssembly(Assembly a) throws IOException { - Files.deleteIfExists(a.getPath()); - } - - public static Assembly loadCustomAssembly(Path assemblyFile) throws IOException, DataFormatException { - log.debug("Loading custom assembly from file: " + assemblyFile); - Assembly a = new Assembly(assemblyFile); - - // TODO: Warn if this assembly is already loaded - - // Copy the assembly file into the built-in assemblies directory - Files.copy(assemblyFile, ResourceManager.getAssembliesDirectory().resolve(assemblyFile.getFileName())); - return a; - } - - /** - * @return the lastUsed - */ - public static Assembly getLastUsed() { - return lastUsed; - } - - /** - * @param lastUsed the lastUsed to set - */ - public static void setLastUsed(Assembly lastUsed) { - AssemblyManager.lastUsed = lastUsed; - } -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/AssemblyManagerDialog.java --- a/gui/edu/unc/genomics/AssemblyManagerDialog.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,135 +0,0 @@ -package edu.unc.genomics; - -import java.awt.BorderLayout; -import java.awt.FlowLayout; - -import javax.swing.JButton; -import javax.swing.JDialog; -import javax.swing.JFileChooser; -import javax.swing.JFrame; -import javax.swing.JOptionPane; -import javax.swing.JPanel; -import javax.swing.JScrollPane; -import javax.swing.JTable; -import javax.swing.border.EmptyBorder; - -import org.apache.log4j.Logger; - -import java.awt.event.ActionListener; -import java.awt.event.ActionEvent; -import java.io.IOException; -import java.nio.file.Path; -import java.util.zip.DataFormatException; - -/** - * View for AssemblyManager - * - * @author timpalpant - * - */ -public class AssemblyManagerDialog extends JDialog { - - public static final int DEFAULT_WIDTH = 400; - public static final int DEFAULT_HEIGHT = 500; - - private static final long serialVersionUID = -1461628562713621064L; - private static final Logger log = Logger.getLogger(AssemblyManagerDialog.class); - - private final JPanel contentPanel = new JPanel(); - private final JFileChooser fcCustomAssembly = new JFileChooser(); - private final JTable assembliesTable = new JTable(); - - private AssemblyTableModel model; - - /** - * Create the dialog. - */ - public AssemblyManagerDialog(JFrame parent) { - super(parent, "Assembly Manager", true); - - setSize(DEFAULT_WIDTH, DEFAULT_HEIGHT); - int centeredX = parent.getX() + (parent.getWidth()-getWidth()) / 2; - int centeredY = parent.getY() + (parent.getHeight()-getHeight()) / 2; - setLocation(centeredX, centeredY); - - getContentPane().setLayout(new BorderLayout()); - contentPanel.setBorder(new EmptyBorder(5, 5, 5, 5)); - getContentPane().add(contentPanel, BorderLayout.CENTER); - contentPanel.setLayout(new BorderLayout(0, 0)); - - // Initialize the assemblies list - model = new AssemblyTableModel(AssemblyManager.getAvailableAssemblies()); - assembliesTable.setModel(model); - assembliesTable.setRowSelectionAllowed(true); - JScrollPane scrollPane = new JScrollPane(assembliesTable); - assembliesTable.setFillsViewportHeight(true); - contentPanel.add(scrollPane); - - JPanel buttonPane = new JPanel(); - buttonPane.setLayout(new FlowLayout(FlowLayout.RIGHT)); - getContentPane().add(buttonPane, BorderLayout.SOUTH); - - JButton removeAssemblyButton = new JButton("Remove"); - removeAssemblyButton.setActionCommand("RemoveAssembly"); - removeAssemblyButton.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - removeCustomAssembly(); - } - }); - buttonPane.add(removeAssemblyButton); - - JButton loadAssemblyButton = new JButton("Load Custom Assembly"); - loadAssemblyButton.setActionCommand("LoadAssembly"); - loadAssemblyButton.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - loadCustomAssembly(); - } - }); - buttonPane.add(loadAssemblyButton); - - JButton doneButton = new JButton("Done"); - doneButton.setActionCommand("Done"); - doneButton.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - closeDialog(); - } - }); - buttonPane.add(doneButton); - getRootPane().setDefaultButton(doneButton); - } - - private void removeCustomAssembly() { - for (int row : assembliesTable.getSelectedRows()) { - try { - Assembly a = model.getRow(row); - AssemblyManager.deleteAssembly(a); - model.removeRow(row); - } catch (IOException e) { - log.error("Error deleting Assembly"); - e.printStackTrace(); - JOptionPane.showMessageDialog(this, "Error deleting assembly", "Assembly Manager Error", JOptionPane.ERROR_MESSAGE); - } - } - } - - private void loadCustomAssembly() { - int returnVal = fcCustomAssembly.showOpenDialog(this); - if (returnVal == JFileChooser.APPROVE_OPTION) { - Path assemblyFile = fcCustomAssembly.getSelectedFile().toPath(); - try { - Assembly a = AssemblyManager.loadCustomAssembly(assemblyFile); - // Add it to the assemblies list model - model.addAssembly(a); - } catch (IOException | DataFormatException e) { - log.error("Error loading custom assembly: " + assemblyFile); - e.printStackTrace(); - JOptionPane.showMessageDialog(this, "Error loading custom assembly", "Assembly Manager Error", JOptionPane.ERROR_MESSAGE); - } - } - } - - private void closeDialog() { - this.dispose(); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/AssemblyTableModel.java --- a/gui/edu/unc/genomics/AssemblyTableModel.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ -package edu.unc.genomics; - -import java.util.List; - -import javax.swing.table.AbstractTableModel; - -/** - * Model for the AssemblyManagerDialog table view - * - * @author timpalpant - * - */ -public class AssemblyTableModel extends AbstractTableModel { - - private static final long serialVersionUID = 8225453782461913732L; - - private static final String[] COLUMN_NAMES = { "Name", "# Contigs" }; - - private final List assemblies; - - public AssemblyTableModel(List assemblies) { - this.assemblies = assemblies; - } - - /* (non-Javadoc) - * @see javax.swing.table.AbstractTableModel#getColumnName(int) - */ - @Override - public String getColumnName(int col) { - return COLUMN_NAMES[col]; - } - - /* (non-Javadoc) - * @see javax.swing.table.AbstractTableModel#isCellEditable(int, int) - */ - @Override - public boolean isCellEditable(int row, int col) { - return false; - } - - /* (non-Javadoc) - * @see javax.swing.table.TableModel#getRowCount() - */ - @Override - public int getRowCount() { - return assemblies.size(); - } - - /* (non-Javadoc) - * @see javax.swing.table.TableModel#getColumnCount() - */ - @Override - public int getColumnCount() { - return 2; - } - - /* (non-Javadoc) - * @see javax.swing.table.TableModel#getValueAt(int, int) - */ - @Override - public Object getValueAt(int rowIndex, int columnIndex) { - Assembly a = assemblies.get(rowIndex); - if (columnIndex == 0) { - return a.toString(); - } else if (columnIndex == 1) { - return a.chromosomes().size(); - } else { - return null; - } - } - - public Assembly getRow(int rowIndex) { - return assemblies.get(rowIndex); - } - - public boolean containsAssembly(Assembly a) { - String aName = a.toString(); - for (Assembly assembly : assemblies) { - if (assembly.toString().equalsIgnoreCase(aName)) { - return true; - } - } - - return false; - } - - public void addAssembly(Assembly a) { - assemblies.add(a); - fireTableRowsInserted(assemblies.size()-1, assemblies.size()-1); - } - - public void removeRow(int rowIndex) { - assemblies.remove(rowIndex); - fireTableRowsDeleted(rowIndex, rowIndex); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ButtonLabel.java --- a/gui/edu/unc/genomics/ButtonLabel.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -package edu.unc.genomics; - -import javax.swing.Action; -import javax.swing.BorderFactory; -import javax.swing.Icon; -import javax.swing.JButton; - -/** - * Act like a button, look like a label - * - * @author timpalpant - * - */ -public class ButtonLabel extends JButton { - - private static final long serialVersionUID = -4449260534784095223L; - - public ButtonLabel() { - init(); - } - - public ButtonLabel(Icon icon) { - super(icon); - init(); - } - - public ButtonLabel(String text) { - super(text); - init(); - } - - public ButtonLabel(Action a) { - super(a); - init(); - } - - public ButtonLabel(String text, Icon icon) { - super(text, icon); - init(); - } - - private void init() { - setBorder(BorderFactory.createEmptyBorder()); - setBorderPainted(false); - setContentAreaFilled(false); - setFocusPainted(false); - setOpaque(false); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/Job.java --- a/gui/edu/unc/genomics/Job.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,207 +0,0 @@ -package edu.unc.genomics; - -import java.io.StringWriter; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; - -import org.apache.log4j.Logger; -import org.apache.log4j.PatternLayout; -import org.apache.log4j.WriterAppender; - -import com.beust.jcommander.JCommander; -import com.beust.jcommander.ParameterDescription; - -/** - * A Job represents an instance of a tool configured with specific arguments - * Attempting to run a Job with invalid arguments will throw a RuntimeException - * If tool execution fails, a RuntimeException will also be thrown - * UncheckedExceptions should be managed by setting the Job's UncheckedExceptionManager - * or providing a ThreadGroup / default UncheckedExceptionManager - * - * @author timpalpant - * - */ -public class Job implements Iterable, Runnable { - - private static final Logger log = Logger.getLogger(Job.class); - - private final Class tool; - private final CommandLineTool app; - private final List parameters; - private final String usageText; - private boolean isRunning = false; - private StringWriter writer = new StringWriter(); - - /** - * Arguments for running this Job - */ - private Map args = new HashMap<>(); - - /** - * Creates a new Job model for the specified tool - * @param tool - * @throws IllegalAccessException - * @throws InstantiationException - */ - public Job(final Class tool) throws InstantiationException, IllegalAccessException { - this.tool = tool; - - // Attempt to instantiate the tool and extract parameter information - app = tool.newInstance(); - JCommander jc = new JCommander(app); - jc.setProgramName(tool.getSimpleName()); - parameters = jc.getParameters(); - StringBuilder sbuilder = new StringBuilder(); - jc.usage(sbuilder); - usageText = sbuilder.toString(); - - // Set default arguments - for (ParameterDescription param : parameters) { - if (param.getDefault() != null) { - setArgument(param, String.valueOf(param.getDefault())); - } - } - } - - /** - * Copy-constructor - * @param job - */ - public Job(final Job job) { - this.tool = job.tool; - this.app = job.app; - this.parameters = job.parameters; - this.args = job.args; - this.usageText = job.usageText; - } - - @Override - public void run() { - // Load the arguments for running the tool - String[] args; - try { - args = getArguments(); - } catch (JobException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - throw new CommandLineToolException("Job arguments are not valid"); - } - - // Attempt to instantiate and run the tool - WriterAppender appender = new WriterAppender(new PatternLayout(), writer); - appender.addFilter(new ThreadFilter(Thread.currentThread().getName())); - Logger.getRootLogger().addAppender(appender); - isRunning = true; - app.toolRunnerMain(args); - isRunning = false; - Logger.getRootLogger().removeAppender(appender); - } - - /** - * Render the arguments for running an instance of this Job - * @return - * @throws JobException - */ - public String[] getArguments() throws JobException { - if (!validateArguments()) { - throw new JobException("Job Arguments are not valid"); - } - - List cmdArgs = new ArrayList<>(); - for (ParameterDescription p : args.keySet()) { - cmdArgs.add(p.getLongestName()); - cmdArgs.add(args.get(p)); - } - - String[] ret = new String[cmdArgs.size()]; - return cmdArgs.toArray(ret); - } - - public String getArgument(final ParameterDescription p) { - return args.get(p); - } - - /** - * Set a value for the given parameter - * @param p - * @param value - */ - public void setArgument(final ParameterDescription p, final String value) { - if (value.length() == 0) { - args.remove(p); - } else { - args.put(p, value); - } - } - - /** - * Remove all set arguments for this Job - */ - public void resetArguments() { - args.clear(); - } - - /** - * Is this parameter set? - * @param p - * @return - */ - public boolean isSet(final ParameterDescription p) { - return args.containsKey(p); - } - - /** - * Validate that this job has all of its parameters set - * and that they are all valid - * @return - */ - public boolean validateArguments() { - // TODO: Better validation based on parameter type - boolean hasAllRequiredParams = true; - for (ParameterDescription param : parameters) { - if (param.getParameter().required() && !isSet(param)) { - log.debug("Job is missing required argument: " + param.getLongestName()); - hasAllRequiredParams = false; - } - } - - return hasAllRequiredParams; - } - - public int numParameters() { - return parameters.size(); - } - - @Override - public Iterator iterator() { - return parameters.iterator(); - } - - public String getName() { - return tool.getSimpleName(); - } - - public boolean isRunning() { - return isRunning; - } - - /** - * @return the usageText - */ - public String getUsageText() { - return usageText; - } - - @Override - public String toString() { - return getName(); - } - - public String getOutput() { - return writer.toString(); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/JobConfigPanel.java --- a/gui/edu/unc/genomics/JobConfigPanel.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,246 +0,0 @@ -package edu.unc.genomics; - -import java.awt.Color; -import java.awt.Component; -import java.awt.Dimension; -import java.awt.FileDialog; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.lang.reflect.Field; -import java.nio.file.Path; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import javax.swing.BorderFactory; -import javax.swing.BoxLayout; -import javax.swing.ImageIcon; -import javax.swing.JButton; -import javax.swing.JComboBox; -import javax.swing.JComponent; -import javax.swing.JFileChooser; -import javax.swing.JFrame; -import javax.swing.JLabel; -import javax.swing.JPanel; -import javax.swing.JTextField; -import javax.swing.SpringLayout; -import javax.swing.SwingUtilities; -import javax.swing.event.DocumentEvent; -import javax.swing.event.DocumentListener; -import javax.swing.layout.SpringUtilities; -import javax.swing.text.BadLocationException; -import javax.swing.text.Document; - -import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; - -import com.beust.jcommander.ParameterDescription; - -import edu.unc.genomics.io.IntervalFile; -import edu.unc.genomics.io.WigFile; - -/** - * View for configuring the parameters of a Job - * Implements databinding between a Job object and the various Swing components - * for configuring each parameter - * - * @author timpalpant - * - */ -public class JobConfigPanel extends JPanel { - - private static final long serialVersionUID = 3336295203155728629L; - private static final Logger log = Logger.getLogger(JobConfigPanel.class); - - private static final ImageIcon fileIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("folder_page.png").toString()); - - /** - * Maps parameters in the Job to GUI components (forward data-binding) - */ - private Map guiMap = new HashMap<>(); - - /** - * Maps GUI components to parameters in the Job (reverse data-binding) - */ - private Map jobMap = new HashMap<>(); - - /** - * The model for the Job that this panel allows you to configure - */ - private Job job; - - /** - * Initialize a new ConfigurationPanel with no Job - */ - public JobConfigPanel() { - this(null); - } - - /** - * Initialize a new ConfigurationPanel for the given Job - * @param job - */ - public JobConfigPanel(final Job job) { - setJob(job); - setLayout(new SpringLayout()); - } - - /** - * Return the Job that this ConfigurationPanel is editing - * @return - */ - public Job getJob() { - return job; - } - - /** - * Set the job for this Configuration panel and re-render - * @param job - */ - public void setJob(final Job job) { - this.job = job; - renderJob(); - } - - /** - * Highlights fields on the Panel that are not set correctly - */ - public void highlightInvalidArguments() { - for (ParameterDescription param : job) { - JComponent guiComponent = guiMap.get(param); - if (param.getParameter().required() && !job.isSet(param)) { - guiComponent.setBorder(BorderFactory.createLineBorder(Color.RED)); - } else { - guiComponent.setBorder(BorderFactory.createEmptyBorder()); - } - } - } - - /** - * Render the parameters from the Job into GUI components - * and set up one-way data binding to map changes to the GUI fields - * back into the Job object's parameters - */ - private void renderJob() { - removeAll(); - guiMap.clear(); - jobMap.clear(); - if (job == null) { - validate(); - repaint(); - return; - } - - // Iterate through the parameters in the Job - // and render them appropriately based on their type - for (ParameterDescription paramDescription : job) { - // Add the parameter name to the configuration panel - String name = paramDescription.getLongestName(); - while (name.startsWith("-")) { - name = name.substring(1); - } - name = StringUtils.capitalize(name); - JLabel label = new JLabel(name); - label.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 5)); - add(label); - - // Add a panel for configuring the parameter - JPanel fieldPanel = new JPanel(); - fieldPanel.setLayout(new BoxLayout(fieldPanel, BoxLayout.LINE_AXIS)); - add(fieldPanel); - Field field = paramDescription.getField(); - Class type = field.getType(); - if (type.equals(Assembly.class)) { - List availableAssemblies = AssemblyManager.getAvailableAssemblies(); - Assembly[] assemblies = new Assembly[availableAssemblies.size()]; - assemblies = availableAssemblies.toArray(assemblies); - final JComboBox cbAssemblyChooser = new JComboBox(assemblies); - cbAssemblyChooser.setPreferredSize(new Dimension(0, 25)); - cbAssemblyChooser.setMaximumSize(new Dimension(Integer.MAX_VALUE, cbAssemblyChooser.getPreferredSize().height)); - cbAssemblyChooser.setSelectedItem(AssemblyManager.getLastUsed()); - cbAssemblyChooser.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - log.debug("Auto-databinding changed assembly into Job argument"); - Assembly selectedAssembly = (Assembly) cbAssemblyChooser.getSelectedItem(); - AssemblyManager.setLastUsed(selectedAssembly); - ParameterDescription param = jobMap.get(cbAssemblyChooser); - job.setArgument(param, selectedAssembly.toString()); - } - }); - fieldPanel.add(cbAssemblyChooser); - guiMap.put(paramDescription, cbAssemblyChooser); - jobMap.put(cbAssemblyChooser, paramDescription); - } else { - final JTextField textField = new JTextField(); - // Set to default parameter, if it exists - if (job.isSet(paramDescription)) { - textField.setText(job.getArgument(paramDescription)); - } - textField.setPreferredSize(new Dimension(0, 20)); - textField.setMaximumSize(new Dimension(Integer.MAX_VALUE, textField.getPreferredSize().height)); - textField.getDocument().addDocumentListener(new DocumentListener() { - public void changedUpdate(DocumentEvent e) { - pushTextToModel(e); - } - - public void removeUpdate(DocumentEvent e) { - pushTextToModel(e); - } - - public void insertUpdate(DocumentEvent e) { - pushTextToModel(e); - } - - private void pushTextToModel(DocumentEvent e) { - log.debug("Auto-databinding changed text into Job argument"); - Document doc = (Document) e.getDocument(); - ParameterDescription param = jobMap.get(textField); - try { - String text = doc.getText(0, doc.getLength()); - job.setArgument(param, text); - } catch (BadLocationException e1) { - log.error("Error pushing changed text into Job model"); - e1.printStackTrace(); - } - } - }); - fieldPanel.add(textField); - guiMap.put(paramDescription, textField); - jobMap.put(textField, paramDescription); - - // For input/output files, add a file chooser button - if (type.equals(Path.class) || type.equals(WigFile.class) || type.equals(IntervalFile.class)) { - // TODO Replace with file icon - JButton btnChooseFile = new JButton(fileIcon); - btnChooseFile.