zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3130 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-04-07 20:39:55 +00:00
parent 918b746798
commit 8fd59c8823
14 changed files with 452 additions and 121 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
ivy.xml
View File

@ -16,7 +16,6 @@
<dependency org="org.simpleframework" name="simple-xml" rev="2.0.4" conf="default"/>
<dependency org="org.apache.bcel" name="bcel" rev="5.2" conf="default"/>
<dependency org="org.broad" name="tribble" rev="latest.integration" conf="default"/>
<dependency org="freemarker" name="freemarker" rev="2.3.8" conf="default"/>
<!-- Dependencies for reflections mvn repository -->
<dependency org="org.reflections" name="reflections" rev="0.9.2" conf="default"/>

29
java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
View File

@ -23,11 +23,8 @@
package org.broadinstitute.sting.playground.utils.report;
import freemarker.template.Configuration;
import freemarker.template.DefaultObjectWrapper;
import freemarker.template.Template;
import freemarker.template.TemplateException;
import org.broadinstitute.sting.oneoffprojects.walkers.varianteval2.CountVariants;
import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.StingException;
@ -46,7 +43,7 @@ import java.util.*;
* marshall report data out of the GATK.
*/
public class ReportMarshaller {
private Template temp;
private ReportFormat temp;
// the aggregation of all our analyses
private Node root;
@ -58,7 +55,7 @@ public class ReportMarshaller {
* @param reportName the report name
* @param template the template to use
*/
public ReportMarshaller(String reportName, File filename, Template template) {
public ReportMarshaller(String reportName, File filename, ReportFormat template) {
try {
init(reportName, new OutputStreamWriter(new FileOutputStream(filename)));
} catch (FileNotFoundException e) {
@ -72,7 +69,7 @@ public class ReportMarshaller {
*
* @param reportName the report name
*/
public ReportMarshaller(String reportName, Writer writer, Template template, List<Node> reportTags) {
public ReportMarshaller(String reportName, Writer writer, ReportFormat template, List<Node> reportTags) {
init(reportName, writer);
temp = template;
for (Node n : reportTags) {
@ -86,7 +83,7 @@ public class ReportMarshaller {
*
* @param reportName the report name
*/
public ReportMarshaller(String reportName, OutputStream writer, Template template, List<Node> reportTags) {
public ReportMarshaller(String reportName, OutputStream writer, ReportFormat template, List<Node> reportTags) {
init(reportName, new PrintWriter(writer));
temp = template;
for (Node n : reportTags) {
@ -152,7 +149,7 @@ public class ReportMarshaller {
}
/**
* output the Params objects we find
* collect the Params objects annotated on the target object
*
* @param toMarshall the object to output
* @param moduleScanner our scanner, which stores the annotated field information
@ -171,7 +168,7 @@ public class ReportMarshaller {
}
/**
* output the DataPoint objects we find
* collect the DataPoint objects annotated on the target object
*
* @param toMarshall the object to output
* @param moduleScanner our scanner, which stores the annotated field information
@ -194,15 +191,11 @@ public class ReportMarshaller {
*/
public void close() {
try {
// add the data to a map
Map map = new HashMap();
map.put("root", root);
temp.process(map, writeLocation);
temp.write(writeLocation, root);
writeLocation.flush();
} catch (TemplateException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
writeLocation.close();
} catch (IOException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
throw new StingException("IO exception", e);
}
}

