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GATK Report code cleanup 

- Updated the documentation on the code
 - Made the table.write() method private and updated necessary files.
 - Added a constructor to GATKReport that takes GATKReportTables
 - Optimized my code

Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
This commit is contained in:
Roger Zurawicki 2012-03-18 01:05:49 -04:00 committed by Mauricio Carneiro
parent 0d4ea30d6d
commit 7afb333811
10 changed files with 73 additions and 131 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
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@ -41,10 +41,10 @@ import java.util.TreeMap;
public class GATKReport {
public static final String GATKREPORT_HEADER_PREFIX = "#:GATKReport.";
public static final GATKReportVersion LATEST_REPORT_VERSION = GATKReportVersion.V1_0;
public static final String SEPARATOR = ":";
private static final String SEPARATOR = ":";
private GATKReportVersion version = LATEST_REPORT_VERSION;
private TreeMap<String, GATKReportTable> tables = new TreeMap<String, GATKReportTable>();
private final TreeMap<String, GATKReportTable> tables = new TreeMap<String, GATKReportTable>();
/**
* Create a new, empty GATKReport.
@ -70,6 +70,15 @@ public class GATKReport {
loadReport(file);
}
/**
* Create a new GATK report from GATK report tables
* @param tables Any number of tables that you want ot add to the report
*/
public GATKReport(GATKReportTable... tables) {
for( GATKReportTable table: tables)
addTable(table);
}
/**
* Load a GATKReport file from disk
*
@ -202,10 +211,6 @@ public class GATKReport {
return version;
}
public void setVersion(GATKReportVersion version) {
this.version = version;
}
/**
* Returns whether or not the two reports have the same format, from columns, to tables, to reports, and everything
* in between. This does not check if the data inside is the same. This is the check to see if the two reports are

2
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
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@ -199,7 +199,7 @@ public class GATKReportColumn extends TreeMap<Object, Object> {
defaultValue.equals(that.defaultValue) );
}
protected boolean equals(GATKReportColumn that) {
boolean equals(GATKReportColumn that) {
if ( !this.keySet().equals(that.keySet()) ) {
return false;
}

6
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumnFormat.java
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@ -1,5 +1,5 @@
/*
* Copyright (c) 2011, The Broad Institute
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
@ -29,8 +29,8 @@ package org.broadinstitute.sting.gatk.report;
*/
public class GATKReportColumnFormat {
public static enum Alignment { LEFT, RIGHT }
public int width;
public Alignment alignment;
private final int width;
private final Alignment alignment;
public GATKReportColumnFormat(int width, Alignment alignment) {
this.width = width;

15
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java
View File

@ -24,13 +24,15 @@
package org.broadinstitute.sting.gatk.report;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.*;
/**
* Tracks a linked list of GATKReportColumn in order by name.
*/
public class GATKReportColumns extends LinkedHashMap<String, GATKReportColumn> implements Iterable<GATKReportColumn> {
private List<String> columnNames = new ArrayList<String>();
private final List<String> columnNames = new ArrayList<String>();
/**
* Returns the column by index
@ -43,9 +45,12 @@ public class GATKReportColumns extends LinkedHashMap<String, GATKReportColumn> i
}
@Override
public GATKReportColumn remove(Object key) {
columnNames.remove(key);
return super.remove(key);
public GATKReportColumn remove(Object columnName) {
if ( !(columnName instanceof String) ) {
throw new ReviewedStingException("The column name must be a String!");
}
columnNames.remove(columnName.toString());
return super.remove(columnName);
}
@Override
@ -85,7 +90,7 @@ public class GATKReportColumns extends LinkedHashMap<String, GATKReportColumn> i
return true;
}
protected boolean equals(GATKReportColumns that) {
boolean equals(GATKReportColumns that) {
for (Map.Entry<String, GATKReportColumn> pair : entrySet()) {
// Make sure that every column is the same, we know that the # of columns
// is the same from isSameFormat()

4
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportDataType.java
View File

@ -67,7 +67,7 @@ public enum GATKReportDataType {
*/
String("%[Ss]");
public final String dataTypeString;
private final String dataTypeString;
private GATKReportDataType(String dataTypeString) {
this.dataTypeString = dataTypeString;
@ -189,7 +189,7 @@ public enum GATKReportDataType {
* @param obj The input string
* @return an object that matches the data type.
*/
protected Object Parse(Object obj) {
Object Parse(Object obj) {
if (obj instanceof String) {
String str = obj.toString();
switch (this) {