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - // AWT FileDialog uses native components, but seems to hang - //Component c = (Component) e.getSource(); - //JFrame frame = (JFrame) SwingUtilities.getRoot(c); - //FileDialog fd = new FileDialog(frame, "Choose File"); - //fd.setVisible(true); - //if (fd.getFile() != null) { - // textField.setText(fd.getDirectory()+fd.getFile()); - //} - - // Swing JFileChooser - JFileChooser fc = new JFileChooser(); - int retValue = fc.showDialog(getParent(), "OK"); - if (retValue == JFileChooser.APPROVE_OPTION) { - textField.setText(fc.getSelectedFile().toString()); - } - } - }); - fieldPanel.add(btnChooseFile); - } - } - } - - // Lay out the panel - SpringUtilities.makeCompactGrid(this, job.numParameters(), 2, 5, 5, 5, 5); - - validate(); - repaint(); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/JobException.java --- a/gui/edu/unc/genomics/JobException.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -package edu.unc.genomics; - -/** - * Exception thrown if attempting to perform an invalid action with a Job - * - * @author timpalpant - * - */ -public class JobException extends Exception { - - private static final long serialVersionUID = -831504993593959450L; - - /** - * - */ - public JobException() { - // TODO Auto-generated constructor stub - } - - /** - * @param message - */ - public JobException(String message) { - super(message); - // TODO Auto-generated constructor stub - } - - /** - * @param cause - */ - public JobException(Throwable cause) { - super(cause); - // TODO Auto-generated constructor stub - } - - /** - * @param message - * @param cause - */ - public JobException(String message, Throwable cause) { - super(message, cause); - // TODO Auto-generated constructor stub - } - - /** - * @param message - * @param cause - * @param enableSuppression - * @param writableStackTrace - */ - public JobException(String message, Throwable cause, - boolean enableSuppression, boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - // TODO Auto-generated constructor stub - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/JobQueue.java --- a/gui/edu/unc/genomics/JobQueue.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -package edu.unc.genomics; - -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import javax.swing.ListModel; -import javax.swing.event.ListDataEvent; -import javax.swing.event.ListDataListener; - -import org.apache.log4j.Logger; - -/** - * Model for the queue of SubmittedJobs - * Should be managed through the JobQueueManager controller - * - * @author timpalpant - * - */ -public class JobQueue implements ListModel, Iterable { - - private static final Logger log = Logger.getLogger(JobQueue.class); - - private final List submittedJobs = new ArrayList<>(); - private final List dataListeners = new ArrayList<>(); - - public void add(SubmittedJob job) { - int N = submittedJobs.size(); - submittedJobs.add(job); - ListDataEvent e = new ListDataEvent(this, ListDataEvent.INTERVAL_ADDED, N, N); - for (ListDataListener l : dataListeners) { - l.intervalAdded(e); - } - } - - public void remove(SubmittedJob job) { - submittedJobs.remove(job); - int N = submittedJobs.size(); - ListDataEvent e = new ListDataEvent(this, ListDataEvent.INTERVAL_REMOVED, N, N); - for (ListDataListener l : dataListeners) { - l.intervalAdded(e); - } - } - - public void update(SubmittedJob job) { - int index = submittedJobs.indexOf(job); - ListDataEvent e = new ListDataEvent(this, ListDataEvent.CONTENTS_CHANGED, index, index); - for (ListDataListener l : dataListeners) { - l.intervalAdded(e); - } - } - - @Override - public int getSize() { - return submittedJobs.size(); - } - - @Override - public SubmittedJob getElementAt(int index) { - return submittedJobs.get(index); - } - - @Override - public void addListDataListener(ListDataListener l) { - dataListeners.add(l); - } - - @Override - public void removeListDataListener(ListDataListener l) { - dataListeners.remove(l); - } - - @Override - public Iterator iterator() { - return submittedJobs.iterator(); - } -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/JobQueueCellRenderer.java --- a/gui/edu/unc/genomics/JobQueueCellRenderer.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,125 +0,0 @@ -package edu.unc.genomics; - -import java.awt.Color; -import java.awt.Component; -import java.awt.Dimension; -import java.awt.FlowLayout; -import java.awt.Font; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; - -import javax.swing.BorderFactory; -import javax.swing.Box; -import javax.swing.BoxLayout; -import javax.swing.ImageIcon; -import javax.swing.JButton; -import javax.swing.JLabel; -import javax.swing.JList; -import javax.swing.JPanel; -import javax.swing.JProgressBar; -import javax.swing.ListCellRenderer; -import javax.swing.SwingConstants; -import javax.swing.border.EtchedBorder; - -/** - * @author timpalpant - * - */ -public class JobQueueCellRenderer extends JPanel implements ListCellRenderer { - - private static final long serialVersionUID = 4270263302075586018L; - - private static final ImageIcon inProgressIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("beachball.png").toString()); - private static final ImageIcon rerunIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("arrow-circle.png").toString()); - private static final ImageIcon infoIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("information-white.png").toString()); - private static final ImageIcon logIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("sticky-note-text.png").toString()); - private static final ImageIcon showFileIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("eye_icon.png").toString()); - - private static final ImageIcon successIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("icon_success_sml.gif").toString()); - private static final ImageIcon errorIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("icon_error_sml.gif").toString()); - private static final ImageIcon warningIcon = new ImageIcon(ResourceManager.getImagesDirectory().resolve("icon_warning_sml.gif").toString()); - - private JLabel statusIconLabel = new JLabel(inProgressIcon); - private JLabel nameLabel = new JLabel(); - - public JobQueueCellRenderer() { - FlowLayout flowLayout = new FlowLayout(FlowLayout.LEADING, 5, 2); - setPreferredSize(new Dimension(190, 48)); - setLayout(flowLayout); - setBorder(BorderFactory.createLineBorder(Color.GRAY, 1, true)); - - JPanel statusPanel = new JPanel(); - statusPanel.setBorder(BorderFactory.createEmptyBorder(0, 3, 16, 0)); - statusPanel.setLayout(new BoxLayout(statusPanel, BoxLayout.PAGE_AXIS)); - statusPanel.add(statusIconLabel); - add(statusPanel); - - JPanel mainPanel = new JPanel(); - mainPanel.setAlignmentX(LEFT_ALIGNMENT); - mainPanel.setLayout(new BoxLayout(mainPanel, BoxLayout.PAGE_AXIS)); - - JPanel namePanel = new JPanel(); - namePanel.setLayout(flowLayout); - nameLabel.setPreferredSize(new Dimension(145, 16)); - nameLabel.setHorizontalTextPosition(SwingConstants.LEFT); - nameLabel.setFont(nameLabel.getFont().deriveFont(Font.BOLD)); - namePanel.add(nameLabel); - mainPanel.add(namePanel); - - JPanel buttonsPanel = new JPanel(); - buttonsPanel.setLayout(flowLayout); - mainPanel.add(buttonsPanel); - - ButtonLabel rerunLabel = new ButtonLabel(rerunIcon); - rerunLabel.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - //addJobToQueue(); - } - }); - buttonsPanel.add(rerunLabel); - ButtonLabel infoLabel = new ButtonLabel(infoIcon); - infoLabel.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - //addJobToQueue(); - } - }); - buttonsPanel.add(infoLabel); - ButtonLabel logLabel = new ButtonLabel(logIcon); - logLabel.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - //addJobToQueue(); - } - }); - buttonsPanel.add(logLabel); - ButtonLabel showFileLabel = new ButtonLabel(showFileIcon); - showFileLabel.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - //addJobToQueue(); - } - }); - buttonsPanel.add(showFileLabel); - - add(mainPanel); - } - - @Override - public Component getListCellRendererComponent( - JList list, SubmittedJob value, int index, - boolean isSelected, boolean cellHasFocus) { - - nameLabel.setText(value.toString()); - if (value.isRunning()) { - statusIconLabel.setIcon(inProgressIcon); - nameLabel.setForeground(Color.BLACK); - } else if (value.succeeded()) { - statusIconLabel.setIcon(successIcon); - nameLabel.setForeground(Color.BLACK); - } else { - statusIconLabel.setIcon(errorIcon); - nameLabel.setForeground(Color.RED); - } - - return this; - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/JobQueueManager.java --- a/gui/edu/unc/genomics/JobQueueManager.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -package edu.unc.genomics; - -import java.util.List; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.Future; - -import org.apache.log4j.Logger; - -/** - * Controller for scheduling and running jobs - * Wrapper for ExcecutorService, although the implementation could change - * - * @author timpalpant - * - */ -public class JobQueueManager { - - private static final Logger log = Logger.getLogger(JobQueueManager.class); - - private final JobQueue queue; - private final ExecutorService exec; - private final Thread monitor; - - public JobQueueManager(JobQueue queue) { - this.queue = queue; - - int numProcessors = Runtime.getRuntime().availableProcessors(); - log.debug("Initializing thread pool with "+numProcessors+" processors"); - exec = Executors.newFixedThreadPool(numProcessors); - - monitor = new Thread(new JobMonitor()); - monitor.start(); - } - - public List shutdownNow() { - return exec.shutdownNow(); - } - - /** - * Add a Job to the queue - * @param job - * @throws JobException - */ - public SubmittedJob submitJob(Job job) throws JobException { - // Refuse to add the Job to the queue if its arguments are not valid - if (!job.validateArguments()) { - throw new JobException("Job arguments are not valid"); - } - - // Submit the job for execution into the thread pool - Future future = exec.submit(job); - SubmittedJob submittedJob = new SubmittedJob(job, future); - log.info("Submitted job " + submittedJob.getId()); - - // Add the SubmittedJob to the JobQueue - queue.add(submittedJob); - return submittedJob; - } - - /** - * Are any jobs running? (not done) - * @return - */ - public boolean isRunning() { - for (SubmittedJob job : queue) { - if (!job.isDone()) { - return true; - } - } - - return false; - } - - - /** - * Background process for polling the status of submitted jobs - * @author timpalpant - * - */ - public class JobMonitor implements Runnable { - - public static final int JOB_POLL_INTERVAL = 1_000; - - public void run() { - try { - while (true) { - // Check Job statuses every 1s - Thread.sleep(JOB_POLL_INTERVAL); - - for (SubmittedJob job : queue) { - if (job.isDone()) { - queue.update(job); - } - } - } - } catch (InterruptedException e) { - log.fatal("JobMonitor crashed"); - e.printStackTrace(); - throw new RuntimeException("JobMonitor crashed"); - } - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ResourceManager.java --- a/gui/edu/unc/genomics/ResourceManager.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -package edu.unc.genomics; - -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; - -/** - * Find resources based on platform/package - * @author timpalpant - * - */ -public class ResourceManager { - - private static final Path ASSEMBLIES_DIR = Paths.get("assemblies"); - private static final Path IMAGES_DIR = Paths.get("images"); - - public static Path getResourceDirectory() { - Path osx = Paths.get("../Resources"); - if (Files.exists(osx)) { - return osx; - } - - return Paths.get("resources"); - } - - public static Path getAssembliesDirectory() { - return getResourceDirectory().resolve(ASSEMBLIES_DIR); - } - - public static Path getImagesDirectory() { - return getResourceDirectory().resolve(IMAGES_DIR); - } -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/SubmittedJob.java --- a/gui/edu/unc/genomics/SubmittedJob.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,103 +0,0 @@ -package edu.unc.genomics; - -import java.util.concurrent.ExecutionException; -import java.util.concurrent.Future; - -/** - * Represents a job that was submitted for processing - * - * @author timpalpant - * - */ -public class SubmittedJob { - private static int numJobs = 0; - - private final Future future; - private final int id; - private final Job job; - - public SubmittedJob(Job job, Future future) { - this.id = ++numJobs; - this.job = job; - this.future = future; - } - - /** - * @return the id - */ - public int getId() { - return id; - } - - /** - * @return the job - */ - public Job getJob() { - return job; - } - - /** - * If the job is currently running - * @return - */ - public boolean isRunning() { - return job.isRunning() && !isDone(); - } - - /** - * If the job is done running - * (it may have failed or succeeded) - * @return - */ - public boolean isDone() { - return future.isDone(); - } - - /** - * If this job completed without any Exceptions - * @return - */ - public boolean succeeded() { - return (future.isDone() && !failed()); - } - - /** - * If this job completed with Exceptions - * @return - */ - public boolean failed() { - if (future.isDone()) { - try { - future.get(); - return false; - } catch (InterruptedException | ExecutionException e) { - return true; - } - } - - return false; - } - - /** - * Return an Exception that occured, or null if there were none - * or the job is not yet done - * @return - */ - public Exception getException() { - if (future.isDone()) { - try { - future.get(); - return null; - } catch (InterruptedException | ExecutionException e) { - return e; - } - } - - return null; - } - - @Override - public String toString() { - return "Job "+id+": "+job.getName(); - } -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ThreadFilter.java --- a/gui/edu/unc/genomics/ThreadFilter.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -package edu.unc.genomics; - -import org.apache.log4j.spi.Filter; -import org.apache.log4j.spi.LoggingEvent; - -/** - * A Log4j filter that filters for messages from a single thread - * @author timpalpant - * - */ -public class ThreadFilter extends Filter { - - private final String threadName; - - public ThreadFilter(String threadName) { - this.threadName = threadName; - } - - @Override - public int decide(LoggingEvent e) { - if(e.getThreadName().equalsIgnoreCase(threadName)) { - return Filter.DENY; - } - - return Filter.NEUTRAL; - } - - /** - * @return the threadName - */ - public String getThreadName() { - return threadName; - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ToolRunner.java --- a/gui/edu/unc/genomics/ToolRunner.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -package edu.unc.genomics; - -import java.awt.EventQueue; - -import javax.swing.JFrame; - -import org.apache.log4j.Logger; - -/** - * The main application for running the genomics toolkit gui - * Could do resource checking, etc. prior to startup - * - * @author timpalpant - * - */ -public class ToolRunner { - - private static final Logger log = Logger.getLogger(ToolRunner.class); - - private JFrame frmToolRunner = new ToolRunnerFrame(); - - /** - * Launch the application. - */ - public static void main(String[] args) { - EventQueue.invokeLater(new Runnable() { - @Override - public void run() { - try { - ToolRunner window = new ToolRunner(); - window.frmToolRunner.setVisible(true); - } catch (Exception e) { - e.printStackTrace(); - } - } - }); - } -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ToolRunnerFrame.java --- a/gui/edu/unc/genomics/ToolRunnerFrame.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,328 +0,0 @@ -package edu.unc.genomics; - -import java.awt.BorderLayout; -import java.awt.Color; -import java.awt.Component; -import java.awt.Container; -import java.awt.Dimension; -import java.awt.Font; - -import javax.swing.JFrame; -import javax.swing.JPanel; - -import javax.swing.BorderFactory; -import javax.swing.JComponent; -import javax.swing.JLabel; -import javax.swing.JList; -import javax.swing.JMenuBar; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JButton; -import javax.swing.JOptionPane; -import javax.swing.JPopupMenu; -import javax.swing.JScrollPane; -import javax.swing.SwingConstants; - -import javax.swing.JProgressBar; -import javax.swing.JSplitPane; -import javax.swing.BoxLayout; -import javax.swing.JTabbedPane; -import javax.swing.JTextPane; - -import javax.swing.event.TreeSelectionListener; -import javax.swing.event.TreeSelectionEvent; -import javax.xml.parsers.ParserConfigurationException; - -import org.apache.log4j.Logger; -import org.simplericity.macify.eawt.Application; -import org.simplericity.macify.eawt.ApplicationEvent; -import org.simplericity.macify.eawt.ApplicationListener; -import org.simplericity.macify.eawt.DefaultApplication; -import org.xml.sax.SAXException; - -import com.beust.jcommander.JCommander; - -import java.awt.event.ActionListener; -import java.awt.event.ActionEvent; -import java.io.IOException; - -/** - * The main ToolRunner window - * and controller for creating, running, and managing Jobs - * - * @author timpalpant - * - */ -public class ToolRunnerFrame extends JFrame implements ApplicationListener { - - private static final long serialVersionUID = 6454774196137357898L; - private static final Logger log = Logger.getLogger(ToolRunnerFrame.class); - - private final Application application = new DefaultApplication(); - - private final JPanel contentPane = new JPanel(); - private final JSplitPane splitPane = new JSplitPane(); - private final JPanel mainPane = new JPanel(); - private final JProgressBar progressBar = new JProgressBar(); - private final JTabbedPane tabbedPane = new JTabbedPane(SwingConstants.TOP); - private final JobConfigPanel configurationPanel = new JobConfigPanel(); - private final JTextPane helpTextPanel = new JTextPane(); - private final ToolsTree toolsTree = new ToolsTree(); - - private final JobQueue queue = new JobQueue(); - private final JobQueueManager queueManager = new JobQueueManager(queue); - private final JList queueList = new JList<>(queue); - - /** - * Create the frame. - */ - public ToolRunnerFrame() { - //application.addPreferencesMenuItem(); - //application.setEnabledPreferencesMenu(true); - application.addApplicationListener(this); - - // set OS X-specific properties - if (application.isMac()) { - setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE); - //toolsTree.putClientProperty("Quaqua.Tree.style", "sourceList"); - } else { - setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - } - setTitle("Genomics Toolkit Tool Runner"); - setBounds(100, 100, 1000, 600); - - contentPane.setBorder(BorderFactory.createEmptyBorder()); - contentPane.setLayout(new BorderLayout(0, 0)); - setContentPane(contentPane); - - initializeChildren(); - initializeMenuBar(); - } - - private void initializeChildren() { - splitPane.setBorder(BorderFactory.createEmptyBorder()); - contentPane.add(splitPane, BorderLayout.CENTER); - - initializeQueuePanel(); - initializeToolsTree(); - - mainPane.setLayout(new BorderLayout(0, 0)); - mainPane.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY)); - mainPane.add(tabbedPane, BorderLayout.CENTER); - - JPanel runPanel = new JPanel(); - runPanel.setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 0)); - runPanel.setLayout(new BoxLayout(runPanel, BoxLayout.X_AXIS)); - runPanel.add(progressBar); - JButton btnRun = new JButton("Run"); - btnRun.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - addJobToQueue(); - } - }); - runPanel.add(btnRun); - mainPane.add(runPanel, BorderLayout.SOUTH); - splitPane.setRightComponent(mainPane); - - initializeConfigurationPanel(); - initializeHelpPanel(); - } - - private void initializeMenuBar() { - JMenuBar menuBar = new JMenuBar(); - setJMenuBar(menuBar); - - JMenu mnFileMenu = new JMenu("File"); - menuBar.add(mnFileMenu); - - JMenuItem mntmAssemblyManager = new JMenuItem("Assembly manager"); - mntmAssemblyManager.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - JMenuItem menuItem = (JMenuItem) e.getSource(); - JPopupMenu popupMenu = (JPopupMenu) menuItem.getParent(); - Component invoker = popupMenu.getInvoker(); //this is the JMenu (in my code) - JComponent invokerAsJComponent = (JComponent) invoker; - Container topLevel = invokerAsJComponent.getTopLevelAncestor(); - AssemblyManagerDialog dialog = new AssemblyManagerDialog((JFrame) topLevel); - //dialog.getRootPane().putClientProperty("Window.style", "small"); - dialog.setVisible(true); - } - }); - mnFileMenu.add(mntmAssemblyManager); - - JMenu mnHelpMenu = new JMenu("Help"); - menuBar.add(mnHelpMenu); - - JMenuItem mntmHelpContents = new JMenuItem("Help Contents"); - mnHelpMenu.add(mntmHelpContents); - - if (!application.isMac()) { - JMenuItem mntmAbout = new JMenuItem("About"); - mnHelpMenu.add(mntmAbout); - mnHelpMenu.