68
java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
View File

@ -1,8 +1,9 @@
package org.broadinstitute.sting.playground.utils.report;
import freemarker.template.Configuration;
import freemarker.template.DefaultObjectWrapper;
import freemarker.template.Template;
import org.broadinstitute.sting.playground.utils.report.templates.CSVFormat;
import org.broadinstitute.sting.playground.utils.report.templates.GrepFormat;
import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
import org.broadinstitute.sting.playground.utils.report.templates.TableFormat;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.StingException;
@ -29,30 +30,17 @@ public class VE2ReportFactory {
/** the types of templates we're aware of for VariantEval2 */
public enum VE2TemplateType {
Table("human_readable.ftl"),
Grep("grep_readable.ftl"),
CSV("csv_readable.ftl");
Table(TableFormat.class),
Grep(GrepFormat.class),
CSV(CSVFormat.class);
public String filename;
public Class underlyingReportType;
VE2TemplateType(String file) {
filename = file;
VE2TemplateType(Class<? extends ReportFormat> type) {
underlyingReportType = type;
}
}
/**
* create a list of RM from an mapping of writer to template type
* @param fileset the mapping of files to types
* @param reportTags the tags to append to each report root node
* @return a list of ReportMarshallers to write data to
*/
public static List<ReportMarshaller> getTemplate(Map<Writer,VE2TemplateType> fileset, List<Node> reportTags) {
List<ReportMarshaller> list = new ArrayList<ReportMarshaller>();
for (Writer writer : fileset.keySet())
list.add(new ReportMarshaller("Variant Eval 2 Report",writer,createTemplate(fileset.get(writer)),reportTags));
return list;
}
/**
* create a report ReportMarshaller from a writer, type, and any report tags
* @param writer the output object
@ -60,27 +48,27 @@ public class VE2ReportFactory {
* @param reportTags the tags to append to each report root node
* @return a list of ReportMarshallers to write data to
*/
public static ReportMarshaller getTemplate(OutputStream writer,VE2TemplateType type, List<Node> reportTags) {
return new ReportMarshaller("Variant Eval 2 Report",writer,createTemplate(type),reportTags);
public static ReportMarshaller createMarhsaller(OutputStream writer,VE2TemplateType type, List<Node> reportTags) {
return new ReportMarshaller("Variant Eval 2 Report",writer,createByType(type.underlyingReportType),reportTags);
}
/**
* create a template from the TemplateType
* @param template the template type
* @return a Template object
* create a report formatter with the given type
*
* @param formatType type of the reporter to create.
*
* @return The reporter object if created; null otherwise.
*/
private static Template createTemplate(VE2TemplateType template) {
Configuration cfg = new Configuration();
cfg.setClassForTemplateLoading(VE2ReportFactory.class,ve2templateDir);
cfg.setObjectWrapper(new DefaultObjectWrapper());
Template temp = null;
try {
temp = cfg.getTemplate(template.filename);
} catch (IOException e) {
throw new StingException("Unable to create template file " + template.filename + " of type " + template,e);
}
return temp;
}
public static ReportFormat createByType(Class formatType) {
try {
return ((Class<? extends ReportFormat>) formatType).newInstance();
}
catch (InstantiationException ex) {
throw new StingException(String.format("Unable to instantiate %s", formatType), ex);
}
catch (IllegalAccessException ex) {
throw new StingException(String.format("Unable to access %s", formatType), ex);
}
}
}

29
java/src/org/broadinstitute/sting/playground/utils/report/templates/CSVFormat.java 100644
View File

@ -0,0 +1,29 @@
package org.broadinstitute.sting.playground.utils.report.templates;
/**
* the basic comma seperated value format
*/
public class CSVFormat extends TableBasedFormat {
private final String DIVIDER = ",";
/**
* format the string according to our internal rules
*
* @param str the string to format
* @return a string, properly formatted
*/
@Override
public String formatColumn(String str) {
return str+DIVIDER;
}
/**
* does the output format want to display line breaks (dotted lines)?
*
* @return true if the format uses them
*/
@Override
public boolean displayDashedLineBreaks() {
return false;
}
}

58
java/src/org/broadinstitute/sting/playground/utils/report/templates/GrepFormat.java 100644
View File

@ -0,0 +1,58 @@
package org.broadinstitute.sting.playground.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import java.io.PrintWriter;
import java.io.Writer;
/**
*
* @author aaron
*
* Class GrepFormat
*
* implements the grep output format
*/
public class GrepFormat implements ReportFormat {
private PrintWriter stream;
/**
* write out to the writer, given the root node
* @param baseFile the writer to write to
* @param baseNode the root node
*/
@Override
public void write(Writer baseFile, Node baseNode) {
stream = new PrintWriter(baseFile);
for (Node analysis : baseNode.getChildren()) {
StringBuilder builder = new StringBuilder();
boolean first = true;
for (Node tag : analysis.getChildren()) {
if (first) first = false;
else if (tag.tag) {
builder.append(".");
}
if ( tag.tag ) builder.append("["+tag.getName() + "=" + tag.getValue()+"]");
}
recursiveTraverse(analysis,builder.toString());
}
}
/**
* recursively get the data. If we hit a final node, output the node plus the trailing text
* @param n the node we're looking at
* @param value the previous text we've seen
*/
public void recursiveTraverse(Node n, String value) {
if (n.tag) return;
if (n.getChildren().size() < 1) {
stream.println(value + " " + n.getValue());
}
else {
String nString = n.getName() + "=" +n.getValue();
for (Node child : n.getChildren())
recursiveTraverse(child,value + ".[" + nString + "]");
}
}
}