31
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
View File

@ -1,3 +1,27 @@
/*
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.report;
import org.broadinstitute.sting.commandline.Gatherer;
@ -8,13 +32,6 @@ import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: roger
* Date: 1/9/12
* Time: 11:17 PM
* To change this template use File | Settings | File Templates.
*/
public class GATKReportGatherer extends Gatherer {
@Override
public void gather(List<File> inputs, File output) {

108
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -34,97 +34,14 @@ import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* A data structure that allows data to be collected over the course of a walker's computation, then have that data
* written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the
* GATKReport loader module).
* <p/>
* The goal of this object is to use the same data structure for both accumulating data during a walker's computation
* and emitting that data to a file for easy analysis in R (or any other program/language that can take in a table of
* results). Thus, all of the infrastructure below is designed simply to make printing the following as easy as
* possible:
* <p/>
* ##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads
* cycle errorrate.61PA8.7 qualavg.61PA8.7
* 0 0.007451835696110506 25.474613284804366
* 1 0.002362777171937477 29.844949954504095
* 2 9.087604507451836E-4 32.87590975254731
* 3 5.452562704471102E-4 34.498999090081895
* 4 9.087604507451836E-4 35.14831665150137
* 5 5.452562704471102E-4 36.07223435225619
* 6 5.452562704471102E-4 36.1217248908297
* 7 5.452562704471102E-4 36.1910480349345
* 8 5.452562704471102E-4 36.00345705967977
* <p/>
* Here, we have a GATKReport table - a well-formatted, easy to read representation of some tabular data. Every single
* table has this same GATKReport.v0.1 header, which permits multiple files from different sources to be cat-ed
* together, which makes it very easy to pull tables from different programs into R via a single file.
* <p/>
* ------------
* Definitions:
* <p/>
* Table info:
* The first line, structured as
* ##:<report version> <table name> : <table description>
* <p/>
* Table header:
* The second line, specifying a unique name for each column in the table.
* <p/>
* The first column mentioned in the table header is the "primary key" column - a column that provides the unique
* identifier for each row in the table. Once this column is created, any element in the table can be referenced by
* the row-column coordinate, i.e. "primary key"-"column name" coordinate.
* <p/>
* When a column is added to a table, a default value must be specified (usually 0). This is the initial value for
* an element in a column. This permits operations like increment() and decrement() to work properly on columns that
* are effectively counters for a particular event.
* <p/>
* Finally, the display property for each column can be set during column creation. This is useful when a given
* column stores an intermediate result that will be used later on, perhaps to calculate the value of another column.
* In these cases, it's obviously necessary to store the value required for further computation, but it's not
* necessary to actually print the intermediate column.
* <p/>
* Table body:
* The values of the table itself.
* <p/>
* ---------------
* Implementation:
* <p/>
* The implementation of this table has two components:
* 1. A TreeSet<Object> that stores all the values ever specified for the primary key. Any get() operation that
* refers to an element where the primary key object does not exist will result in its implicit creation. I
* haven't yet decided if this is a good idea...
* <p/>
* 2. A HashMap<String, GATKReportColumn> that stores a mapping from column name to column contents. Each
* GATKReportColumn is effectively a map (in fact, GATKReportColumn extends TreeMap<Object, Object>) between
* primary key and the column value. This means that, given N columns, the primary key information is stored
* N+1 times. This is obviously wasteful and can likely be handled much more elegantly in future implementations.
* <p/>
* ------------------------------
* Element and column operations:
* <p/>
* In addition to simply getting and setting values, this object also permits some simple operations to be applied to
* individual elements or to whole columns. For instance, an element can be easily incremented without the hassle of
* calling get(), incrementing the obtained value by 1, and then calling set() with the new value. Also, some vector
* operations are supported. For instance, two whole columns can be divided and have the result be set to a third
* column. This is especially useful when aggregating counts in two intermediate columns that will eventually need to
* be manipulated row-by-row to compute the final column.
* <p/>
* Note: I've made no attempt whatsoever to make these operations efficient. Right now, some of the methods check the
* type of the stored object using an instanceof call and attempt to do the right thing. Others cast the contents of
* the cell to a Number, call the Number.toDouble() method and compute a result. This is clearly not the ideal design,
* but at least the prototype contained herein works.
*
* @author Kiran Garimella
* @author Khalid Shakir
*/
public class GATKReportTable {
/**
* REGEX that matches any table with an invalid name
*/
public static final String INVALID_TABLE_NAME_REGEX = "[^a-zA-Z0-9_\\-\\.]";
public static final String GATKTABLE_HEADER_PREFIX = "#:GATKTable";
public static final String SEPARATOR = ":";
public static final String ENDLINE = ":;";
private static final String GATKTABLE_HEADER_PREFIX = "#:GATKTable";
private static final String SEPARATOR = ":";
private static final String ENDLINE = ":;";
private String tableName;
private String tableDescription;
@ -418,8 +335,8 @@ public class GATKReportTable {
* output file), and the format string used to display the data.
*
* @param columnName the name of the column
* @param defaultValue if true - the column will be displayed; if false - the column will be hidden
* @param display
* @param defaultValue the default value of a blank cell
* @param display if true - the column will be displayed; if false - the column will be hidden
* @param format the format string used to display data
*/
public void addColumn(String columnName, Object defaultValue, boolean display, String format) {
@ -429,12 +346,6 @@ public class GATKReportTable {
columns.put(columnName, new GATKReportColumn(columnName, defaultValue, display, format));
}
public GATKReportVersion getVersion() {
return GATKReport.LATEST_REPORT_VERSION;
}
/**
* Check if the requested element exists, and if not, create it.
*
@ -508,8 +419,7 @@ public class GATKReportTable {
value = newValue;
if (column.getDataType().equals(GATKReportDataType.fromObject(value)) ||
column.getDataType().equals(GATKReportDataType.Unknown) ||
value == null)
column.getDataType().equals(GATKReportDataType.Unknown) )
columns.get(columnName).put(primaryKey, value);
else
throw new ReviewedStingException(String.format("Tried to add an object of type: %s to a column of type: %s",
@ -795,7 +705,7 @@ public class GATKReportTable {
*
* @return the width of the primary key column
*/
public int getPrimaryKeyColumnWidth() {
int getPrimaryKeyColumnWidth() {
int maxWidth = getPrimaryKeyName().length();
for (Object primaryKey : primaryKeyColumn) {
@ -814,7 +724,7 @@ public class GATKReportTable {
*
* @param out the PrintStream to which the table should be written
*/
public void write(PrintStream out) {
void write(PrintStream out) {
/*
* Table header:
@ -912,7 +822,7 @@ public class GATKReportTable {
*
* @param input Another GATK table
*/
protected void combineWith(GATKReportTable input) {
void combineWith(GATKReportTable input) {
/*
* This function is different from addRowsFrom because we will add the ability to sum,average, etc rows
* TODO: Add other combining algorithms