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent e) { - handleAbout(null); - } - }); - } - } - - private void initializeQueuePanel() { - JPanel queuePanel = new JPanel(); - queuePanel.setLayout(new BoxLayout(queuePanel, BoxLayout.PAGE_AXIS)); - queuePanel.setBorder(BorderFactory.createEmptyBorder()); - contentPane.add(queuePanel, BorderLayout.EAST); - - JLabel queueLabel = new JLabel("Job Queue"); - queueLabel.setBorder(BorderFactory.createEmptyBorder(5, 0, 5, 0)); - queueLabel.setAlignmentX(JLabel.CENTER_ALIGNMENT); - queuePanel.add(queueLabel); - - queueList.setBackground(contentPane.getBackground()); - queueList.setCellRenderer(new JobQueueCellRenderer()); - JScrollPane queueListScrollPane = new JScrollPane(queueList); - queueListScrollPane.setBorder(BorderFactory.createEmptyBorder()); - queueListScrollPane.setBackground(contentPane.getBackground()); - queueListScrollPane.setPreferredSize(new Dimension(200, Integer.MAX_VALUE)); - queuePanel.add(queueListScrollPane); - } - - private void initializeConfigurationPanel() { - JScrollPane configScrollPane = new JScrollPane(configurationPanel); - configScrollPane.setBorder(BorderFactory.createEmptyBorder()); - tabbedPane.addTab("Tool Configuration", null, configScrollPane, "Configure tool"); - } - - private void initializeHelpPanel() { - JPanel helpPanel = new JPanel(); - tabbedPane.addTab("Help", null, helpPanel, null); - helpPanel.setLayout(new BorderLayout(0, 0)); - - helpTextPanel.setEditable(false); - helpTextPanel.setBackground(tabbedPane.getBackground()); - Font mono = new Font("Monospaced", helpTextPanel.getFont().getStyle(), helpTextPanel.getFont().getSize()); - helpTextPanel.setFont(mono); - JScrollPane helpScrollPane = new JScrollPane(helpTextPanel); - helpScrollPane.setBorder(BorderFactory.createEmptyBorder()); - helpPanel.add(helpScrollPane); - } - - private void initializeToolsTree() { - try { - ToolsTreeModel model = ToolsTreeModel.loadDefaultConfig(); - toolsTree.setModel(model); - } catch (ParserConfigurationException | SAXException | IOException e1) { - log.error("Error loading tool configuration file"); - e1.printStackTrace(); - System.exit(-1); - } catch (ClassNotFoundException e) { - log.error("Error loading tool: " + e.getMessage()); - e.printStackTrace(); - System.exit(-1); - } - - toolsTree.addTreeSelectionListener(new TreeSelectionListener() { - public void valueChanged(TreeSelectionEvent e) { - changeTool(); - } - }); - - JScrollPane toolsTreeScrollPane = new JScrollPane(toolsTree); - toolsTreeScrollPane.setBorder(BorderFactory.createMatteBorder(0, 0, 0, 1, Color.LIGHT_GRAY)); - splitPane.setLeftComponent(toolsTreeScrollPane); - } - - /** - * Change the configuration panel to the currently selected tool - * to configure a new Job - */ - private void changeTool() { - // Returns the last path element of the selection. - Object node = toolsTree.getLastSelectedPathComponent(); - // Nothing is selected - if (node == null) { - return; - } - - if (node instanceof ToolsTreeNode) { - ToolsTreeNode toolNode = (ToolsTreeNode) node; - try { - Class tool = toolNode.getClazz(); - - // Set up the configuration panel to configure this tool - Job job = new Job(tool); - configurationPanel.setJob(job); - // Set the help text to the usage - helpTextPanel.setText(job.getUsageText()); - } catch (InstantiationException | IllegalAccessException e) { - log.error("Error initializing Job"); - e.printStackTrace(); - JOptionPane.showMessageDialog(this, "Error initializing job", "Job Initialization Error", JOptionPane.ERROR_MESSAGE); - } - - } - } - - private void addJobToQueue() { - Job currentJob = configurationPanel.getJob(); - if (currentJob == null) return; - - // Validate the required parameters - log.info("Validating parameters for tool"); - if (!currentJob.validateArguments()) { - configurationPanel.highlightInvalidArguments(); - return; - } - - // Add the job to the queue - try { - queueManager.submitJob(currentJob); - configurationPanel.setJob(null); - } catch (JobException e) { - log.error("Error adding Job to queue"); - e.printStackTrace(); - JOptionPane.showMessageDialog(this, "Error adding job to queue", "Job Queue Error", JOptionPane.ERROR_MESSAGE); - } - } - - public void handleAbout(ApplicationEvent event) { - JOptionPane.showMessageDialog(this, "Java Genomics Toolkit v1.0"); - if (event != null) { - event.setHandled(true); - } - } - - public void handleOpenApplication(ApplicationEvent event) { - // Application was opened - } - - public void handleOpenFile(ApplicationEvent event) { - //JOptionPane.showMessageDialog(frmToolRunner, "OS X told us to open " + event.getFilename()); - } - - public void handlePreferences(ApplicationEvent event) { - //JOptionPane.showMessageDialog(frmToolRunner, "No preferences available"); - } - - public void handlePrintFile(ApplicationEvent event) { - //JOptionPane.showMessageDialog(frmToolRunner, "OS X told us to print " + event.getFilename()); - } - - public void handleQuit(ApplicationEvent event) { - boolean confirm = true; - if (queueManager.isRunning()) { - int result = JOptionPane.showConfirmDialog(this, "Jobs are currently running. Are you sure you want to quit?", "Confirm Quit", JOptionPane.OK_CANCEL_OPTION); - confirm = (result == JOptionPane.OK_OPTION); - } - - if (confirm) { - dispose(); - System.exit(0); - } - } - - public void handleReOpenApplication(ApplicationEvent event) { - //JOptionPane.showMessageDialog(frmToolRunner, "OS X told the application was reopened"); - setVisible(true); - } -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ToolsTree.java --- a/gui/edu/unc/genomics/ToolsTree.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -package edu.unc.genomics; - -import java.awt.Dimension; - -import javax.swing.BorderFactory; -import javax.swing.JTree; -import javax.swing.tree.TreeSelectionModel; - -/** - * Tree view of the available tools - * - * @author timpalpant - * - */ -public class ToolsTree extends JTree { - - private static final long serialVersionUID = -2591915754191263660L; - - public ToolsTree() { - super(); - initialize(); - } - - public ToolsTree(ToolsTreeModel model) { - super(model); - initialize(); - } - - private void initialize() { - getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION); - - setBorder(BorderFactory.createEmptyBorder()); - setRootVisible(false); - setShowsRootHandles(true); - setPreferredSize(new Dimension(200, 0)); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ToolsTreeModel.java --- a/gui/edu/unc/genomics/ToolsTreeModel.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -package edu.unc.genomics; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; - -import javax.swing.tree.DefaultMutableTreeNode; -import javax.swing.tree.DefaultTreeModel; -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; -import javax.xml.parsers.ParserConfigurationException; - -import org.apache.log4j.Logger; -import org.w3c.dom.Document; -import org.w3c.dom.Node; -import org.w3c.dom.NodeList; -import org.xml.sax.SAXException; - -/** - * Model for the ToolsTree - * Essentially just a DefaultTreeModel, but provides methods for - * loading the available tools from a configuration file - * - * @author timpalpant - * - */ -public class ToolsTreeModel extends DefaultTreeModel { - - public static final Path DEFAULT_CONFIGURATION_FILE = Paths.get("toolConf.xml"); - - private static final Logger log = Logger.getLogger(ToolsTreeModel.class); - - private static final long serialVersionUID = -6587614270922489960L; - - public ToolsTreeModel() { - super(new DefaultMutableTreeNode("Tools")); - } - - public static ToolsTreeModel loadDefaultConfig() throws ClassNotFoundException, ParserConfigurationException, SAXException, IOException { - return loadConfig(ResourceManager.getResourceDirectory().resolve(DEFAULT_CONFIGURATION_FILE)); - } - - public static ToolsTreeModel loadConfig(Path p) throws ParserConfigurationException, SAXException, IOException, ClassNotFoundException { - ToolsTreeModel model = new ToolsTreeModel(); - DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot(); - - // Populate the TreeModel with the tools in the default configuration file - log.debug("Loading tools from: " + DEFAULT_CONFIGURATION_FILE.toAbsolutePath()); - DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); - DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); - Document doc = dBuilder.parse(p.toFile()); - - // Iterate over the sections - NodeList sections = doc.getElementsByTagName("section"); - log.debug("Found "+sections.getLength()+" sections"); - for (int i = 0; i < sections.getLength(); i++) { - Node section = sections.item(i); - String sectionName = section.getAttributes().getNamedItem("name").getNodeValue(); - log.debug("Loading section: " + sectionName); - DefaultMutableTreeNode sectionNode = new DefaultMutableTreeNode(sectionName); - root.add(sectionNode); - NodeList tools = section.getChildNodes(); - - // Iterate over the tools in each section - for (int j = 0; j < tools.getLength(); j++) { - Node tool = tools.item(j); - if (tool.getNodeType() == Node.ELEMENT_NODE && tool.getNodeName().equalsIgnoreCase("tool")) { - String toolName = tool.getAttributes().getNamedItem("name").getNodeValue(); - log.debug("Loading tool: " + toolName); - String toolClassName = tool.getAttributes().getNamedItem("class").getNodeValue(); - Class toolClass = (Class) Class.forName(toolClassName); - ToolsTreeNode toolNode = new ToolsTreeNode(toolName, toolClass); - sectionNode.add(toolNode); - } - } - } - - return model; - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/edu/unc/genomics/ToolsTreeNode.java --- a/gui/edu/unc/genomics/ToolsTreeNode.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -package edu.unc.genomics; - -import javax.swing.tree.DefaultMutableTreeNode; - -/** - * A node in the ToolsTreeModel - * Contains a class and a name for the tool - * TODO Add help for each tool - * - * @author timpalpant - * - */ -public class ToolsTreeNode extends DefaultMutableTreeNode { - - private static final long serialVersionUID = -9067416927466519457L; - - private final String name; - private final Class clazz; - - /** - * @param userObject - */ - public ToolsTreeNode(String name, Class clazz) { - super(name, false); - - this.name = name; - this.clazz = clazz; - } - - /** - * @return the name - */ - public String getName() { - return name; - } - - /** - * @return the clazz - */ - public Class getClazz() { - return clazz; - } - -} diff -r e16016635b2a -r 4b610dc8f6ba gui/javax/swing/layout/SpringUtilities.java --- a/gui/javax/swing/layout/SpringUtilities.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,225 +0,0 @@ -/* - * Copyright (c) 1995, 2008, Oracle and/or its affiliates. All rights reserved. - * - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions - * are met: - * - * - Redistributions of source code must retain the above copyright - * notice, this list of conditions and the following disclaimer. - * - * - Redistributions in binary form must reproduce the above copyright - * notice, this list of conditions and the following disclaimer in the - * documentation and/or other materials provided with the distribution. - * - * - Neither the name of Oracle or the names of its - * contributors may be used to endorse or promote products derived - * from this software without specific prior written permission. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS - * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, - * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR - * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR - * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, - * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, - * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR - * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF - * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING - * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - -package javax.swing.layout; - -import javax.swing.*; -import javax.swing.SpringLayout; -import java.awt.*; - -/** - * A 1.4 file that provides utility methods for - * creating form- or grid-style layouts with SpringLayout. - * These utilities are used by several programs, such as - * SpringBox and SpringCompactGrid. - */ -public class SpringUtilities { - /** - * A debugging utility that prints to stdout the component's - * minimum, preferred, and maximum sizes. - */ - public static void printSizes(Component c) { - System.out.println("minimumSize = " + c.getMinimumSize()); - System.out.println("preferredSize = " + c.getPreferredSize()); - System.out.println("maximumSize = " + c.getMaximumSize()); - } - - /** - * Aligns the first rows * cols - * components of parent in - * a grid. Each component is as big as the maximum - * preferred width and height of the components. - * The parent is made just big enough to fit them all. - * - * @param rows number of rows - * @param cols number of columns - * @param initialX x location to start the grid at - * @param initialY y location to start the grid at - * @param xPad x padding between cells - * @param yPad y padding between cells - */ - public static void makeGrid(Container parent, - int rows, int cols, - int initialX, int initialY, - int xPad, int yPad) { - SpringLayout layout; - try { - layout = (SpringLayout)parent.getLayout(); - } catch (ClassCastException exc) { - System.err.println("The first argument to makeGrid must use SpringLayout."); - return; - } - - Spring xPadSpring = Spring.constant(xPad); - Spring yPadSpring = Spring.constant(yPad); - Spring initialXSpring = Spring.constant(initialX); - Spring initialYSpring = Spring.constant(initialY); - int max = rows * cols; - - //Calculate Springs that are the max of the width/height so that all - //cells have the same size. - Spring maxWidthSpring = layout.getConstraints(parent.getComponent(0)). - getWidth(); - Spring maxHeightSpring = layout.getConstraints(parent.getComponent(0)). - getHeight(); - for (int i = 1; i < max; i++) { - SpringLayout.Constraints cons = layout.getConstraints( - parent.getComponent(i)); - - maxWidthSpring = Spring.max(maxWidthSpring, cons.getWidth()); - maxHeightSpring = Spring.max(maxHeightSpring, cons.getHeight()); - } - - //Apply the new width/height Spring. This forces all the - //components to have the same size. - for (int i = 0; i < max; i++) { - SpringLayout.Constraints cons = layout.getConstraints( - parent.getComponent(i)); - - cons.setWidth(maxWidthSpring); - cons.setHeight(maxHeightSpring); - } - - //Then adjust the x/y constraints of all the cells so that they - //are aligned in a grid. - SpringLayout.Constraints lastCons = null; - SpringLayout.Constraints lastRowCons = null; - for (int i = 0; i < max; i++) { - SpringLayout.Constraints cons = layout.getConstraints( - parent.getComponent(i)); - if (i % cols == 0) { //start of new row - lastRowCons = lastCons; - cons.setX(initialXSpring); - } else { //x position depends on previous component - cons.setX(Spring.sum(lastCons.getConstraint(SpringLayout.EAST), - xPadSpring)); - } - - if (i / cols == 0) { //first row - cons.setY(initialYSpring); - } else { //y position depends on previous row - cons.setY(Spring.sum(lastRowCons.getConstraint(SpringLayout.SOUTH), - yPadSpring)); - } - lastCons = cons; - } - - //Set the parent's size. - SpringLayout.Constraints pCons = layout.getConstraints(parent); - pCons.setConstraint(SpringLayout.SOUTH, - Spring.sum( - Spring.constant(yPad), - lastCons.getConstraint(SpringLayout.SOUTH))); - pCons.setConstraint(SpringLayout.EAST, - Spring.sum( - Spring.constant(xPad), - lastCons.getConstraint(SpringLayout.EAST))); - } - - /* Used by makeCompactGrid. */ - private static SpringLayout.Constraints getConstraintsForCell( - int row, int col, - Container parent, - int cols) { - SpringLayout layout = (SpringLayout) parent.getLayout(); - Component c = parent.getComponent(row * cols + col); - return layout.getConstraints(c); - } - - /** - * Aligns the first rows * cols - * components of parent in - * a grid. Each component in a column is as wide as the maximum - * preferred width of the components in that column; - * height is similarly determined for each row. - * The parent is made just big enough to fit them all. - * - * @param rows number of rows - * @param cols number of columns - * @param initialX x location to start the grid at - * @param initialY y location to start the grid at - * @param xPad x padding between cells - * @param yPad y padding between cells - */ - public static void makeCompactGrid(Container parent, - int rows, int cols, - int initialX, int initialY, - int xPad, int yPad) { - SpringLayout layout; - try { - layout = (SpringLayout)parent.getLayout(); - } catch (ClassCastException exc) { - System.err.println("The first argument to makeCompactGrid must use SpringLayout."); - return; - } - - //Align all cells in each column and make them the same width. - Spring x = Spring.constant(initialX); - for (int c = 0; c < cols; c++) { - Spring width = Spring.constant(0); - for (int r = 0; r < rows; r++) { - width = Spring.max(width, - getConstraintsForCell(r, c, parent, cols). - getWidth()); - } - for (int r = 0; r < rows; r++) { - SpringLayout.Constraints constraints = - getConstraintsForCell(r, c, parent, cols); - constraints.setX(x); - constraints.setWidth(width); - } - x = Spring.sum(x, Spring.sum(width, Spring.constant(xPad))); - } - - //Align all cells in each row and make them the same height. - Spring y = Spring.constant(initialY); - for (int r = 0; r < rows; r++) { - Spring height = Spring.constant(0); - for (int c = 0; c < cols; c++) { - height = Spring.max(height, - getConstraintsForCell(r, c, parent, cols). - getHeight()); - } - for (int c = 0; c < cols; c++) { - SpringLayout.Constraints constraints = - getConstraintsForCell(r, c, parent, cols); - constraints.setY(y); - constraints.setHeight(height); - } - y = Spring.sum(y, Spring.sum(height, Spring.constant(yPad))); - } - - //Set the parent's size. - SpringLayout.Constraints pCons = layout.getConstraints(parent); - pCons.setConstraint(SpringLayout.SOUTH, y); - pCons.setConstraint(SpringLayout.EAST, x); - } -} diff -r e16016635b2a -r 4b610dc8f6ba launch4j.xml --- a/launch4j.xml Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - false - gui - dist/java-genomics-toolkit.jar - dist/Genomics Toolkit.exe - - - - normal - http://java.com/download - http://github.com/timpalpant/java-genomics-toolkit - false - false - META-INF/MANIFEST.MF - - - edu.unc.genomics.GenomicsToolkit - ../lib/* - - - - 1.7.0 - - preferJre - - \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba lib/BigWig.jar Binary file lib/BigWig.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/commons-lang3-3.1.jar Binary file lib/commons-lang3-3.1.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/commons-math-2.2.jar Binary file lib/commons-math-2.2.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/jarbundler-2.2.0.jar Binary file lib/jarbundler-2.2.0.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/java-genomics-io.jar Binary file lib/java-genomics-io.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/jcommander-1.20.jar Binary file lib/jcommander-1.20.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/jtransforms-2.4.jar Binary file lib/jtransforms-2.4.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/launch4j.jar Binary file lib/launch4j.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/log4j-1.2.15.jar Binary file lib/log4j-1.2.15.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/macify-1.4.jar Binary file lib/macify-1.4.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/sam-1.56.jar Binary file lib/sam-1.56.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/swing-layout.jar Binary file lib/swing-layout.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba lib/xstream.jar Binary file lib/xstream.jar has changed diff -r e16016635b2a -r 4b610dc8f6ba log4j.properties --- a/log4j.properties Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -log4j.rootLogger=debug, stdout - -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout - -# Pattern to output the caller's file name and line number. -log4j.appender.stdout.layout.ConversionPattern=%5p - %m%n - -# Only output errors from the BigWig library -log4j.logger.org.broad.igv.bbfile=ERROR \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce2.len --- a/resources/assemblies/ce2.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrI 15080483 -chrII 15279308 -chrIII 13783313 -chrIV 17493791 -chrM 13794 -chrV 20922231 -chrX 17718849 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce3.len --- a/resources/assemblies/ce3.