17
java/src/org/broadinstitute/sting/playground/utils/report/templates/ReportFormat.java 100644
View File

@ -0,0 +1,17 @@
package org.broadinstitute.sting.playground.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import java.io.File;
import java.io.Writer;
/**
* @author aaron
* <p/>
* Interface ReportFormat
* <p/>
* The basics of a report formatter
*/
public interface ReportFormat {
public void write(Writer baseFile, Node baseNode);
}

212
java/src/org/broadinstitute/sting/playground/utils/report/templates/TableBasedFormat.java 100644
View File

@ -0,0 +1,212 @@
package org.broadinstitute.sting.playground.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import java.io.PrintWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* an abstract class to share the basics of a table based format; many methods
* overlap in different output types.
*/
public abstract class TableBasedFormat implements ReportFormat {
private Map<String, List<Node>> analyses = new HashMap<String, List<Node>>();
private PrintWriter stream;
@Override
public void write(Writer writeTo, Node baseNode) {
getAnalyses(baseNode);
stream = new PrintWriter(writeTo);
for (String s : analyses.keySet()) {
writeAnalysis(analyses.get(s));
outputTables(analyses.get(s));
}
}
/**
* break out the analyses by type, given the base node
* @param baseNode the root node
*/
private void getAnalyses(Node baseNode) {
for (Node n : baseNode.getChildren())
if (!n.tag && n.getComplex()) {
if (!analyses.containsKey(n.getValue()))
analyses.put(n.getValue(),new ArrayList<Node>());
analyses.get(n.getValue()).add(n);
}
}
/**
* write the analysis nodes out, only outputting the simple data points (non-table data)
* @param nodes a list of nodes, of the same analysis type
*/
private void writeAnalysis(List<Node> nodes) {
if (nodes.size() < 1 || !nodes.get(0).getName().equals("analysis")) return;
Node forTitle = nodes.get(0);
stream.println(niceDivider(80));
stream.println("Analysis Name: \t" + forTitle.getValue());
stream.println("Analysis Description: \t" + forTitle.getDescription());
stream.println();
String header = extractHeaderString(forTitle);
if (header == null) return; // a null here indicates we don't have any unique columns to display
stream.println(header);
stream.println(niceDivider(header.length()));
for (Node analysis : nodes) {
String dataString = dataPointNodesToValues(analysis);
if (dataString.length() > 0 && !dataString.equals("<null>")) {
stream.print(getTagValues(analysis));
stream.println(dataString);
}
}
stream.println();
stream.println();
}
/**
* output the tables: look at list of analysis nodes (all from the same analysis) and output the table
* @param nodes the list of analysis nodes (of the same underlying type)
*/
public void outputTables(List<Node> nodes) {
Map<String,List<String>> tableRows = new HashMap<String,List<String>>();
Map<String,String> tableHeaders = new HashMap<String,String>();
for (Node analysis : nodes)
for (Node n : analysis.getChildren()) {
if (n.table) {
StringBuilder columnBuilder = new StringBuilder();
getTagNames(analysis,columnBuilder);
for (Node row : n.getChildren()) {
StringBuilder rowBuilder = new StringBuilder();
rowBuilder.append(getTagValues(analysis));
rowBuilder.append(formatColumn(row.getValue()));
columnBuilder.append(formatColumn(row.getName()));
for (Node column : row.getChildren()) {
columnBuilder.append(formatColumn(column.getValue()));
if (column.getChildren().size() == 1) {
String value = formatColumn(column.getChildren().iterator().next().getValue());