4
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
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@ -1,5 +1,5 @@
/*
* Copyright (c) 2011, The Broad Institute
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
@ -50,7 +50,7 @@ public enum GATKReportVersion {
*/
V1_0("v1.0");
public final String versionString;
private final String versionString;
private GATKReportVersion(String versionString) {
this.versionString = versionString;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
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@ -1,5 +1,5 @@
/*
* Copyright (c) 2011, The Broad Institute
* Copyright (c) 2012, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
@ -244,7 +244,8 @@ public class DiffEngine {
table.set(diff.getPath(), "NumberOfOccurrences", diff.getCount());
table.set(diff.getPath(), "ExampleDifference", diff.valueDiffString());
}
table.write(params.out);
GATKReport output = new GATKReport(table);
output.print(params.out);
}
protected static int longestCommonPostfix(String[] diffPath1, String[] diffPath2) {

12
public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java
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@ -80,11 +80,15 @@ public class GATKReportUnitTest extends BaseTest {
@Test
public void testSimpleGATKReport() {
GATKReport report = GATKReport.newSimpleReport("TableName", "a", "b", "Roger", "is", "Awesome");
report.addRow("a", 'F', 12, 23.45, true);
report.addRow("ans", '3', 24.5, 456L, 2345);
report.addRow("hi", null, null, "", 2.3);
// Create a new simple GATK report named "TableName" with columns: Roger, is, and Awesome
GATKReport report = GATKReport.newSimpleReport("TableName", "Roger", "is", "Awesome");
// Add data to simple GATK report
report.addRow( 12, 23.45, true);
report.addRow("ans", '3', 24.5);
report.addRow("hi", "", 2.3);
// Print the report to console
//report.print(System.out);
try {