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrI 15080552 -chrII 15279311 -chrIII 13783317 -chrIV 17493785 -chrM 13794 -chrV 20922231 -chrX 17718850 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce4.len --- a/resources/assemblies/ce4.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrI 15072419 -chrII 15279316 -chrIII 13783681 -chrIV 17493784 -chrM 13794 -chrV 20919398 -chrX 17718852 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce5.len --- a/resources/assemblies/ce5.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrV 20919568 -chrX 17718851 -chrIV 17493785 -chrII 15279316 -chrI 15072421 -chrIII 13783681 -chrM 13794 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce6.len --- a/resources/assemblies/ce6.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrV 20919568 -chrX 17718854 -chrIV 17493785 -chrII 15279323 -chrI 15072421 -chrIII 13783681 -chrM 13794 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce7.len --- a/resources/assemblies/ce7.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrV 20924143 -chrX 17718854 -chrIV 17493784 -chrII 15279324 -chrI 15072421 -chrIII 13783682 -chrM 13794 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce8.len --- a/resources/assemblies/ce8.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrV 20924143 -chrX 17718854 -chrIV 17493784 -chrII 15279323 -chrI 15072421 -chrIII 13783685 -chrM 13794 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/ce9.len --- a/resources/assemblies/ce9.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -chrV 20924143 -chrX 17718854 -chrIV 17493784 -chrII 15279323 -chrI 15072421 -chrIII 13783685 -chrM 13794 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/dm1.len --- a/resources/assemblies/dm1.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -chr4 1237870 -chrU 8248647 -chrX 21780003 -chr2L 22217931 -chr2R 20302755 -chr2h 1651714 -chr3L 23352213 -chr3R 27890790 -chr3h 1961095 -chrXh 359526 -chrYh 321294 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/dm2.len --- a/resources/assemblies/dm2.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -chr4 1281640 -chrM 19517 -chrU 8724946 -chrX 22224390 -chr2L 22407834 -chr2R 20766785 -chr2h 1694122 -chr3L 23771897 -chr3R 27905053 -chr3h 2955737 -chr4h 88110 -chrXh 359526 -chrYh 396896 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/dm3.len --- a/resources/assemblies/dm3.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -chr2L 23011544 -chr2LHet 368872 -chr2R 21146708 -chr2RHet 3288761 -chr3L 24543557 -chr3LHet 2555491 -chr3R 27905053 -chr3RHet 2517507 -chr4 1351857 -chrU 10049037 -chrUextra 29004656 -chrX 22422827 -chrXHet 204112 -chrYHet 347038 -chrM 19517 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/hg15.len --- a/resources/assemblies/hg15.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -chr1 245203898 -chr2 243315028 -chr3 199411731 -chr4 191610523 -chr5 180967295 -chr6 170740541 -chr7 158431299 -chr8 145908738 -chr9 134505819 -chrM 16571 -chrX 152634166 -chrY 50961097 -chr1_random 12562665 -chr2_random 1464032 -chr3_random 423185 -chr4_random 1219494 -chr6_random 12061844 -chr7_random 1057565 -chr8_random 427716 -chr9_random 2536476 -chrX_random 4859112 -chrY_random 191708 -chr10 135480874 -chr11 134978784 -chr12 133464434 -chr13 114151656 -chr14 105311216 -chr15 100114055 -chr16 89995999 -chr17 81691216 -chr18 77753510 -chr19 63790860 -chr20 63644868 -chr21 46976537 -chr22 49476972 -chr10_random 710249 -chr11_random 150110 -chr12_random 590431 -chr13_random 414659 -chr15_random 366089 -chr16_random 24360 -chr17_random 337440 -chr19_random 301858 -chrUn_random 611077 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/hg16.len --- a/resources/assemblies/hg16.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -chr1 246127941 -chr2 243615958 -chr3 199344050 -chr4 191731959 -chr5 181034922 -chr6 170914576 -chr7 158545518 -chr8 146308819 -chr9 136372045 -chrM 16571 -chrX 153692391 -chrY 50286555 -chr1_random 6515988 -chr2_random 1104831 -chr3_random 749256 -chr4_random 648024 -chr5_random 143687 -chr6_random 2055751 -chr7_random 632637 -chr8_random 1499381 -chr9_random 2766341 -chrX_random 3403558 -chr10 135037215 -chr11 134482954 -chr12 132078379 -chr13 113042980 -chr14 105311216 -chr15 100256656 -chr16 90041932 -chr17 81860266 -chr18 76115139 -chr19 63811651 -chr20 63741868 -chr21 46976097 -chr22 49396972 -chr10_random 1043775 -chr13_random 189598 -chr15_random 1132826 -chr17_random 2549222 -chr18_random 4262 -chr19_random 92689 -chrUn_random 3349625 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/hg17.len --- a/resources/assemblies/hg17.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -chr10 135413628 -chr10_random 113275 -chr11 134452384 -chr12 132449811 -chr12_random 466818 -chr13 114142980 -chr13_random 186858 -chr14 106368585 -chr15 100338915 -chr15_random 784346 -chr16 88827254 -chr16_random 105485 -chr17 78774742 -chr17_random 2618010 -chr18 76117153 -chr18_random 4262 -chr19 63811651 -chr19_random 301858 -chr1 245522847 -chr1_random 3897131 -chr20 62435964 -chr21 46944323 -chr22 49554710 -chr22_random 257318 -chr2 243018229 -chr2_random 418158 -chr3 199505740 -chr3_random 970716 -chr4 191411218 -chr4_random 1030282 -chr5 180857866 -chr5_random 143687 -chr6 170975699 -chr6_random 1875562 -chr6_hla_hap1 139182 -chr6_hla_hap2 150447 -chr7 158628139 -chr7_random 778964 -chr8 146274826 -chr8_random 943810 -chr9 138429268 -chr9_random 1312665 -chrM 16571 -chrX 154824264 -chrX_random 1719168 -chrY 57701691 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/hg18.len --- a/resources/assemblies/hg18.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -chr1 247249719 -chr1_random 1663265 -chr10 135374737 -chr10_random 113275 -chr11 134452384 -chr11_random 215294 -chr12 132349534 -chr13 114142980 -chr13_random 186858 -chr14 106368585 -chr15 100338915 -chr15_random 784346 -chr16 88827254 -chr16_random 105485 -chr17 78774742 -chr17_random 2617613 -chr18 76117153 -chr18_random 4262 -chr19 63811651 -chr19_random 301858 -chr2 242951149 -chr2_random 185571 -chr20 62435964 -chr21 46944323 -chr21_random 1679693 -chr22 49691432 -chr22_random 257318 -chr22_h2_hap1 63661 -chr3 199501827 -chr3_random 749256 -chr4 191273063 -chr4_random 842648 -chr5 180857866 -chr5_random 143687 -chr5_h2_hap1 1794870 -chr6 170899992 -chr6_random 1875562 -chr6_cox_hap1 4731698 -chr6_qbl_hap2 4565931 -chr7 158821424 -chr7_random 549659 -chr8 146274826 -chr8_random 943810 -chr9 140273252 -chr9_random 1146434 -chrM 16571 -chrX 154913754 -chrX_random 1719168 -chrY 57772954 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/hg19.len --- a/resources/assemblies/hg19.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -chr1 249250621 -chr2 243199373 -chr3 198022430 -chr4 191154276 -chr5 180915260 -chr6 171115067 -chr7 159138663 -chrX 155270560 -chr8 146364022 -chr9 141213431 -chr10 135534747 -chr11 135006516 -chr12 133851895 -chr13 115169878 -chr14 107349540 -chr15 102531392 -chr16 90354753 -chr17 81195210 -chr18 78077248 -chr20 63025520 -chrY 59373566 -chr19 59128983 -chr22 51304566 -chr21 48129895 -chr6_ssto_hap7 4928567 -chr6_mcf_hap5 4833398 -chr6_cox_hap2 4795371 -chr6_mann_hap4 4683263 -chr6_apd_hap1 4622290 -chr6_qbl_hap6 4611984 -chr6_dbb_hap3 4610396 -chr17_ctg5_hap1 1680828 -chr4_ctg9_hap1 590426 -chr1_gl000192_random 547496 -chrUn_gl000225 211173 -chr4_gl000194_random 191469 -chr4_gl000193_random 189789 -chr9_gl000200_random 187035 -chrUn_gl000222 186861 -chrUn_gl000212 186858 -chr7_gl000195_random 182896 -chrUn_gl000223 180455 -chrUn_gl000224 179693 -chrUn_gl000219 179198 -chr17_gl000205_random 174588 -chrUn_gl000215 172545 -chrUn_gl000216 172294 -chrUn_gl000217 172149 -chr9_gl000199_random 169874 -chrUn_gl000211 166566 -chrUn_gl000213 164239 -chrUn_gl000220 161802 -chrUn_gl000218 161147 -chr19_gl000209_random 159169 -chrUn_gl000221 155397 -chrUn_gl000214 137718 -chrUn_gl000228 129120 -chrUn_gl000227 128374 -chr1_gl000191_random 106433 -chr19_gl000208_random 92689 -chr9_gl000198_random 90085 -chr17_gl000204_random 81310 -chrUn_gl000233 45941 -chrUn_gl000237 45867 -chrUn_gl000230 43691 -chrUn_gl000242 43523 -chrUn_gl000243 43341 -chrUn_gl000241 42152 -chrUn_gl000236 41934 -chrUn_gl000240 41933 -chr17_gl000206_random 41001 -chrUn_gl000232 40652 -chrUn_gl000234 40531 -chr11_gl000202_random 40103 -chrUn_gl000238 39939 -chrUn_gl000244 39929 -chrUn_gl000248 39786 -chr8_gl000196_random 38914 -chrUn_gl000249 38502 -chrUn_gl000246 38154 -chr17_gl000203_random 37498 -chr8_gl000197_random 37175 -chrUn_gl000245 36651 -chrUn_gl000247 36422 -chr9_gl000201_random 36148 -chrUn_gl000235 34474 -chrUn_gl000239 33824 -chr21_gl000210_random 27682 -chrUn_gl000231 27386 -chrUn_gl000229 19913 -chrM 16571 -chrUn_gl000226 15008 -chr18_gl000207_random 4262 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/hg19Haps.len --- a/resources/assemblies/hg19Haps.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -chr6_ssto_hap7 4928567 -chr6_mcf_hap5 4833398 -chr6_cox_hap2 4795371 -chr6_mann_hap4 4683263 -chr6_apd_hap1 4622290 -chr6_qbl_hap6 4611984 -chr6_dbb_hap3 4610396 -chr17_ctg5_hap1 1680828 -chr4_ctg9_hap1 590426 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/hg19Patch2.len --- a/resources/assemblies/hg19Patch2.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -chr6_ssto_hap7 4928567 -chr6_mcf_hap5 4833398 -chr6_cox_hap2 4795371 -chr6_mann_hap4 4683263 -chr6_apd_hap1 4622290 -chr6_qbl_hap6 4611984 -chr6_dbb_hap3 4610396 -chr17_ctg5_hap1 1680828 -chr5_ctg1_gl339449 1620324 -chr4_ctg9_hap1 590426 -chr17_gl383560 534288 -chr17_gl383558 457041 -chr8_gl383535 429806 -chr17_gl383561 406963 -chr10_gl383543 392792 -chr15_ctg8_gl383555 388773 -chr19_ctg3_gl383573 385657 -chr4_ctg6_gl383528 376187 -chr1_ctg31_gl383520 366579 -chr17_gl383559 338640 -chr9_gl339450 330164 -chr10_ctg5_gl383546 309802 -chr15_ctg4_gl383554 296527 -chr18_ctg1_gl383567 289831 -chr17_ctg1_gl383563 270261 -chr17_ctg4_gl383565 223995 -chr8_gl383536 203777 -chr21_ctg1_gl383579 201198 -chr18_ctg2_gl383571 198278 -chr16_ctg3_gl383556 192462 -chr19_ctg3_gl383576 188024 -chr12_ctg5_gl383551 184319 -chr1_ctg31_gl383518 182439 -chr3_ctg2_gl383526 180671 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-chr3_gl383525 65063 -chr21_ctg1_gl383578 63917 -chr9_gl383537 62435 -chr9_ctg35_gl383542 60032 -chr1_gl383517 49352 -chr1_gl383516 49316 -chr9_gl383538 49281 -chr17_gl383562 45551 -chrM_rCRS 16569 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/klac.len --- a/resources/assemblies/klac.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -1 1062590 -2 1320834 -3 1753957 -4 1715506 -5 2234072 -6 2602197 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/kwal.len --- a/resources/assemblies/kwal.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,459 +0,0 @@ -0 2534 -1 125497 -2 14630 -3 14849 -4 21406 -5 143962 -6 27307 -7 88161 -8 132901 -9 16396 -10 8070 -11 186703 -12 36232 -13 51137 -14 15683 -15 19814 -16 24938 -17 58820 -18 38681 -19 5673 -20 23346 -21 4497 -22 41879 -23 29929 -24 38007 -25 7906 -26 32971 -27 213938 -28 44808 -29 35672 -30 18684 -31 57206 -32 39731 -33 128244 -34 41627 -35 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-447 2611 -448 1179 -449 5365 -450 1259 -451 5395 -452 1972 -453 3195 -454 816 -455 7081 -456 1241 -457 21922 -458 1100 -459 927 -460 1100 -461 5552 -462 5577 -463 5460 -665 2006 -666 1381 -667 1781 -668 1407 -690 4541 -691 2971 -692 1226 -693 1100 -694 1218 -695 5394 -696 4542 -697 14183 -698 5428 -699 577 -700 2530 -710 16854 -711 2634 -712 5627 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/sacCer1.len --- a/resources/assemblies/sacCer1.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -chr1 230208 -chr10 745446 -chr11 666445 -chr12 1078173 -chr13 924430 -chr14 784328 -chr15 1091285 -chr16 948060 -chr2 813136 -chr3 316613 -chr4 1531914 -chr5 576869 -chr6 270148 -chr7 1090944 -chr8 562639 -chr9 439885 -chrM 85779 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/sacCer2.len --- a/resources/assemblies/sacCer2.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -chrIV 1531919 -chrXV 1091289 -chrVII 1090947 -chrXII 1078175 -chrXVI 948062 -chrXIII 924429 -chrII 813178 -chrXIV 784333 -chrX 745742 -chrXI 666454 -chrV 576869 -chrVIII 562643 -chrIX 439885 -chrIII 316617 -chrVI 270148 -chrI 230208 -chrM 85779 -2micron 6318 diff -r e16016635b2a -r 4b610dc8f6ba resources/assemblies/sacCer3.len --- a/resources/assemblies/sacCer3.len Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -chrI 230218 -chrII 813184 -chrIII 316620 -chrIV 1531933 -chrIX 439888 -chrV 576874 -chrVI 270161 -chrVII 1090940 -chrVIII 562643 -chrX 745751 -chrXI 666816 -chrXII 1078177 -chrXIII 924431 -chrXIV 784333 -chrXV 1091291 -chrXVI 948066 -chrM 85779 diff -r e16016635b2a -r 4b610dc8f6ba resources/images/add_icon.png Binary file resources/images/add_icon.png has changed diff -r e16016635b2a -r 4b610dc8f6ba resources/images/add_icon_dark.png Binary file resources/images/add_icon_dark.png has changed diff -r e16016635b2a -r 4b610dc8f6ba 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- - -

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- - - - - - - -

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- \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/config/GalaxyConfig.java --- a/src/edu/unc/config/GalaxyConfig.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -package edu.unc.config; - -import java.io.IOException; -import java.nio.file.Path; - -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; -import javax.xml.parsers.ParserConfigurationException; - -import org.w3c.dom.Document; -import org.xml.sax.SAXException; - -public class GalaxyConfig { - - /** - * Parse a Galaxy configuration file - * @param p - * @return - * @throws ParserConfigurationException - * @throws IOException - * @throws SAXException - */ - public static GalaxyConfig parse(Path p) throws ParserConfigurationException, SAXException, IOException { - DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); - DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); - Document doc = dBuilder.parse(p.toFile()); - return parse(doc); - } - - /** - * Parse a Galaxy configuration XML - * @param doc - * @return - */ - public static GalaxyConfig parse(Document doc) { - GalaxyConfig config = new GalaxyConfig(); - - // TODO Implement parser - - return config; - } -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/AssemblyConverter.java --- a/src/edu/unc/genomics/AssemblyConverter.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -package edu.unc.genomics; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.zip.DataFormatException; - -import com.beust.jcommander.IStringConverter; -import com.beust.jcommander.ParameterException; - -/** - * @author timpalpant - * - */ -public class AssemblyConverter implements IStringConverter { - - public static final Path ASSEMBLIES_DIR = Paths.get("resources", "assemblies"); - - @Override - public Assembly convert(String value) throws ParameterException { - // Look for the assembly in the resources/assemblies directory - Path p = ASSEMBLIES_DIR.resolve(value+".len"); - - // If it does not exist in the assemblies directory, check if it is a path to a file - if (!Files.isReadable(p)) { - PathConverter converter = new PathConverter(); - p = converter.convert(value); - // If it does not exist, then throw an exception that the assembly cannot be found - if (!Files.isReadable(p)) { - throw new ParameterException("Cannot find Assembly file: " + value); - } - } - - // Attempt to load the assembly from file - try { - return new Assembly(p); - } catch (IOException | DataFormatException e) { - throw new ParameterException("Error loading Assembly from file: " + p); - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/AssemblyFactory.java --- a/src/edu/unc/genomics/AssemblyFactory.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -/** - * - */ -package edu.unc.genomics; - -import com.beust.jcommander.IStringConverterFactory; - -/** - * @author timpalpant - * - */ -public class AssemblyFactory implements IStringConverterFactory { - - /* (non-Javadoc) - * @see com.beust.jcommander.IStringConverterFactory#getConverter(java.lang.Class) - */ - @Override - public Class getConverter(Class forType) { - if (forType.equals(Assembly.class)) { - return AssemblyConverter.class; - } else { - return null; - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/CommandLineTool.java --- a/src/edu/unc/genomics/CommandLineTool.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -package edu.unc.genomics; - -import java.io.IOException; - -import com.beust.jcommander.JCommander; -import com.beust.jcommander.ParameterException; - -/** - * A command-line script - * @author timpalpant - * - */ -public abstract class CommandLineTool { - - /** - * JCommander command-line argument parser - */ - private final JCommander jc = new JCommander(this); - - public CommandLineTool() { - // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles - jc.addConverterFactory(new PathFactory()); - jc.addConverterFactory(new AssemblyFactory()); - jc.addConverterFactory(new IntervalFileFactory()); - jc.addConverterFactory(new WigFileFactory()); - - // Set the program name to be the class name - jc.setProgramName(this.getClass().getSimpleName()); - } - - /** - * The default bite-size to use for applications that process files in chunks - */ - public static final int DEFAULT_CHUNK_SIZE = 500_000; - - /** - * Do the main computation of this tool - * @throws IOException - */ - public abstract void run() throws IOException; - - /** - * Parse command-line arguments and run the tool - * Exit on parameter exceptions - * @param args - */ - public void instanceMain(String[] args) throws CommandLineToolException { - try { - toolRunnerMain(args); - } catch (ParameterException e) { - System.err.println(e.getMessage()); - jc.usage(); - System.exit(-1); - } - } - - /** - * Parse command-line arguments and run the tool - * @param args - * @throws ParameterException if there are invalid/missing parameters - * @throws CommandLineToolException if an exception occurs while running the tool - */ - public void toolRunnerMain(String[] args) throws ParameterException, CommandLineToolException { - jc.parse(args); - - try { - run(); - } catch (IOException e) { - e.printStackTrace(); - throw new CommandLineToolException("IO error while running tool"); - } - } -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/CommandLineToolException.java --- a/src/edu/unc/genomics/CommandLineToolException.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ -package edu.unc.genomics; - -/** - * @author timpalpant - * - */ -public class CommandLineToolException extends RuntimeException { - - /** - * - */ - private static final long serialVersionUID = 4740440799806133636L; - - /** - * - */ - public CommandLineToolException() { - // TODO Auto-generated constructor stub - } - - /** - * @param message - */ - public CommandLineToolException(String message) { - super(message); - // TODO Auto-generated constructor stub - } - - /** - * @param cause - */ - public CommandLineToolException(Throwable cause) { - super(cause); - // TODO Auto-generated constructor stub - } - - /** - * @param message - * @param cause - */ - public CommandLineToolException(String message, Throwable cause) { - super(message, cause); - // TODO Auto-generated constructor stub - } - - /** - * @param message - * @param cause - * @param enableSuppression - * @param writableStackTrace - */ - public CommandLineToolException(String message, Throwable cause, - boolean enableSuppression, boolean writableStackTrace) { - super(message, cause, enableSuppression, writableStackTrace); - // TODO Auto-generated constructor stub - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/IntervalFileConverter.java --- a/src/edu/unc/genomics/IntervalFileConverter.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -package edu.unc.genomics; - -import java.io.IOException; -import java.nio.file.Path; - -import com.beust.jcommander.IStringConverter; -import com.beust.jcommander.ParameterException; - -import edu.unc.genomics.io.IntervalFile; - -/** - * @author timpalpant - * - */ -public class IntervalFileConverter implements IStringConverter> { - - @Override - public IntervalFile convert(String value) throws ParameterException { - PathConverter converter = new PathConverter(); - Path p = converter.convert(value); - try { - return IntervalFile.autodetect(p); - } catch (IOException e) { - throw new ParameterException("IOException while attempting to autodetect interval file type"); - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/IntervalFileFactory.java --- a/src/edu/unc/genomics/IntervalFileFactory.