rowBuilder.append(value);
}
}
if (!tableRows.containsKey(n.getValue()))
tableRows.put(n.getValue(),new ArrayList<String>());
tableRows.get(n.getValue()).add(rowBuilder.toString());
if (!tableHeaders.containsKey(n.getValue()))
tableHeaders.put(n.getValue(),columnBuilder.toString());
}
}
}
// output the tables
for (String tableName : tableHeaders.keySet()) {
stream.println("Table Name : " + tableName);
stream.println();
stream.println(tableHeaders.get(tableName));
stream.println(niceDivider(tableHeaders.get(tableName).length()));
List<String> rows = tableRows.get(tableName);
for (String row : rows)
stream.println(row);
stream.println();
}
}
/**
* get the header (tag) names
* @param analysis the analysis node
* @return a string representing the tag names
*/
private String getTagValues(Node analysis) {
StringBuilder buffer = new StringBuilder();
for (Node s : analysis.getChildren())
if (s.tag) buffer.append(formatColumn(s.getValue()));
return buffer.toString();
}
/**
* simple data points describe themselves, and have one child that stores their value and it's description. Extract the value and
* convert the list of nodes to a string
* @param analysis the analysis
* @return a String representing the values
*/
private String dataPointNodesToValues(Node analysis) {
StringBuilder builder = new StringBuilder();
for (Node n : analysis.getChildren()) {
if (!n.tag && !n.table) {
if (n.getChildren().size() > 1) throw new IllegalStateException("Simple data points shouldn't have more than one value");
if (n.getChildren().size() == 1)
builder.append(formatColumn(n.getChildren().iterator().next().getValue()));
}
}
return builder.toString();
}
/**
* extract the header string from the base analysis node
*/
private String extractHeaderString(Node analysisNode) {
StringBuilder buffer = new StringBuilder();
// first get the tags
getTagNames(analysisNode, buffer);
if (!getColumnNames(analysisNode, buffer))
return null;
return buffer.toString();
}
/**
* get the column names from the analysis node
* @param analysisNode the node
* @param buffer the buffer to append to
* @return true if there was data fields to output, false if we dont add data to the column header list
*/
private boolean getColumnNames(Node analysisNode, StringBuilder buffer) {
// now get the simple data points
boolean addedValue = false;
for (Node n : analysisNode.getChildren())
if (!n.tag && !n.table) {
addedValue = true;
buffer.append(formatColumn(n.getValue()));
}
return addedValue;
}
/**
* get the tags names from an analysis node
* @param analysisNode the node
* @param buffer the StringBuilder to append to
*/
private void getTagNames(Node analysisNode, StringBuilder buffer) {
for (Node n : analysisNode.getChildren())
if (n.tag) buffer.append(formatColumn(n.getName()));
}
/**
* create a correct-length divider string
* @param length the length for the divider
* @return a string with the divider text of length "length"
*/
private String niceDivider(int length) {
if (!displayDashedLineBreaks()) return "";
StringBuilder builder = new StringBuilder();
for (int x = 0; x < length; x++) builder.append("-");
return builder.toString();
}
/**
* format the string according to our internal rules
* @param str the string to format
* @return a string, properly formatted
*/
public abstract String formatColumn(String str);
/**
* does the output format want to display line breaks (dotted lines)?
* @return true if the format uses them
*/
public abstract boolean displayDashedLineBreaks();
}