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -package edu.unc.genomics; - -import com.beust.jcommander.IStringConverterFactory; - -import edu.unc.genomics.io.IntervalFile; - -/** - * @author timpalpant - * - */ -public class IntervalFileFactory implements IStringConverterFactory { - - /* (non-Javadoc) - * @see com.beust.jcommander.IStringConverterFactory#getConverter(java.lang.Class) - */ - @Override - public Class getConverter(Class forType) { - if (forType.equals(IntervalFile.class)) { - return IntervalFileConverter.class; - } else { - return null; - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/PathConverter.java --- a/src/edu/unc/genomics/PathConverter.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -package edu.unc.genomics; - -import java.nio.file.Path; -import java.nio.file.Paths; - -import com.beust.jcommander.IStringConverter; - -/** - * @author timpalpant - * - */ -public class PathConverter implements IStringConverter { - - @Override - public Path convert(String value) { - return Paths.get(value); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/PathFactory.java --- a/src/edu/unc/genomics/PathFactory.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -/** - * - */ -package edu.unc.genomics; - -import java.nio.file.Path; - -import com.beust.jcommander.IStringConverterFactory; - -/** - * @author timpalpant - * - */ -public class PathFactory implements IStringConverterFactory { - /* (non-Javadoc) - * @see com.beust.jcommander.IStringConverterFactory#getConverter(java.lang.Class) - */ - @Override - public Class getConverter(Class forType) { - if (forType.equals(Path.class)) { - return PathConverter.class; - } else { - return null; - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/PositiveIntegerValidator.java --- a/src/edu/unc/genomics/PositiveIntegerValidator.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -package edu.unc.genomics; - -import com.beust.jcommander.IParameterValidator; -import com.beust.jcommander.ParameterException; - -/** - * @author timpalpant - * - */ -public class PositiveIntegerValidator implements IParameterValidator { - - /* (non-Javadoc) - * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String, java.lang.String) - */ - @Override - public void validate(String name, String value) throws ParameterException { - int n = Integer.parseInt(value); - if (n <= 0) { - throw new ParameterException("Parameter "+name+" must be > 0 (was "+value+")"); - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ReadablePathValidator.java --- a/src/edu/unc/genomics/ReadablePathValidator.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -/** - * - */ -package edu.unc.genomics; - -import java.nio.file.Files; -import java.nio.file.Path; - -import com.beust.jcommander.IParameterValidator; -import com.beust.jcommander.ParameterException; - -/** - * @author timpalpant - * - */ -public class ReadablePathValidator implements IParameterValidator { - - /* (non-Javadoc) - * @see com.beust.jcommander.IParameterValidator#validate(java.lang.String, java.lang.String) - */ - @Override - public void validate(String name, String value) throws ParameterException { - PathConverter converter = new PathConverter(); - Path p = converter.convert(value); - if (!Files.isReadable(p)) { - throw new ParameterException("Parameter " + name + " should be a readable file"); - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/WigFileConverter.java --- a/src/edu/unc/genomics/WigFileConverter.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -package edu.unc.genomics; - -import java.io.IOException; -import java.nio.file.Path; - -import com.beust.jcommander.IStringConverter; -import com.beust.jcommander.ParameterException; - -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -/** - * @author timpalpant - * - */ -public class WigFileConverter implements IStringConverter { - - @Override - public WigFile convert(String value) throws ParameterException { - PathConverter converter = new PathConverter(); - Path p = converter.convert(value); - try { - return WigFile.autodetect(p); - } catch (WigFileException | IOException e) { - throw new ParameterException("Error autodetecting and initializing BigWig/Wig file"); - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/WigFileFactory.java --- a/src/edu/unc/genomics/WigFileFactory.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -package edu.unc.genomics; - -import com.beust.jcommander.IStringConverterFactory; - -import edu.unc.genomics.io.WigFile; - -/** - * @author timpalpant - * - */ -public class WigFileFactory implements IStringConverterFactory { - - /* (non-Javadoc) - * @see com.beust.jcommander.IStringConverterFactory#getConverter(java.lang.Class) - */ - @Override - public Class getConverter(Class forType) { - if (forType.equals(WigFile.class)) { - return WigFileConverter.class; - } else { - return null; - } - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/converters/IntervalToWig.java --- a/src/edu/unc/genomics/converters/IntervalToWig.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,91 +0,0 @@ -package edu.unc.genomics.converters; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.ucsc.genome.TrackHeader; -import edu.unc.genomics.Assembly; -import edu.unc.genomics.Interval; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.ValuedInterval; -import edu.unc.genomics.io.IntervalFile; - -public class IntervalToWig extends CommandLineTool { - - private static final Logger log = Logger.getLogger(IntervalToWig.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (Bed/BedGraph)", required = true) - public IntervalFile intervalFile; - @Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true) - public Assembly assembly; - @Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true) - public Path outputFile; - - @Override - public void run() throws IOException { - log.info(intervalFile.count() + " entries in input"); - - log.debug("Initializing output file"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - // Write the Wiggle track header to the output file - TrackHeader header = new TrackHeader("wiggle_0"); - header.setName("Converted " + intervalFile.getPath().getFileName()); - header.setDescription("Converted " + intervalFile.getPath().getFileName()); - writer.write(header.toString()); - writer.newLine(); - - // Process each chromosome in the assembly - for (String chr : assembly) { - log.debug("Processing chromosome " + chr); - // Write the contig header to the output file - writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1"); - writer.newLine(); - - int start = 1; - while (start < assembly.getChrLength(chr)) { - int stop = start + DEFAULT_CHUNK_SIZE - 1; - int length = stop - start + 1; - int[] count = new int[length]; - float[] sum = new float[length]; - - Iterator it = intervalFile.query(chr, start, stop); - while (it.hasNext()) { - ValuedInterval entry = (ValuedInterval) it.next(); - if (entry.getValue() != null) { - for (int i = entry.getStart(); i <= entry.getStop(); i++) { - sum[i-start] += entry.getValue().floatValue(); - count[i-start]++; - } - } - } - - // Write the average at each base pair to the output file - for (int i = 0; i < sum.length; i++) { - if (count[i] == 0) { - writer.write(String.valueOf(Float.NaN)); - } else { - writer.write(String.valueOf(sum[i]/count[i])); - } - writer.newLine(); - } - - // Process the next chunk - start = stop + 1; - } - } - } - } - - public static void main(String[] args) { - new IntervalToWig().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/converters/RomanNumeralize.java --- a/src/edu/unc/genomics/converters/RomanNumeralize.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -package edu.unc.genomics.converters; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.ReadablePathValidator; -import edu.unc.utils.RomanNumeral; - -public class RomanNumeralize extends CommandLineTool { - - private static final Logger log = Logger.getLogger(RomanNumeralize.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true, validateWith = ReadablePathValidator.class) - public Path inputFile; - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - - /** - * Pattern for finding "chr12" tokens (will find "chr1" through "chr99") - */ - Pattern p = Pattern.compile("/chr[\\d]{1,2}/i"); - - @Override - public void run() throws IOException { - try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset()); - BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - log.debug("Copying input to output and replacing with Roman Numerals"); - String line; - while ((line = reader.readLine()) != null) { - Matcher m = p.matcher(line); - StringBuffer converted = new StringBuffer(line.length()); - while (m.find()) { - String chrNum = line.substring(m.start()+3, m.end()); - int arabic = Integer.parseInt(chrNum); - String roman = RomanNumeral.int2roman(arabic); - m.appendReplacement(converted, "chr"+roman); - } - m.appendTail(converted); - - writer.write(converted.toString()); - writer.newLine(); - } - } - } - - public static void main(String[] args) { - new RomanNumeralize().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ngs/Autocorrelation.java --- a/src/edu/unc/genomics/ngs/Autocorrelation.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -package edu.unc.genomics.ngs; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; - -import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.emory.mathcs.jtransforms.fft.FloatFFT_1D; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.PositiveIntegerValidator; -import edu.unc.genomics.io.IntervalFile; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Autocorrelation extends CommandLineTool { - - private static final Logger log = Logger.getLogger(Autocorrelation.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) - public WigFile wig; - @Parameter(names = {"-l", "--loci"}, description = "Genomic loci (Bed format)", required = true) - public IntervalFile loci; - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - @Parameter(names = {"-m", "--max"}, description = "Autocorrelation limit (bp)", validateWith = PositiveIntegerValidator.class) - public int limit = 200; - - private void abs2(float[] data) { - for (int i = 0; i < data.length; i+=2) { - data[i] = data[i]*data[i] + data[i+1]*data[i+1]; - data[i+1] = 0; - } - } - - @Override - public void run() throws IOException { - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - log.debug("Computing autocorrelation for each window"); - int skipped = 0; - for (Interval interval : loci) { - if (interval.length() < limit) { - log.debug("Skipping interval: " + interval.toString()); - skipped++; - continue; - } - - Iterator wigIter; - try { - wigIter = wig.query(interval); - } catch (IOException | WigFileException e) { - log.debug("Skipping interval: " + interval.toString()); - skipped++; - continue; - } - - float[] data = WigFile.flattenData(wigIter, interval.getStart(), interval.getStop()); - - // Compute the autocorrelation with the Wiener-Khinchin theorem - FloatFFT_1D fft = new FloatFFT_1D(data.length); - fft.realForward(data); - abs2(data); - fft.realInverse(data, true); - - writer.write(StringUtils.join(data, "\t")); - writer.newLine(); - } - - log.info("Skipped " + skipped + " intervals"); - } - } - - public static void main(String[] args) { - new Autocorrelation().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ngs/BaseAlignCounts.java --- a/src/edu/unc/genomics/ngs/BaseAlignCounts.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -package edu.unc.genomics.ngs; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.ucsc.genome.TrackHeader; -import edu.unc.genomics.Assembly; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.io.IntervalFile; - -public class BaseAlignCounts extends CommandLineTool { - - private static final Logger log = Logger.getLogger(BaseAlignCounts.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true) - public IntervalFile intervalFile; - @Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true) - public Assembly assembly; - @Parameter(names = {"-x", "--extend"}, description = "Extend reads from 5' end (default = read length)") - public Integer extend; - @Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true) - public Path outputFile; - - @Override - public void run() throws IOException { - log.debug("Initializing output file"); - int mapped = 0; - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - // Write the Wiggle track header to the output file - TrackHeader header = new TrackHeader("wiggle_0"); - header.setName("Converted " + intervalFile.getPath().getFileName()); - header.setDescription("Converted " + intervalFile.getPath().getFileName()); - writer.write(header.toString()); - writer.newLine(); - - // Process each chromosome in the assembly - for (String chr : assembly) { - log.debug("Processing chromosome " + chr); - // Write the contig header to the output file - writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1"); - writer.newLine(); - - int start = 1; - while (start < assembly.getChrLength(chr)) { - int stop = start + DEFAULT_CHUNK_SIZE - 1; - int length = stop - start + 1; - int[] count = new int[length]; - - Iterator it = intervalFile.query(chr, start, stop); - while (it.hasNext()) { - Interval entry = it.next(); - int entryStop = entry.getStop(); - if (extend != null) { - if (entry.isWatson()) { - entryStop = entry.getStart() + extend; - } else { - entryStop = entry.getStart() - extend; - } - } - - for (int i = entry.getStart(); i <= entryStop; i++) { - count[i-start]++; - } - mapped++; - } - - // Write the count at each base pair to the output file - for (int i = 0; i < count.length; i++) { - writer.write(count[i]); - writer.newLine(); - } - - // Process the next chunk - start = stop + 1; - } - } - } - - log.info("Mapped "+mapped+" reads"); - } - - public static void main(String[] args) { - new BaseAlignCounts().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java --- a/src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ -package edu.unc.genomics.ngs; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.io.IntervalFile; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class FindAbsoluteMaxima extends CommandLineTool { - - private static final Logger log = Logger.getLogger(FindAbsoluteMaxima.class); - - @Parameter(description = "Input files", required = true) - public List inputFiles = new ArrayList(); - @Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true) - public IntervalFile lociFile; - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - - private List wigs = new ArrayList<>(); - - @Override - public void run() throws IOException { - log.debug("Initializing input Wig file(s)"); - for (String inputFile : inputFiles) { - try { - WigFile wig = WigFile.autodetect(Paths.get(inputFile)); - wigs.add(wig); - } catch (WigFileException e) { - log.error("Error initializing Wig input file: " + inputFile); - e.printStackTrace(); - throw new RuntimeException("Error initializing Wig input file: " + inputFile); - } - } - - log.debug("Initializing output file"); - int count = 0, skipped = 0; - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - writer.write("#Chr\tStart\tStop\tID\tValue\tStrand"); - for (String inputFile : inputFiles) { - Path p = Paths.get(inputFile); - writer.write("\t" + p.getFileName().toString()); - } - writer.newLine(); - - log.debug("Iterating over all intervals and finding maxima"); - for (Interval interval : lociFile) { - writer.write(interval.toBed()); - for (WigFile wig : wigs) { - float maxValue = -Float.MAX_VALUE; - int maxima = -1; - try { - Iterator results = wig.query(interval); - while (results.hasNext()) { - WigItem item = results.next(); - if (item.getWigValue() > maxValue) { - maxValue = item.getWigValue(); - maxima = (item.getStartBase() + item.getEndBase()) / 2; - } - } - writer.write("\t" + maxima); - } catch (WigFileException e) { - writer.write("\t" + Float.NaN); - skipped++; - } - } - writer.newLine(); - count++; - } - } - - lociFile.close(); - for (WigFile wig : wigs) { - wig.close(); - } - log.info(count + " intervals processed"); - log.info(skipped + " interval skipped"); - } - - public static void main(String[] args) { - new FindAbsoluteMaxima().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ngs/IntervalLengthDistribution.java --- a/src/edu/unc/genomics/ngs/IntervalLengthDistribution.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -package edu.unc.genomics.ngs; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.commons.math.stat.Frequency; -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.io.IntervalFile; - -public class IntervalLengthDistribution extends CommandLineTool { - - private static final Logger log = Logger.getLogger(IntervalLengthDistribution.class); - - @Parameter(names = {"-i", "--input"}, description = "Interval file", required = true) - public IntervalFile inputFile; - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - - - @Override - public void run() throws IOException { - log.debug("Generating histogram of interval lengths"); - Frequency freq = new Frequency(); - int min = Integer.MAX_VALUE; - int max = -1; - for (Interval i : inputFile) { - int L = i.length(); - freq.addValue(L); - - if (L < min) { - min = L; - } - if (L > max) { - max = L; - } - } - - log.debug("Writing histogram output"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - for (int i = min; i <= max; i++) { - writer.write(i+"\t"+freq.getCount(i)); - writer.newLine(); - } - } - } - - public static void main(String[] args) { - new IntervalLengthDistribution().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ngs/IntervalStats.java --- a/src/edu/unc/genomics/ngs/IntervalStats.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ -package edu.unc.genomics.ngs; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.math.stat.descriptive.SummaryStatistics; -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.io.IntervalFile; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class IntervalStats extends CommandLineTool { - - private static final Logger log = Logger.getLogger(IntervalStats.class); - - @Parameter(description = "Input files", required = true) - public List inputFiles = new ArrayList(); - @Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true) - public IntervalFile lociFile; - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - - private List wigs = new ArrayList<>(); - - @Override - public void run() throws IOException { - log.debug("Initializing input Wig file(s)"); - for (String inputFile : inputFiles) { - try { - WigFile wig = WigFile.autodetect(Paths.get(inputFile)); - wigs.add(wig); - } catch (WigFileException e) { - log.error("Error initializing Wig input file: " + inputFile); - e.printStackTrace(); - throw new RuntimeException("Error initializing Wig input file: " + inputFile); - } - } - - log.debug("Initializing output file"); - int count = 0, skipped = 0; - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - writer.write("#Chr\tStart\tStop\tID\tValue\tStrand"); - for (String inputFile : inputFiles) { - Path p = Paths.get(inputFile); - writer.write("\t" + p.getFileName().toString()); - } - writer.newLine(); - - log.debug("Iterating over all intervals and computing statistics"); - SummaryStatistics stats = new SummaryStatistics(); - for (Interval interval : lociFile) { - List means = new ArrayList<>(wigs.size()); - for (WigFile wig : wigs) { - stats.clear(); - try { - Iterator result = wig.query(interval); - while(result.hasNext()) { - WigItem item = result.next(); - for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { - stats.addValue(item.getWigValue()); - } - } - means.add(stats.getMean()); - } catch (WigFileException e) { - means.add(Double.NaN); - skipped++; - } - } - - writer.write(interval.toBed() + "\t" + StringUtils.join(means, "\t")); - writer.newLine(); - count++; - } - } - - lociFile.close(); - for (WigFile wig : wigs) { - wig.close(); - } - log.info(count + " intervals processed"); - log.info(skipped + " interval skipped"); - } - - public static void main(String[] args) { - new IntervalStats().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ngs/PowerSpectrum.java --- a/src/edu/unc/genomics/ngs/PowerSpectrum.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ -package edu.unc.genomics.ngs; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.emory.mathcs.jtransforms.fft.FloatFFT_1D; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.io.IntervalFile; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class PowerSpectrum extends CommandLineTool { - - private static final Logger log = Logger.getLogger(PowerSpectrum.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (Wig)", required = true) - public WigFile inputFile; - @Parameter(names = {"-l", "--loci"}, description = "Genomic loci (Bed format)", required = true) - public IntervalFile loci; - @Parameter(names = {"-o", "--output"}, description = "Output file (tabular)", required = true) - public Path outputFile; - - /** - * Computes the power spectrum from FFT data - * taking into accound even/odd length arrays - * refer to JTransforms documentation for layout of the FFT data - * @param f - * @return - */ - private float[] abs2(float[] f) { - int n = f.length; - float[] ps = new float[n/2+1]; - // DC component - ps[0] = (f[0]*f[0]) / (n*n); - - // Even - if (n % 2 == 0) { - for (int k = 1; k < n/2; k++) { - ps[k] = f[2*k]*f[2*k] + f[2*k+1]*f[2*k+1]; - } - ps[n/2] = f[1]*f[1]; - // Odd - } else { - for (int k = 1; k < (n-1)/2; k++) { - ps[k] = f[2*k]*f[2*k] + f[2*k+1]*f[2*k+1]; - } - - ps[(n-1)/2] = f[n-1]*f[n-1] + f[1]*f[1]; - } - - return ps; - } - - public void run() throws IOException { - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - log.debug("Computing power spectrum for each window"); - int skipped = 0; - for (Interval interval : loci) { - Iterator wigIter; - try { - wigIter = inputFile.query(interval); - } catch (IOException | WigFileException e) { - log.debug("Skipping interval: " + interval.toString()); - skipped++; - continue; - } - - float[] data = WigFile.flattenData(wigIter, interval.getStart(), interval.getStop()); - // Compute the power spectrum - FloatFFT_1D fft = new FloatFFT_1D(data.length); - fft.realForward(data); - float[] ps = abs2(data); - // and normalize the power spectrum - float sum = 0; - for (int i = 1; i < ps.length; i++) { - sum += ps[i]; - } - for (int i = 1; i < ps.length; i++) { - ps[i] /= sum; - } - - writer.write(interval.toBed()); - for (int i = 1; i < Math.min(ps.length, 40); i++) { - writer.write("\t"+ps[i]); - } - writer.newLine(); - } - - log.info("Skipped " + skipped + " intervals"); - } - } - - public static void main(String[] args) { - new PowerSpectrum().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/ngs/RollingReadLength.java --- a/src/edu/unc/genomics/ngs/RollingReadLength.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,89 +0,0 @@ -package edu.unc.genomics.ngs; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.ucsc.genome.TrackHeader; -import edu.unc.genomics.Assembly; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.io.IntervalFile; - -public class RollingReadLength extends CommandLineTool { - - private static final Logger log = Logger.getLogger(RollingReadLength.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true) - public IntervalFile intervalFile; - @Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true) - public Assembly assembly; - @Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true) - public Path outputFile; - - @Override - public void run() throws IOException { - log.debug("Initializing output file"); - int mapped = 0; - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - // Write the Wiggle track header to the output file - TrackHeader header = new TrackHeader("wiggle_0"); - header.setName("Converted " + intervalFile.getPath().getFileName()); - header.setDescription("Converted " + intervalFile.getPath().getFileName()); - writer.write(header.toString()); - writer.newLine(); - - // Process each chromosome in the assembly - for (String chr : assembly) { - log.debug("Processing chromosome " + chr); - // Write the contig header to the output file - writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1"); - writer.newLine(); - - int start = 1; - while (start < assembly.getChrLength(chr)) { - int stop = start + DEFAULT_CHUNK_SIZE - 1; - int length = stop - start + 1; - int[] sum = new int[length]; - int[] count = new int[length]; - - Iterator it = intervalFile.query(chr, start, stop); - while (it.hasNext()) { - Interval entry = it.next(); - for (int i = entry.getStart(); i <= entry.getStop(); i++) { - sum[i-start] += entry.length(); - count[i-start]++; - } - mapped++; - } - - // Write the average at each base pair to the output file - for (int i = 0; i < sum.length; i++) { - if (count[i] == 0) { - writer.write(String.valueOf(Float.NaN)); - } else { - writer.write(String.valueOf(sum[i]/count[i])); - } - writer.newLine(); - } - - // Process the next chunk - start = stop + 1; - } - } - } - - log.info("Mapped "+mapped+" reads"); - } - - public static void main(String[] args) { - new RollingReadLength().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/nucleosomes/FindBoundaryNucleosomes.java --- a/src/edu/unc/genomics/nucleosomes/FindBoundaryNucleosomes.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,98 +0,0 @@ -package edu.unc.genomics.nucleosomes; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.ReadablePathValidator; -import edu.unc.genomics.io.IntervalFile; - -public class FindBoundaryNucleosomes extends CommandLineTool { - - private static final Logger log = Logger.getLogger(FindBoundaryNucleosomes.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (nucleosome calls)", required = true, validateWith = ReadablePathValidator.class) - public Path inputFile; - @Parameter(names = {"-l", "--loci"}, description = "Boundary loci (Bed format)", required = true) - public IntervalFile lociFile; - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - - private Map> nucs = new HashMap<>(); - - private List getIntervalNucleosomes(Interval i) { - List intervalNucs = new ArrayList<>(); - for (NucleosomeCall call : nucs.get(i.getChr())) { - if (call.getDyad() >= i.low() && call.getDyad() <= i.high()) { - intervalNucs.add(call); - } - } - - return intervalNucs; - } - - @Override - public void run() throws IOException { - log.debug("Initializing input file"); - NucleosomeCallsFile nucsFile = new NucleosomeCallsFile(inputFile); - log.debug("Loading all nucleosomes"); - for (NucleosomeCall nuc : nucsFile) { - if (nuc == null) continue; - if (!nucs.containsKey(nuc.getChr())) { - nucs.put(nuc.getChr(), new ArrayList()); - } - nucs.get(nuc.getChr()).add(nuc); - } - nucsFile.close(); - - log.debug("Initializing output file"); - int skipped = 0; - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - log.debug("Finding boundary nucleosomes for each interval"); - NucleosomeCall.DyadComparator comparator = new NucleosomeCall.DyadComparator(); - for (Interval interval : lociFile) { - writer.write(interval.toBed()); - - // Get all of the nucleosomes within this interval - List intervalNucs = getIntervalNucleosomes(interval); - - if (intervalNucs.size() > 0) { - // Sort the list by nucleosome position - Collections.sort(intervalNucs, comparator); - if (interval.isCrick()) { - Collections.reverse(intervalNucs); - } - - int fivePrime = intervalNucs.get(0).getDyad(); - int threePrime = intervalNucs.get(intervalNucs.size()-1).getDyad(); - writer.write("\t"+fivePrime+"\t"+threePrime); - } else { - skipped++; - writer.write("\tNA\tNA"); - } - - writer.newLine(); - } - } - - lociFile.close(); - log.info("Skipped "+skipped+" intervals with 0 nucleosomes"); - } - - public static void main(String[] args) { - new FindBoundaryNucleosomes().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/nucleosomes/GreedyCaller.java --- a/src/edu/unc/genomics/nucleosomes/GreedyCaller.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,120 +0,0 @@ -package edu.unc.genomics.nucleosomes; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.CommandLineToolException; -import edu.unc.genomics.ReadablePathValidator; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; -import edu.unc.utils.SortUtils; - -public class GreedyCaller extends CommandLineTool { - - private static final Logger log = Logger.getLogger(GreedyCaller.class); - - private static final int CHUNK_SIZE = 500_000; - - @Parameter(names = {"-d", "--dyads"}, description = "Dyad counts file", required = true, validateWith = ReadablePathValidator.class) - public WigFile dyadsFile; - @Parameter(names = {"-s", "--smoothed"}, description = "Smoothed dyad counts file", required = true, validateWith = ReadablePathValidator.class) - public WigFile smoothedDyadsFile; - @Parameter(names = {"-n", "--size"}, description = "Nucleosome size (bp)") - public int nucleosomeSize = 147; - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - - public void run() throws IOException { - int halfNuc = nucleosomeSize / 2; - - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - for (String chr : smoothedDyadsFile.chromosomes()) { - log.debug("Processing chromosome "+chr); - int chunkStart = smoothedDyadsFile.getChrStart(chr); - int chrStop = smoothedDyadsFile.getChrStop(chr); - while (chunkStart < chrStop) { - int chunkStop = chunkStart + CHUNK_SIZE; - int paddedStart = chunkStart - nucleosomeSize; - int paddedStop = chunkStop + nucleosomeSize; - log.debug("Processing chunk "+chunkStart+"-"+chunkStop); - - log.debug("Loading data and sorting"); - Iterator dyadsIter; - Iterator smoothedIter; - try { - dyadsIter = dyadsFile.query(chr, paddedStart, paddedStop); - smoothedIter = smoothedDyadsFile.query(chr, paddedStart, paddedStop); - } catch (IOException | WigFileException e) { - e.printStackTrace(); - throw new CommandLineToolException("Error loading data from Wig file"); - } - - float[] dyads = WigFile.flattenData(dyadsIter, paddedStart, paddedStop); - float[] smoothed = WigFile.flattenData(smoothedIter, paddedStart, paddedStop); - int[] sortedIndices = SortUtils.indexSort(smoothed); - - // Proceed through the data in descending order - log.debug("Calling nucleosomes"); - for (int j = sortedIndices.length; j >= 0; j++) { - int i = sortedIndices[j]; - int dyad = paddedStart + i; - - if (smoothed[i] > 0) { - int nucStart = Math.max(1, dyad-halfNuc); - int nucStop = Math.min(dyad+halfNuc, chrStop); - NucleosomeCall call = new NucleosomeCall(chr, nucStart, nucStop); - call.setDyad(dyad); - - double occupancy = 0; - double weightedSum = 0; - double smoothedSum = 0; - double sumOfSquares = 0; - for (int bp = nucStart; bp <= nucStop; bp++) { - occupancy += dyads[bp-paddedStart]; - weightedSum += bp * dyads[bp-paddedStart]; - smoothedSum += smoothed[bp-paddedStart]; - sumOfSquares += bp * bp * dyads[bp-paddedStart]; - } - call.setOccupancy(occupancy); - - if (occupancy > 0) { - call.setDyadMean(Math.round(weightedSum/occupancy)); - call.setConditionalPosition(smoothed[i] / smoothedSum); - double variance = (sumOfSquares - weightedSum*call.getDyadMean()) / occupancy; - call.setDyadStdev(Math.sqrt(variance)); - - // Only write nucleosomes within the current chunk to disk - if (chunkStart <= dyad && dyad <= chunkStop) { - writer.write(call.toString()); - writer.newLine(); - } - - // Don't allow nucleosome calls overlapping this nucleosome - int low = Math.max(i-nucleosomeSize, 0); - int high = Math.min(i-nucleosomeSize, paddedStop-1); - for (int k = low; k <= high; k++) { - smoothed[k] = 0; - } - } - } - } - - chunkStart = chunkStop + 1; - } - } - } - } - - public static void main(String[] args) { - new GreedyCaller().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/nucleosomes/MapDyads.java --- a/src/edu/unc/genomics/nucleosomes/MapDyads.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,88 +0,0 @@ -package edu.unc.genomics.nucleosomes; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.ucsc.genome.TrackHeader; -import edu.unc.genomics.Assembly; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.PositiveIntegerValidator; -import edu.unc.genomics.io.IntervalFile; - -public class MapDyads extends CommandLineTool { - - private static final Logger log = Logger.getLogger(MapDyads.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true) - public IntervalFile inputFile; - @Parameter(names = {"-s", "--size"}, description = "Mononucleosome length (default: read length)", validateWith = PositiveIntegerValidator.class) - public Integer nucleosomeSize; - @Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true) - public Assembly assembly; - @Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true) - public Path outputFile; - - @Override - public void run() throws IOException { - log.debug("Initializing output file"); - int mapped = 0; - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - // Write the Wiggle track header to the output file - TrackHeader header = new TrackHeader("wiggle_0"); - header.setName("Converted " + inputFile.getPath().getFileName()); - header.setDescription("Converted " + inputFile.getPath().getFileName()); - writer.write(header.toString()); - writer.newLine(); - - // Process each chromosome in the assembly - for (String chr : assembly) { - log.debug("Processing chromosome " + chr); - // Write the contig header to the output file - writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1"); - writer.newLine(); - - int start = 1; - while (start < assembly.getChrLength(chr)) { - int stop = start + DEFAULT_CHUNK_SIZE - 1; - int length = stop - start + 1; - int[] count = new int[length]; - - Iterator it = inputFile.query(chr, start, stop); - while (it.hasNext()) { - Interval entry = it.next(); - if (nucleosomeSize == null) { - count[entry.center()-start]++; - } else { - count[entry.getStart()+nucleosomeSize-start]++; - } - mapped++; - } - - // Write the average at each base pair to the output file - for (int i = 0; i < count.length; i++) { - writer.write(count[i]); - writer.newLine(); - } - - // Process the next chunk - start = stop + 1; - } - } - } - - log.info("Mapped "+mapped+" reads"); - } - - public static void main(String[] args) { - new MapDyads().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/nucleosomes/NRLCalculator.java --- a/src/edu/unc/genomics/nucleosomes/NRLCalculator.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -package edu.unc.genomics.nucleosomes; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.Interval; -import edu.unc.genomics.ReadablePathValidator; -import edu.unc.genomics.io.IntervalFile; - -public class NRLCalculator extends CommandLineTool { - - private static final Logger log = Logger.getLogger(NRLCalculator.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (nucleosome calls)", required = true, validateWith = ReadablePathValidator.class) - public Path inputFile; - @Parameter(names = {"-l", "--loci"}, description = "Genomic loci (Bed format)", required = true) - public IntervalFile lociFile; - @Parameter(names = {"-o", "--output"}, description = "Output file (NRL for each gene)", required = true) - public Path outputFile; - - private Map> nucs = new HashMap<>(); - - private List getIntervalNucleosomes(Interval i) { - List intervalNucs = new ArrayList<>(); - for (NucleosomeCall call : nucs.get(i.getChr())) { - if (call.getDyad() >= i.low() && call.getDyad() <= i.high()) { - intervalNucs.add(call); - } - } - - return intervalNucs; - } - - @Override - public void run() throws IOException { - log.debug("Initializing input file"); - NucleosomeCallsFile nucsFile = new NucleosomeCallsFile(inputFile); - log.debug("Loading all nucleosomes"); - for (NucleosomeCall nuc : nucsFile) { - if (nuc == null) continue; - if (!nucs.containsKey(nuc.getChr())) { - nucs.put(nuc.getChr(), new ArrayList()); - } - nucs.get(nuc.getChr()).add(nuc); - } - nucsFile.close(); - - log.debug("Initializing output file"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - log.debug("Calculating nucleosome spacing for each interval"); - NucleosomeCall.DyadComparator comparator = new NucleosomeCall.DyadComparator(); - for (Interval interval : lociFile) { - writer.write(interval.toBed()); - - // Get all of the nucleosomes within this interval - List intervalNucs = getIntervalNucleosomes(interval); - - if (intervalNucs.size() > 1) { - // Sort the list by nucleosome position - Collections.sort(intervalNucs, comparator); - if (interval.isCrick()) { - Collections.reverse(intervalNucs); - } - - for (int i = 1; i < Math.min(intervalNucs.size(), 10); i++) { - writer.write("\t" + Math.abs(intervalNucs.get(i).getDyad()-intervalNucs.get(i-1).getDyad())); - } - } - - writer.newLine(); - } - } - - lociFile.close(); - } - - public static void main(String[] args) throws IOException { - new NRLCalculator().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/nucleosomes/NucleosomeCall.java --- a/src/edu/unc/genomics/nucleosomes/NucleosomeCall.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,174 +0,0 @@ -package edu.unc.genomics.nucleosomes; - -import java.util.Comparator; - -import edu.unc.genomics.ValuedInterval; -import edu.unc.genomics.io.IntervalFileFormatException; - -/** - * @author timpalpant - * - */ -public class NucleosomeCall extends ValuedInterval implements Comparable { - - private static final long serialVersionUID = 6522702303121259979L; - - private int dyad; - private double dyadStdev; - private double dyadMean; - private double conditionalPosition; - private int length; - private double lengthStdev; - - /** - * @param chr - * @param start - * @param stop - */ - public NucleosomeCall(String chr, int start, int stop) { - super(chr, start, stop); - } - - public static NucleosomeCall parse(String line) { - if (line.startsWith("#")) return null; - - String[] entry = line.split("\t"); - if (entry.length < 10) { - throw new IntervalFileFormatException("Invalid nucleosome call has < 10 columns"); - } - - String chr = entry[0]; - int start = Integer.parseInt(entry[1]); - int stop = Integer.parseInt(entry[2]); - - NucleosomeCall call = new NucleosomeCall(chr, start, stop); - call.setLength(Integer.parseInt(entry[3])); - call.setLengthStdev(Double.parseDouble(entry[4])); - call.setDyad(Integer.parseInt(entry[5])); - call.setDyadStdev(Double.parseDouble(entry[6])); - call.setConditionalPosition(Double.parseDouble(entry[7])); - call.setDyadMean(Double.parseDouble(entry[8])); - call.setValue(Double.parseDouble(entry[9])); - - return call; - } - - @Override - public String toString() { - return chr+"\t"+start+"\t"+stop+"\t"+length()+"\t"+lengthStdev+"\t"+dyad+"\t"+dyadStdev+"\t"+conditionalPosition+"\t"+dyadMean+"\t"+occupancy(); - } - - /** - * @return the dyad - */ - public int getDyad() { - return dyad; - } - - /** - * @param dyad the dyad to set - */ - public void setDyad(int dyad) { - this.dyad = dyad; - } - - /** - * @return the dyadStdev - */ - public double getDyadStdev() { - return dyadStdev; - } - - /** - * @param dyadStdev the dyadStdev to set - */ - public void setDyadStdev(double dyadStdev) { - this.dyadStdev = dyadStdev; - } - - /** - * @return the dyadMean - */ - public double getDyadMean() { - return dyadMean; - } - - /** - * @param dyadMean the dyadMean to set - */ - public void setDyadMean(double dyadMean) { - this.dyadMean = dyadMean; - } - - /** - * @return the conditionalPosition - */ - public double getConditionalPosition() { - return conditionalPosition; - } - - /** - * @param conditionalPosition the conditionalPosition to set - */ - public void setConditionalPosition(double conditionalPosition) { - this.conditionalPosition = conditionalPosition; - } - - /** - * @return the length - */ - public int getLength() { - return length; - } - - /** - * @param length the length to set - */ - public void setLength(int length) { - this.length = length; - } - - /** - * @return the lengthStdev - */ - public double getLengthStdev() { - return lengthStdev; - } - - /** - * @param lengthStdev the lengthStdev to set - */ - public void setLengthStdev(double lengthStdev) { - this.lengthStdev = lengthStdev; - } - - public double occupancy() { - return value; - } - - public void setOccupancy(double value) { - this.value = value; - } - - @Override - public int compareTo(NucleosomeCall o) { - DyadComparator comparator = new DyadComparator(); - return comparator.compare(this, o); - } - - public static class DyadComparator implements Comparator { - - @Override - public int compare(NucleosomeCall o1, NucleosomeCall o2) { - if (o1.getDyad() == o2.getDyad()) { - return 0; - } else if (o1.getDyad() < o2.getDyad()) { - return -1; - } else { - return 1; - } - } - - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/nucleosomes/NucleosomeCallsFile.java --- a/src/edu/unc/genomics/nucleosomes/NucleosomeCallsFile.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -/** - * - */ -package edu.unc.genomics.nucleosomes; - -import java.io.IOException; -import java.nio.file.Path; - -import edu.unc.genomics.IntervalFactory; -import edu.unc.genomics.io.TextIntervalFile; - -/** - * @author timpalpant - * - */ -public class NucleosomeCallsFile extends TextIntervalFile { - - public NucleosomeCallsFile(Path p) throws IOException { - super(p, new NucleosomeCallFactory()); - } - - public static class NucleosomeCallFactory implements IntervalFactory { - - @Override - public NucleosomeCall parse(String line) { - return NucleosomeCall.parse(line); - } - - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/nucleosomes/Phasogram.java --- a/src/edu/unc/genomics/nucleosomes/Phasogram.