42
java/src/org/broadinstitute/sting/playground/utils/report/templates/TableFormat.java 100644
View File

@ -0,0 +1,42 @@
package org.broadinstitute.sting.playground.utils.report.templates;
import org.broadinstitute.sting.playground.utils.report.utils.Node;
import org.broadinstitute.sting.utils.Pair;
import java.io.*;
import java.util.*;
/**
*
* @author aaron
*
* Class TableFormat
*
* implements the table (human readable) format.
*/
public class TableFormat extends TableBasedFormat {
private static final int COLUMN_WIDTH = 25;
/**
* format the string according to our internal rules
*
* @param str the string to format
* @return a string, properly formatted
*/
@Override
public String formatColumn(String str) {
return String.format("%-"+COLUMN_WIDTH+"s",str);
}
/**
* does the output format want to display line breaks (dotted lines)?
*
* @return true if the format uses them
*/
@Override
public boolean displayDashedLineBreaks() {
return true;
}
}

69
java/src/org/broadinstitute/sting/playground/utils/report/templates/human_readable.ftl
View File

@ -6,23 +6,26 @@
Report: ${root.value}
Description: ${root.description}
<#-- get any tags on the root node -->
<#-- get any tags on the root node (any information we've tagged the report with) -->
<#list root.children as tagNode>
<#if tagNode.tag>
Tag: ${tagNode.name} = ${tagNode.value}
</#if>
</#list>
<#list root.children as analysis>
<#list root.childresn as analysis>
<#if analysis.complex>
<#if analysis.value!=currentAnalysis>
<#if analysis.value!=currentAnalysi>
<#assign currentAnalysis=analysis.value>
Analysis: ${analysis.value}
Column names specific to the analysis:
<@emit_column_names_with_descriptions analysis=analysis/>
<@emit_tables analysis=analysis/>
<@emit_tags analysis=analysis/>
<@emit_column_names analysis=analysis/>
@ -32,16 +35,32 @@ Column names specific to the analysis:
</#if>
</#list>
<#-- -------------------- -->
<#-- emit only tables -->
<#macro emit_tables analysis>
<#if analysis.complex && !analysis.tag>
<#list analysis.children as child>
<#if child.table>
<@emit_tags analysis=analysis/>
<#list child.tableRows as rows>
<@emit_tag_values analysis=analysis/>
----------------------------------------------------------------------------------------------------------------------------------------
<#list rows as node>
<@emit_name value=node.value/>
</#list>
</#list>
</#if>
</#list>
</#if>
</#macro>
<#-- -------------------- -->
<#-- get the data tag values -->
<#macro emit_row_values analysis>
<#list analysis.tableRows as rows>
<#list analysis.tableRowsNoTables as rows>
<@emit_tag_values analysis=analysis/>
<#list rows as node>
<#if (node.value?length > colTextWidth)>
<#lt>${(node.value?substring(0, colTextWidth)+"..")?right_pad(colWidth)}<#rt>
<#else>
<#lt>${node.value?right_pad(colWidth)}<#rt>
</#if>
<@emit_name value=node.value/>
</#list>
</#list>
@ -49,38 +68,22 @@ Column names specific to the analysis:
<#-- -------------------- -->
<#-- get the column names -->
<#macro emit_column_names analysis>
<#if analysis.complex && analysis.display>
<#if analysis.complex && !analysis.tag>
<#list analysis.children as child>
<#if child.complex && !child.table>
<@emit_name value=child.value/>
<#elseif child.table>
<#list child.children as rows>
<@emit_name value=rows.name/>
<#list rows.children as cols>
<@emit_name value=cols.value/>
</#list>
<#break>
</#list>
<@emit_name value=child.value/>
</#if>
</#list>
</#if>
</#macro>
<#-- -------------------- -->
<#-- get the column names -->
<#-- get the column names to display at the top of the analysis -->
<#macro emit_column_names_with_descriptions analysis>
<#if analysis.complex && analysis.display>
<#if analysis.complex && !analysis.tag>
<#list analysis.children as child>
<#if child.complex && !child.table>
${child.value?right_pad(40)}${child.description}
<#elseif child.table>
<#list child.children as rows>
${rows.name?right_pad(40)}${rows.description}
<#list rows.children as cols>
${cols.value?right_pad(40)}${cols.description}
</#list>
<#break>
</#list>
</#if>
${child.value?right_pad(40)}${child.description}
</#if>
</#list>
</#if>
</#macro>
@ -104,7 +107,7 @@ Column names specific to the analysis:
</#macro>
<#-- -------------------- -->
<#-- a macro for cleaning up emitted names -->
<#-- a macro for formatting emitted names -->
<#macro emit_name value>
<#if (value?length > colTextWidth)>
<#lt>${(value?substring(0, colTextWidth)+"..")?right_pad(colWidth)}<#rt>

17
java/src/org/broadinstitute/sting/playground/utils/report/utils/ComplexDataUtils.java
View File

@ -31,7 +31,7 @@ public class ComplexDataUtils {
// try to handle maps
else if (obj instanceof Map) {
extractMap(obj, nodes);
throw new UnsupportedOperationException("The report generation system is currently unable to output Maps, due to their ambiguity");
// handle collections
} else if (obj instanceof Collection)
@ -49,21 +49,6 @@ public class ComplexDataUtils {
return nodes;
}
/**
* extract a map object
* @param obj the object (instance of Map)
* @param nodes the node list to add our key->values to
*/
private static void extractMap(Object obj, Collection<Node> nodes) {
for (Object key : ((Map) obj).keySet()) {
Node keyNode = new Node("key", key.toString(), "map key");
nodes.add(keyNode);
keyNode.addAllChildren(resolveObjects(((Map) obj).get(key)));
}
// special case: if the map is empty, add a null node
if (nodes.isEmpty()) nodes.add(new Node("<null>", "<null>", "<null>"));
}
/**
* extract a (hopefully) primitive value
* @param obj the object

7
java/src/org/broadinstitute/sting/playground/utils/report/utils/Node.java
View File