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -package edu.unc.genomics.nucleosomes; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.CommandLineToolException; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Phasogram extends CommandLineTool { - - private static final Logger log = Logger.getLogger(Phasogram.class); - - @Parameter(names = {"-i", "--input"}, description = "Input wig file (read counts)", required = true) - public WigFile inputFile; - @Parameter(names = {"-m", "--max"}, description = "Maximum phase shift", required = true) - public int maxPhase; - @Parameter(names = {"-o", "--output"}, description = "Output file (histogram)", required = true) - public Path outputFile; - - public void run() throws IOException { - long[] phaseCounts = new long[maxPhase+1]; - - // Process each chromosome in the assembly - for (String chr : inputFile.chromosomes()) { - log.debug("Processing chromosome " + chr); - - int start = inputFile.getChrStart(chr); - while (start < inputFile.getChrStop(chr)) { - int stop = start + DEFAULT_CHUNK_SIZE - 1; - - try { - float[] data = WigFile.flattenData(inputFile.query(chr, start, stop), start, stop); - for (int i = 0; i < data.length-maxPhase; i++) { - for (int j = 0; j <= maxPhase; j++) { - phaseCounts[j] += data[i]; - } - } - - } catch (WigFileException e) { - log.fatal("Error querying data from Wig file!"); - e.printStackTrace(); - throw new CommandLineToolException("Error querying data from Wig file!"); - } - - // Process the next chunk - start = stop - maxPhase + 1; - } - } - - log.debug("Writing output to disk"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - for (int i = 0; i < phaseCounts.length; i++) { - writer.write(i+"\t"+phaseCounts[i]); - writer.newLine(); - } - } - } - - public static void main(String[] args) { - new Phasogram().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/visualization/IntervalAverager.java --- a/src/edu/unc/genomics/visualization/IntervalAverager.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,118 +0,0 @@ -package edu.unc.genomics.visualization; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Iterator; -import java.util.List; - -import org.apache.commons.lang3.ArrayUtils; -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.BedEntry; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.ReadablePathValidator; -import edu.unc.genomics.io.BedFile; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class IntervalAverager extends CommandLineTool { - - private static final Logger log = Logger.getLogger(IntervalAverager.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (Wig)", required = true) - public WigFile inputFile; - @Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class) - public Path lociFile; - @Parameter(names = {"-o", "--output"}, description = "Output file (matrix2png format)", required = true) - public Path outputFile; - - private List loci; - - @Override - public void run() throws IOException { - log.debug("Loading alignment intervals"); - try (BedFile bed = new BedFile(lociFile)) { - loci = bed.loadAll(); - } - - // Compute the matrix dimensions - int leftMax = Integer.MIN_VALUE; - int rightMax = Integer.MIN_VALUE; - for (BedEntry entry : loci) { - int left = Math.abs(entry.getValue().intValue()-entry.getStart()); - int right = Math.abs(entry.getValue().intValue()-entry.getStop()); - if (left > leftMax) { - leftMax = left; - } - if (right > rightMax) { - rightMax = right; - } - } - - int m = loci.size(); - int n = leftMax + rightMax + 1; - int alignmentPoint = leftMax; - log.info("Intervals aligned into: " + m+"x"+n + " matrix"); - log.info("Alignment point: " + alignmentPoint); - - float[] sum = new float[n]; - int[] counts = new int[n]; - int count = 0, skipped = 0; - log.debug("Iterating over all intervals"); - for (BedEntry entry : loci) { - Iterator result = null; - try { - result = inputFile.query(entry); - } catch (WigFileException e) { - skipped++; - continue; - } - - float[] data = WigFile.flattenData(result, entry.getStart(), entry.getStop()); - // Reverse if on the Crick strand - if (entry.isCrick()) { - ArrayUtils.reverse(data); - } - - // Locus alignment point (entry value) should be positioned over the global alignment point - int n1 = alignmentPoint - Math.abs(entry.getValue().intValue()-entry.getStart()); - int n2 = alignmentPoint + Math.abs(entry.getValue().intValue()-entry.getStop()); - for (int bp = n1; bp <= n2; bp++) { - sum[bp] += data[bp-n1]; - counts[bp]++; - } - } - - inputFile.close(); - log.info(count + " intervals processed"); - log.info(skipped + " intervals skipped"); - - log.debug("Computing average"); - float[] avg = new float[n]; - for (int i = 0; i < n; i++) { - if (counts[i] == 0) { - avg[i] = Float.NaN; - } else { - avg[i] = sum[i] / counts[i]; - } - } - - log.debug("Writing average to output"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - for (int i = 0; i < n; i++) { - writer.write(i-alignmentPoint + "\t" + avg[i]); - writer.newLine(); - } - } - } - - public static void main(String[] args) { - new IntervalAverager().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/visualization/KMeans.java --- a/src/edu/unc/genomics/visualization/KMeans.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,120 +0,0 @@ -package edu.unc.genomics.visualization; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Random; - -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.math.stat.clustering.Cluster; -import org.apache.commons.math.stat.clustering.KMeansPlusPlusClusterer; -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.ReadablePathValidator; -import edu.unc.genomics.io.IntervalFileSnifferException; -import edu.unc.genomics.io.WigFileException; - -public class KMeans extends CommandLineTool { - - private static final Logger log = Logger.getLogger(KMeans.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (matrix2png format)", required = true, validateWith = ReadablePathValidator.class) - public Path inputFile; - @Parameter(names = {"-k", "--clusters"}, description = "Number of clusters") - public int k = 10; - @Parameter(names = {"-1", "--min"}, description = "Minimum column to use for clustering") - public int minCol = 1; - @Parameter(names = {"-2", "--max"}, description = "Maximum column to use for clustering") - public Integer maxCol; - @Parameter(names = {"-o", "--output"}, description = "Output file (clustered matrix2png format)", required = true) - public Path outputFile; - - private Map rows = new HashMap(); - private List data = new ArrayList(); - - @Override - public void run() throws IOException { - log.debug("Loading data from the input matrix"); - String headerLine = ""; - try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset())) { - // Header line - int lineNum = 1; - headerLine = reader.readLine(); - int numColsInMatrix = StringUtils.countMatches(headerLine, "\t"); - - // Validate the range info - if (maxCol != null) { - if (maxCol > numColsInMatrix) { - throw new RuntimeException("Invalid range of data specified for clustering ("+maxCol+" > "+numColsInMatrix+")"); - } - } else { - maxCol = numColsInMatrix; - } - - // Loop over the rows and load the data - String line; - while ((line = reader.readLine()) != null) { - lineNum++; - if (StringUtils.countMatches(line, "\t") != numColsInMatrix) { - throw new RuntimeException("Irregular input matrix does not have same number of columns on line " + lineNum); - } - - int delim = line.indexOf('\t'); - String id = line.substring(0, delim); - String[] row = line.substring(delim+1).split("\t"); - String[] subset = Arrays.copyOfRange(row, minCol, maxCol); - float[] rowData = new float[subset.length]; - for (int i = 0; i < subset.length; i++) { - try { - rowData[i] = Float.parseFloat(subset[i]); - } catch (NumberFormatException e) { - rowData[i] = Float.NaN; - } - } - data.add(new KMeansRow(id, rowData)); - rows.put(id, line); - } - } - - // Perform the clustering - log.debug("Clustering the data"); - Random rng = new Random(); - KMeansPlusPlusClusterer clusterer = new KMeansPlusPlusClusterer(rng); - List> clusters = clusterer.cluster(data, k, 50); - - // Write to output - log.debug("Writing clustered data to output file"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - writer.write(headerLine); - writer.newLine(); - int n = 1; - int count = 1; - for (Cluster cluster : clusters) { - int numRowsInCluster = cluster.getPoints().size(); - int stop = count + numRowsInCluster - 1; - log.info("Cluster "+(n++)+": rows "+count+"-"+stop); - count = stop+1; - for (KMeansRow row : cluster.getPoints()) { - writer.write(rows.get(row.getId())); - writer.newLine(); - } - } - } - } - - public static void main(String[] args) throws IOException, WigFileException, IntervalFileSnifferException { - new KMeans().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/visualization/KMeansRow.java --- a/src/edu/unc/genomics/visualization/KMeansRow.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -package edu.unc.genomics.visualization; - -import java.io.Serializable; -import java.util.Collection; - -import org.apache.commons.math.stat.clustering.Clusterable; - -/** - * @author timpalpant - * Holds a row of data for the KMeans program - */ -class KMeansRow implements Clusterable, Serializable { - - private static final long serialVersionUID = -323598431692368500L; - - private final String id; - /** Point coordinates. */ - private final float[] point; - - /** - * Build an instance wrapping an float array. - *

The wrapped array is referenced, it is not copied.

- * @param point the n-dimensional point in integer space - */ - public KMeansRow(final String id, final float[] point) { - this.point = point; - this.id = id; - } - - /** - * Get the n-dimensional point in float space. - * @return a reference (not a copy!) to the wrapped array - */ - public float[] getPoint() { - return point; - } - - /** {@inheritDoc} */ - public double distanceFrom(final KMeansRow p) { - double sumSquares = 0; - float[] otherPoint = p.getPoint(); - for (int i = 0; i < point.length; i++) { - sumSquares += Math.pow(point[i]-otherPoint[i], 2); - } - return Math.sqrt(sumSquares); - } - - /** {@inheritDoc} */ - public KMeansRow centroidOf(final Collection points) { - float[] centroid = new float[getPoint().length]; - for (KMeansRow p : points) { - for (int i = 0; i < centroid.length; i++) { - centroid[i] += p.getPoint()[i]; - } - } - for (int i = 0; i < centroid.length; i++) { - centroid[i] /= points.size(); - } - return new KMeansRow(id, centroid); - } - - /** {@inheritDoc} */ - @Override - public boolean equals(final Object other) { - if (!(other instanceof KMeansRow)) { - return false; - } - final float[] otherPoint = ((KMeansRow) other).getPoint(); - if (point.length != otherPoint.length) { - return false; - } - for (int i = 0; i < point.length; i++) { - if (point[i] != otherPoint[i]) { - return false; - } - } - return true; - } - - /** {@inheritDoc} */ - @Override - public int hashCode() { - int hashCode = 0; - for (Float i : point) { - hashCode += i.hashCode() * 13 + 7; - } - return hashCode; - } - - /** - * {@inheritDoc} - * @since 2.1 - */ - @Override - public String toString() { - final StringBuilder buff = new StringBuilder(id); - for (float value : getPoint()) { - buff.append("\t").append(value); - } - return buff.toString(); - } - - /** - * @return the id - */ - public String getId() { - return id; - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/visualization/MatrixAligner.java --- a/src/edu/unc/genomics/visualization/MatrixAligner.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -package edu.unc.genomics.visualization; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Arrays; -import java.util.Iterator; -import java.util.List; - -import org.apache.commons.lang3.ArrayUtils; -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.BedEntry; -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.ReadablePathValidator; -import edu.unc.genomics.io.BedFile; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class MatrixAligner extends CommandLineTool { - - private static final Logger log = Logger.getLogger(MatrixAligner.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (Wig)", required = true) - public WigFile inputFile; - @Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class) - public Path lociFile; - @Parameter(names = {"-m", "--max"}, description = "Truncate width (base pairs)") - public Integer maxWidth; - @Parameter(names = {"-o", "--output"}, description = "Output file (matrix2png format)", required = true) - public Path outputFile; - - private List loci; - - @Override - public void run() throws IOException { - log.debug("Loading alignment intervals"); - try (BedFile bed = new BedFile(lociFile)) { - loci = bed.loadAll(); - } - - // Compute the matrix dimensions - int leftMax = Integer.MIN_VALUE; - int rightMax = Integer.MIN_VALUE; - for (BedEntry entry : loci) { - int left = Math.abs(entry.getValue().intValue()-entry.getStart()); - int right = Math.abs(entry.getValue().intValue()-entry.getStop()); - if (left > leftMax) { - leftMax = left; - } - if (right > rightMax) { - rightMax = right; - } - } - - int m = loci.size(); - int n = leftMax + rightMax + 1; - int alignmentPoint = leftMax; - log.info("Intervals aligned into: " + m+"x"+n + " matrix"); - log.info("Alignment point: " + alignmentPoint); - - int leftBound = 0; - int rightBound = n-1; - if (maxWidth != null && maxWidth < n) { - log.info("Truncated to: " + m+"x"+maxWidth); - int leftAlignDistance = alignmentPoint; - int rightAlignDistance = n - alignmentPoint - 1; - int halfMax = maxWidth / 2; - - if (halfMax < leftAlignDistance && halfMax < rightAlignDistance) { - leftBound = alignmentPoint - halfMax; - rightBound = alignmentPoint + halfMax; - } else { - if (leftAlignDistance <= rightAlignDistance) { - rightBound = maxWidth; - } else { - leftBound = n - maxWidth; - } - } - } - - log.debug("Initializing output file"); - int count = 0, skipped = 0; - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - writer.write("ID"); - for (int i = leftBound-alignmentPoint; i <= rightBound-alignmentPoint; i++) { - writer.write("\t"+i); - } - writer.newLine(); - - log.debug("Iterating over all intervals"); - String[] row = new String[n]; - for (BedEntry entry : loci) { - Iterator result = null; - try { - result = inputFile.query(entry); - } catch (WigFileException e) { - skipped++; - continue; - } - - float[] data = WigFile.flattenData(result, entry.getStart(), entry.getStop()); - // Reverse if on the crick strand - if (entry.isCrick()) { - ArrayUtils.reverse(data); - } - - // Position the data in the matrix - // Locus alignment point (entry value) should be positioned over the matrix alignment point - int n1 = alignmentPoint - Math.abs(entry.getValue().intValue()-entry.getStart()); - int n2 = alignmentPoint + Math.abs(entry.getValue().intValue()-entry.getStop()); - assert data.length == n2-n1+1; - - Arrays.fill(row, "-"); - for (int i = 0; i < data.length; i++) { - if (!Float.isNaN(data[i])) { - row[n1+i] = String.valueOf(data[i]); - } - } - - // Write to output - String id = ((entry.getId() == null) ? entry.getId() : "Row "+(count++)); - writer.write(id); - for (int i = leftBound; i <= rightBound; i++) { - writer.write("\t"+row[i]); - } - writer.newLine(); - } - } - - inputFile.close(); - log.info(count + " intervals processed"); - log.info(skipped + " intervals skipped"); - } - - public static void main(String[] args) { - new MatrixAligner().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/visualization/StripMatrix.java --- a/src/edu/unc/genomics/visualization/StripMatrix.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -package edu.unc.genomics.visualization; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.ReadablePathValidator; - -public class StripMatrix extends CommandLineTool { - - private static final Logger log = Logger.getLogger(StripMatrix.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file (matrix2png format)", required = true, validateWith = ReadablePathValidator.class) - public Path inputFile; - @Parameter(names = {"-o", "--output"}, description = "Output file (tabular)", required = true) - public Path outputFile; - - public void run() throws IOException { - try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset())) { - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - String line = reader.readLine(); - // Always copy the first (header) line - writer.write(line); - writer.newLine(); - while ((line = reader.readLine()) != null) { - String[] row = line.split("\t"); - for (int i = 1; i < row.length; i++) { - String cell = row[i]; - if (cell.equalsIgnoreCase("-")) { - writer.write("NaN"); - } else { - writer.write(cell); - } - - if (i > 1) { - writer.write("\t"); - } - } - writer.newLine(); - } - } - } - } - - public static void main(String[] args) { - new StripMatrix().instanceMain(args); - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/Add.java --- a/src/edu/unc/genomics/wigmath/Add.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineToolException; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Add extends WigMathTool { - - private static final Logger log = Logger.getLogger(Add.class); - - @Parameter(description = "Input files", required = true) - public List inputFiles = new ArrayList(); - - @Override - public void setup() { - if (inputFiles.size() < 2) { - throw new CommandLineToolException("No reason to add < 2 files."); - } - - log.debug("Initializing input files"); - for (String inputFile : inputFiles) { - try { - addInputFile(WigFile.autodetect(Paths.get(inputFile))); - } catch (IOException | WigFileException e) { - log.error("Error initializing input Wig file: " + inputFile); - e.printStackTrace(); - throw new CommandLineToolException(e.getMessage()); - } - } - log.debug("Initialized " + inputs.size() + " input files"); - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing sum for chunk "+chr+":"+start+"-"+stop); - - int length = stop - start + 1; - float[] sum = new float[length]; - - for (WigFile wig : inputs) { - Iterator data = wig.query(chr, start, stop); - while (data.hasNext()) { - WigItem item = data.next(); - for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { - if (i-start >= 0 && i-start < sum.length) { - sum[i-start] += item.getWigValue(); - } - } - } - } - - return sum; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new Add().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/Average.java --- a/src/edu/unc/genomics/wigmath/Average.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineToolException; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Average extends WigMathTool { - - private static final Logger log = Logger.getLogger(Average.class); - - @Parameter(description = "Input files", required = true) - public List inputFiles = new ArrayList(); - - int numFiles; - - @Override - public void setup() { - if (inputFiles.size() < 2) { - throw new CommandLineToolException("No reason to add < 2 files."); - } - - log.debug("Initializing input files"); - for (String inputFile : inputFiles) { - try { - addInputFile(WigFile.autodetect(Paths.get(inputFile))); - } catch (IOException | WigFileException e) { - log.error("Error initializing input Wig file: " + inputFile); - e.printStackTrace(); - throw new CommandLineToolException(e.getMessage()); - } - } - log.debug("Initialized " + inputs.size() + " input files"); - - numFiles = inputs.size(); - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing average for chunk "+chr+":"+start+"-"+stop); - - int length = stop - start + 1; - float[] avg = new float[length]; - - for (WigFile wig : inputs) { - Iterator data = wig.query(chr, start, stop); - while (data.hasNext()) { - WigItem item = data.next(); - for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { - if (i-start >= 0 && i-start < avg.length) { - avg[i-start] += item.getWigValue(); - } - } - } - } - - for (int i = 0; i < avg.length; i++) { - avg[i] = avg[i] / numFiles; - } - - return avg; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new Average().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/Divide.java --- a/src/edu/unc/genomics/wigmath/Divide.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Divide extends WigMathTool { - - private static final Logger log = Logger.getLogger(Divide.class); - - @Parameter(names = {"-n", "--numerator"}, description = "Dividend / Numerator (file 1)", required = true) - public WigFile dividendFile; - @Parameter(names = {"-d", "--denominator"}, description = "Divisor / Denominator (file 2)", required = true) - public WigFile divisorFile; - - @Override - public void setup() { - inputs.add(dividendFile); - inputs.add(divisorFile); - log.debug("Initialized " + inputs.size() + " input files"); - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop); - - Iterator dividendData = dividendFile.query(chr, start, stop); - Iterator divisorData = divisorFile.query(chr, start, stop); - - float[] result = WigFile.flattenData(dividendData, start, stop); - while (divisorData.hasNext()) { - WigItem item = divisorData.next(); - for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { - if (i-start >= 0 && i-start < result.length) { - if (item.getWigValue() != 0) { - result[i-start] /= item.getWigValue(); - } else { - result[i-start] = Float.NaN; - } - } - } - } - - return result; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new Divide().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/GaussianSmooth.java --- a/src/edu/unc/genomics/wigmath/GaussianSmooth.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class GaussianSmooth extends WigMathTool { - - private static final Logger log = Logger.getLogger(GaussianSmooth.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) - public WigFile inputFile; - @Parameter(names = {"-s", "--stdev"}, description = "Standard deviation of Gaussian (bp)") - public int stdev = 20; - - float[] filter; - - @Override - public void setup() { - inputs.add(inputFile); - - // Use a window size equal to +/- 3 SD's - filter = new float[6*stdev+1]; - float sum = 0; - for (int i = 0; i < filter.length; i++) { - float x = i - 3*stdev; - float value = (float) Math.exp(-(x*x) / (2*stdev*stdev)); - filter[i] = value; - sum += value; - } - for (int i = 0; i < filter.length; i++) { - filter[i] /= sum; - } - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Smoothing chunk "+chr+":"+start+"-"+stop); - - // Pad the query for smoothing - int paddedStart = Math.max(start-3*stdev, inputFile.getChrStart(chr)); - int paddedStop = Math.min(stop+3*stdev, inputFile.getChrStop(chr)); - Iterator result = inputFile.query(chr, paddedStart, paddedStop); - float[] data = WigFile.flattenData(result, start-3*stdev, stop+3*stdev); - - // Convolve the data with the filter - float[] smoothed = new float[stop-start+1]; - for (int i = 0; i < smoothed.length; i++) { - for (int j = 0; j < filter.length; j++) { - smoothed[i] += data[i+j] * filter[j]; - } - } - - return smoothed; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new GaussianSmooth().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/LogTransform.java --- a/src/edu/unc/genomics/wigmath/LogTransform.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class LogTransform extends WigMathTool { - - private static final Logger log = Logger.getLogger(LogTransform.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) - public WigFile inputFile; - @Parameter(names = {"-b", "--base"}, description = "Logarithm base (default = 2)") - public double base = 2; - - private double baseChange; - - @Override - public void setup() { - baseChange = Math.log(base); - inputs.add(inputFile); - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop); - - Iterator data = inputFile.query(chr, start, stop); - float[] result = WigFile.flattenData(data, start, stop); - - for (int i = 0; i < result.length; i++) { - result[i] = (float) (Math.log(result[i]) / baseChange); - } - - return result; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new LogTransform().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/MovingAverageSmooth.java --- a/src/edu/unc/genomics/wigmath/MovingAverageSmooth.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.util.Iterator; - -import org.apache.commons.math.stat.descriptive.DescriptiveStatistics; -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.PositiveIntegerValidator; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class MovingAverageSmooth extends WigMathTool { - - private static final Logger log = Logger.getLogger(MovingAverageSmooth.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) - public WigFile inputFile; - @Parameter(names = {"-w", "--width"}, description = "Width of kernel (bp)") - public int width = 10; - - WigFile input; - DescriptiveStatistics stats; - - @Override - public void setup() { - inputs.add(inputFile); - - log.debug("Initializing statistics"); - stats = new DescriptiveStatistics(); - stats.setWindowSize(width); - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Smoothing chunk "+chr+":"+start+"-"+stop); - // Pad the query so that we can provide values for the ends - int queryStart = Math.max(start-width/2, input.getChrStart(chr)); - int queryStop = Math.min(stop+width/2, input.getChrStop(chr)); - Iterator result = input.query(chr, queryStart, queryStop); - float[] data = WigFile.flattenData(result, queryStart, queryStop); - - float[] smoothed = new float[stop-start+1]; - for (int bp = start; bp <= stop; bp++) { - stats.addValue(data[bp-queryStart]); - if (bp-start-width/2 >= 0) { - smoothed[bp-start-width/2] = (float) stats.getMean(); - } - } - - return smoothed; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new MovingAverageSmooth().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/Multiply.java --- a/src/edu/unc/genomics/wigmath/Multiply.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Iterator; -import java.util.List; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Multiply extends WigMathTool { - - private static final Logger log = Logger.getLogger(Multiply.class); - - @Parameter(description = "Input files", required = true) - public List inputFiles = new ArrayList(); - - @Override - public void setup() { - log.debug("Initializing input files"); - for (String inputFile : inputFiles) { - try { - addInputFile(WigFile.autodetect(Paths.get(inputFile))); - } catch (IOException | WigFileException e) { - log.error("Error initializing input Wig file: " + inputFile); - e.printStackTrace(); - System.exit(-1); - } - } - log.debug("Initialized " + inputs.size() + " input files"); - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing sum for chunk "+chr+":"+start+"-"+stop); - - int length = stop - start + 1; - float[] product = new float[length]; - Arrays.fill(product, 1); - - for (WigFile wig : inputs) { - Iterator data = wig.query(chr, start, stop); - while (data.hasNext()) { - WigItem item = data.next(); - for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { - if (i-start >= 0 && i-start < product.length) { - product[i-start] *= item.getWigValue(); - } - } - } - } - - return product; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new Multiply().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/Scale.java --- a/src/edu/unc/genomics/wigmath/Scale.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Scale extends WigMathTool { - - private static final Logger log = Logger.getLogger(Scale.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) - public WigFile inputFile; - @Parameter(names = {"-m", "--multiplier"}, description = "Multiplier (scale factor, default = 1/mean)") - public Double multiplier; - - - @Override - public void setup() { - inputs.add(inputFile); - - if (multiplier == null) { - multiplier = inputFile.numBases() / inputFile.total(); - } - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop); - - Iterator data = inputFile.query(chr, start, stop); - float[] result = WigFile.flattenData(data, start, stop); - - for (int i = 0; i < result.length; i++) { - result[i] = (float) (multiplier * result[i]); - } - - return result; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new Scale().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/Subtract.java --- a/src/edu/unc/genomics/wigmath/Subtract.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class Subtract extends WigMathTool { - - private static final Logger log = Logger.getLogger(Subtract.class); - - @Parameter(names = {"-m", "--minuend"}, description = "Minuend (top - file 1)", required = true) - public WigFile minuendFile; - @Parameter(names = {"-s", "--subtrahend"}, description = "Subtrahend (bottom - file 2)", required = true) - public WigFile subtrahendFile; - - @Override - public void setup() { - log.debug("Initializing input files"); - inputs.add(minuendFile); - inputs.add(subtrahendFile); - log.debug("Initialized " + inputs.size() + " input files"); - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop); - - Iterator minuendData = minuendFile.query(chr, start, stop); - Iterator subtrahendData = subtrahendFile.query(chr, start, stop); - - float[] result = WigFile.flattenData(minuendData, start, stop); - while (subtrahendData.hasNext()) { - WigItem item = subtrahendData.next(); - for (int i = item.getStartBase(); i <= item.getEndBase(); i++) { - if (i-start >= 0 && i-start < result.length) { - result[i-start] -= item.getWigValue(); - } - } - } - - return result; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new Subtract().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/WigMathTool.java --- a/src/edu/unc/genomics/wigmath/WigMathTool.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,170 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.HashSet; -import java.util.Iterator; -import java.util.List; -import java.util.Set; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -/** - * Abstract class for writing programs to do computation on Wig files - * Concrete subclasses must implement the compute method - * - * @author timpalpant - * - */ -public abstract class WigMathTool extends CommandLineTool { - - private static final Logger log = Logger.getLogger(WigMathTool.class); - - public static final int DEFAULT_CHUNK_SIZE = 500_000; - - // TODO: Variable resolution output - - @Parameter(names = {"-o", "--output"}, description = "Output file", required = true) - public Path outputFile; - - protected List inputs = new ArrayList(); - - public void addInputFile(WigFile wig) { - inputs.add(wig); - } - - /** - * Setup the computation. Should add all input Wig files - * with addInputFile() during setup - */ - public abstract void setup(); - - /** - * Do the computation on a chunk and return the results - * Must return (stop-start+1) values - * - * @param chr - * @param start - * @param stop - * @return the results of the computation for this chunk - * @throws IOException - * @throws WigFileException - */ - public abstract float[] compute(String chr, int start, int stop) - throws IOException, WigFileException; - - @Override - public void run() throws IOException { - log.debug("Executing setup operations"); - setup(); - - log.debug("Processing files and writing result to disk"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - // Write the Wig header - writer.write("track type=wiggle_0"); - writer.newLine(); - - Set chromosomes = getCommonChromosomes(inputs); - log.debug("Found " + chromosomes.size() + " chromosomes in common between all inputs"); - for (String chr : chromosomes) { - int start = getMaxChrStart(inputs, chr); - int stop = getMinChrStop(inputs, chr); - log.debug("Processing chromosome " + chr + " region " + start + "-" + stop); - - // Write the chromosome header to output - writer.write("fixedStep chrom="+chr+" start="+start+" step=1 span=1"); - writer.newLine(); - - // Process the chromosome in chunks - int bp = start; - while (bp < stop) { - int chunkStart = bp; - int chunkStop = Math.min(bp+DEFAULT_CHUNK_SIZE-1, stop); - int expectedLength = chunkStop - chunkStart + 1; - log.debug("Processing chunk "+chr+":"+chunkStart+"-"+chunkStop); - - float[] result = null; - try { - result = compute(chr, chunkStart, chunkStop); - } catch (WigFileException e) { - log.fatal("Wig file error while processing chunk " + chr + " region " + start + "-" + stop); - e.printStackTrace(); - throw new RuntimeException("Wig file error while processing chunk " + chr + " region " + start + "-" + stop); - } - - if (result.length != expectedLength) { - log.error("Expected result length="+expectedLength+", got="+result.length); - throw new RuntimeException("Result is not the expected length!"); - } - - for (int i = 0; i < result.length; i++) { - writer.write(Float.toString(result[i])); - writer.newLine(); - } - - bp = chunkStop + 1; - } - } - } - - for (WigFile wig : inputs) { - wig.close(); - } - } - - public int getMaxChrStart(List wigs, String chr) { - int max = -1; - for (WigFile wig : wigs) { - if (wig.getChrStart(chr) > max) { - max = wig.getChrStart(chr); - } - } - - return max; - } - - public int getMinChrStop(List wigs, String chr) { - if (wigs.size() == 0) { - return -1; - } - - int min = Integer.MAX_VALUE; - for (WigFile wig : wigs) { - if (wig.getChrStop(chr) < min) { - min = wig.getChrStop(chr); - } - } - - return min; - } - - public Set getCommonChromosomes(List wigs) { - if (wigs.size() == 0) { - return new HashSet(); - } - - Set chromosomes = wigs.get(0).chromosomes(); - Iterator it = chromosomes.iterator(); - while(it.hasNext()) { - String chr = it.next(); - for (WigFile wig : wigs) { - if (!wig.includes(chr)) { - it.remove(); - break; - } - } - } - - return chromosomes; - } -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/WigSummary.java --- a/src/edu/unc/genomics/wigmath/WigSummary.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.log4j.Logger; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineTool; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; -import edu.unc.genomics.ngs.Autocorrelation; - -public class WigSummary extends CommandLineTool { - - private static final Logger log = Logger.getLogger(Autocorrelation.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) - public WigFile inputFile; - @Parameter(names = {"-o", "--output"}, description = "Output file") - public Path outputFile; - - public void run() throws IOException { - String summary = inputFile.toString(); - - if (outputFile != null) { - log.debug("Writing to output file"); - try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { - writer.write(summary); - } - } else { - System.out.println(summary); - } - } - - public static void main(String[] args) throws IOException, WigFileException { - new WigSummary().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/genomics/wigmath/ZScore.java --- a/src/edu/unc/genomics/wigmath/ZScore.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -package edu.unc.genomics.wigmath; - -import java.io.IOException; -import java.util.Iterator; - -import org.apache.log4j.Logger; -import org.broad.igv.bbfile.WigItem; - -import com.beust.jcommander.Parameter; - -import edu.unc.genomics.CommandLineToolException; -import edu.unc.genomics.io.WigFile; -import edu.unc.genomics.io.WigFileException; - -public class ZScore extends WigMathTool { - - private static final Logger log = Logger.getLogger(ZScore.class); - - @Parameter(names = {"-i", "--input"}, description = "Input file", required = true) - public WigFile inputFile; - - double mean; - double stdev; - - @Override - public void setup() { - inputs.add(inputFile); - - mean = inputFile.mean(); - stdev = inputFile.stdev(); - if(stdev == 0) { - log.error("Cannot Z-score a file with stdev = 0!"); - throw new CommandLineToolException("Cannot Z-score a file with stdev = 0!"); - } - } - - @Override - public float[] compute(String chr, int start, int stop) throws IOException, WigFileException { - log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop); - Iterator data = inputFile.query(chr, start, stop); - float[] result = WigFile.flattenData(data, start, stop); - - for (int i = 0; i < result.length; i++) { - result[i] = (float)((result[i] - mean) / stdev); - } - - return result; - } - - - /** - * @param args - * @throws WigFileException - * @throws IOException - */ - public static void main(String[] args) throws IOException, WigFileException { - new ZScore().instanceMain(args); - } - -} diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/utils/RomanNumeral.java --- a/src/edu/unc/utils/RomanNumeral.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -package edu.unc.utils; - -// Rudimentary Class for doing Arabic Integer -> Roman Numeral conversion -// Adapted by Timothy Palpant -// File : gui/componenents/calculators/Roman.java -// Description: A static method for converting binary integers to Roman numbers. -// Illustrates: Static inner value class, StringBuffer, throw exceptions. -// Author : Fred Swartz - 2006-12-29 - Placed in public domain. -public class RomanNumeral { - - // This could be alternatively be done with parallel arrays. - // Another alternative would be Pair - final static RomanValue[] ROMAN_VALUE_TABLE = { - new RomanValue(1000, "M"), - new RomanValue( 900, "CM"), - new RomanValue( 500, "D"), - new RomanValue( 400, "CD"), - new RomanValue( 100, "C"), - new RomanValue( 90, "XC"), - new RomanValue( 50, "L"), - new RomanValue( 40, "XL"), - new RomanValue( 10, "X"), - new RomanValue( 9, "IX"), - new RomanValue( 5, "V"), - new RomanValue( 4, "IV"), - new RomanValue( 1, "I") - }; - - public static String int2roman(int n) { - if (n >= 4000 || n < 1) { - throw new NumberFormatException("Numbers must be in range 1-3999"); - } - StringBuilder result = new StringBuilder(10); - - //... Start with largest value, and work toward smallest. - for (RomanValue equiv : ROMAN_VALUE_TABLE) { - //... Remove as many of this value as possible (maybe none). - while (n >= equiv.intVal) { - n -= equiv.intVal; // Subtract value. - result.append(equiv.romVal); // Add roman equivalent. - } - } - return result.toString(); - } - - private static class RomanValue { - //... No need to make this fields private because they are - // used only in this private value class. - int intVal; // Integer value. - String romVal; // Equivalent roman numeral. - - RomanValue(int dec, String rom) { - this.intVal = dec; - this.romVal = rom; - } - } -} \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba src/edu/unc/utils/SortUtils.java --- a/src/edu/unc/utils/SortUtils.java Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -package edu.unc.utils; - -/** - * Custom sorting utilities - * see: http://stackoverflow.com/questions/951848/java-array-sort-quick-way-to-get-a-sorted-list-of-indices-of-an-array - * @author timpalpant - * - */ -public class SortUtils { - public static int[] indexSort(float[] main) { - int[] index = new int[main.length]; - for (int i = 0; i < index.length; i++) { - index[i] = i; - } - - quicksort(main, index, 0, index.length-1); - - return index; - } - - // quicksort a[left] to a[right] - public static void quicksort(float[] a, int[] index, int left, int right) { - if (right <= left) - return; - int i = partition(a, index, left, right); - quicksort(a, index, left, i - 1); - quicksort(a, index, i + 1, right); - } - - // partition a[left] to a[right], assumes left < right - private static int partition(float[] a, int[] index, int left, int right) { - int i = left - 1; - int j = right; - while (true) { - while (a[index[++i]] < a[index[right]]) - // find item on left to swap - ; // a[right] acts as sentinel - while (a[index[right]] < a[index[--j]]) - // find item on right to swap - if (j == left) - break; // don't go out-of-bounds - if (i >= j) - break; // check if pointers cross - exch(a, index, i, j); // swap two elements into place - } - exch(a, index, i, right); // swap with partition element - return i; - } - - // exchange a[i] and a[j] - private static void exch(float[] a, int[] index, int i, int j) { - // Don't swap the data - // float swap = a[i]; - // a[i] = a[j]; - // a[j] = swap; - int b = index[i]; - index[i] = index[j]; - index[j] = b; - } -} diff -r e16016635b2a -r 4b610dc8f6ba stubFile.sh --- a/stubFile.sh Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/usr/bin/env bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -java -Dlog4j.configuration=log4j.properties -cp "$DIR/../Resources/Java/*" edu.unc.genomics.ToolRunner \ No newline at end of file diff -r e16016635b2a -r 4b610dc8f6ba toolRunner.sh --- a/toolRunner.sh Mon Feb 13 22:12:06 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#!/usr/bin/env bash - -if [ $# -eq 0 ] -then - echo "USAGE: toolRunner.sh APPNAME [ARGS]"; - exit; -fi - -if [ "$1" = "list" ] -then - find src/edu/unc/genomics/**/*.java -exec basename -s .java {} \; -fi - -java -Dlog4j.configuration=log4j.properties -cp .:build:lib/* edu.unc.genomics."$@" \ No newline at end of file