@ -103,7 +103,12 @@ public class Node {
}
public List<List<Node>> getTableRows() {
List<List<Node>> ret = NodeUtils.flattenToRow(this);
List<List<Node>> ret = NodeUtils.flattenToRow(this,false);
return ret;
}
public List<List<Node>> getTableRowsNoTables() {
List<List<Node>> ret = NodeUtils.flattenToRow(this,true);
return ret;
}

12
java/src/org/broadinstitute/sting/playground/utils/report/utils/NodeUtils.java
View File

@ -42,7 +42,7 @@ public class NodeUtils {
return list;
}
public List<List<Node>> toRow(List<List<Node>> oldList) {
public List<List<Node>> toRow(List<List<Node>> oldList, boolean excludeTables) {
// if we're a leaf node that isn't a tag, add it to each list
if (validLeafNode())
addToEachList(oldList);
@ -50,10 +50,10 @@ public class NodeUtils {
// special case: if we've just got a single node, traverse into it
else if (node.getChildren().size() > 0 && !node.table)
for (Node n : node.children) {
oldList = new NodeMarker(n).toRow(oldList);
oldList = new NodeMarker(n).toRow(oldList, excludeTables);
}
// when we encounter a table we want to branch into multiple rows
else if (node.table) {
else if (node.table && !excludeTables) {
List<List<Node>> newList = new ArrayList<List<Node>>();
for (Node child : node.children) {
if (child.display && !child.tag) {
@ -61,7 +61,7 @@ public class NodeUtils {
tempList.add(new ArrayList<Node>());
tempList.get(0).add(child);
NodeMarker marker = new NodeMarker(child);
List<List<Node>> carry = marker.toRow(tempList);
List<List<Node>> carry = marker.toRow(tempList, excludeTables);
newList.addAll(carry);
}
}
@ -90,10 +90,10 @@ public class NodeUtils {
}
// given a node, generate rows (flattening tables)
public static List<List<Node>> flattenToRow(Node n) {
public static List<List<Node>> flattenToRow(Node n, boolean excludeTables) {
NodeMarker fn = new NodeMarker(n);
List<List<Node>> nodesList = new ArrayList<List<Node>>();
nodesList.add(new ArrayList<Node>());
return fn.toRow(nodesList);
return fn.toRow(nodesList, excludeTables);
}
}

10
java/test/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2IntegrationTest.java
View File

@ -18,8 +18,8 @@ public class VariantEval2IntegrationTest extends WalkerTest {
@Test
public void testVE2Simple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000", "d5a8c6550236e971ffe29f7f254ad076");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "529b56760da952741e9d843453a8eb73");
expectations.put("-L 1:1-10,000,000", "32d771b62dadc1c164f19bf3a1efc018");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "de42a239847e3466f4526e4781710ce7");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -39,10 +39,10 @@ public class VariantEval2IntegrationTest extends WalkerTest {
" -B dbsnp_130,dbSNP," + GATKDataLocation + "dbsnp_130_b36.rod" +
" -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
String eqMD5s = "13d2de47f9fe56a4ddfeca10d9c1d5a9"; // next two examples should be the same!
String eqMD5s = "0e961437bec3d4ad28b1511c0c45d13a"; // next two examples should be the same!
expectations.put("", eqMD5s);
expectations.put(" -known comp_hapmap -known dbsnp", eqMD5s);
expectations.put(" -known comp_hapmap", "edd1f32a7f2f0390fdd0cc4c5ff14bf1");
expectations.put(" -known comp_hapmap", "139b10dc0ea968dc035798492ef4ef97");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs2 = entry.getKey();
@ -60,7 +60,7 @@ public class VariantEval2IntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
2,
Arrays.asList("31f8cf5010d4b73b1520acef88207214", "a3ce1d70d8ae3874807e9d61994d42af"));
Arrays.asList("3d4de331f90ef49792d3da3ee9509edc", "a3ce1d70d8ae3874807e9d61994d42af"));
executeTest("testVE2WriteVCF", spec);
}
}

2
java/test/org/broadinstitute/sting/playground/utils/report/ReportMarshallerTest.java
View File

@ -46,7 +46,7 @@ public class ReportMarshallerTest extends BaseTest {
cfg.setObjectWrapper(new DefaultObjectWrapper());
Template temp = null;
try {
temp = cfg.getTemplate("myTestTemp.ftl");
temp = cfg.createMarhsaller("myTestTemp.ftl");
} catch (IOException e) {
e.printStackTrace();
}