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rod's now have names. Use getName() to access it. Next step is better interface to accessing rods 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-03 16:41:33 +00:00
parent 5019971290
commit edc44807af
8 changed files with 52 additions and 17 deletions
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21
doc/Genome Analysis TK plan.omniplan/contents.xml
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@ -28,9 +28,9 @@
<key>GanttGroupShading</key> <key>GanttGroupShading</key>
<false/> <false/>
<key>GanttVisibleRect</key> <key>GanttVisibleRect</key>
<string>{{-35, 124}, {1025, 1033}}</string> <string>{{-35, 141}, {1025, 1033}}</string>
<key>OutlineVisibleRect</key> <key>OutlineVisibleRect</key>
<string>{{0, 124}, {789, 1033}}</string> <string>{{0, 141}, {789, 1033}}</string>
<key>ScaleWidths</key> <key>ScaleWidths</key>
<dict> <dict>
<key>Automatic</key> <key>Automatic</key>
@ -587,7 +587,7 @@
<key>taskDifferenceEngine</key> <key>taskDifferenceEngine</key>
<dict> <dict>
<key>nextId</key> <key>nextId</key>
<integer>111</integer> <integer>112</integer>
</dict> </dict>
<key>taskUserKeys</key> <key>taskUserKeys</key>
<array/> <array/>
@ -1373,6 +1373,7 @@
<integer>83</integer> <integer>83</integer>
<integer>95</integer> <integer>95</integer>
<integer>96</integer> <integer>96</integer>
<integer>111</integer>
</array> </array>
<key>objectId</key> <key>objectId</key>
<integer>41</integer> <integer>41</integer>
@ -2391,6 +2392,18 @@
<key>workTime</key> <key>workTime</key>
<real>8</real> <real>8</real>
</dict> </dict>
<dict>
<key>effort</key>
<real>28800</real>
<key>objectId</key>
<integer>111</integer>
<key>task</key>
<string>Fix rodDBSNP</string>
<key>workSeconds</key>
<real>28800</real>
<key>workTime</key>
<real>8</real>
</dict>
</array> </array>
<key>topResources</key> <key>topResources</key>
<array> <array>
@ -2401,7 +2414,7 @@
<integer>-1</integer> <integer>-1</integer>
</array> </array>
<key>uuid</key> <key>uuid</key>
<string>E50852A9-C0BE-452A-A050-4FF83DEF06D7</string> <string>85860500-DAB8-4D75-95EE-F86F00907D5D</string>
<key>version</key> <key>version</key>
<integer>2</integer> <integer>2</integer>
</dict> </dict>

8
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -158,21 +158,21 @@ public class GenomeAnalysisTK extends CommandLineProgram {
List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum> >(); List<ReferenceOrderedData<? extends ReferenceOrderedDatum> > rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum> >();
if ( TEST_ROD ) { if ( TEST_ROD ) {
ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>(new File("trunk/data/gFFTest.gff"), rodGFF.class ); ReferenceOrderedData<rodGFF> gff = new ReferenceOrderedData<rodGFF>("test", new File("trunk/data/gFFTest.gff"), rodGFF.class );
gff.testMe(); gff.testMe();
//ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class ); //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class );
ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class ); ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>("dbSNP", new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class );
//dbsnp.testMe(); //dbsnp.testMe();
rods.add(dbsnp); // { gff, dbsnp }; rods.add(dbsnp); // { gff, dbsnp };
} else { } else {
if ( DBSNP_FILE != null ) { if ( DBSNP_FILE != null ) {
ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>(new File(DBSNP_FILE), rodDbSNP.class ); ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>("dbSNP", new File(DBSNP_FILE), rodDbSNP.class );
//dbsnp.testMe(); //dbsnp.testMe();
rods.add(dbsnp); // { gff, dbsnp }; rods.add(dbsnp); // { gff, dbsnp };
} }
if ( HAPMAP_FILE != null ) { if ( HAPMAP_FILE != null ) {
ReferenceOrderedData<HapMapAlleleFrequenciesROD> hapmap = new ReferenceOrderedData<HapMapAlleleFrequenciesROD>(new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class ); ReferenceOrderedData<HapMapAlleleFrequenciesROD> hapmap = new ReferenceOrderedData<HapMapAlleleFrequenciesROD>("hapmap", new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class );
//dbsnp.testMe(); //dbsnp.testMe();
rods.add(hapmap); // { gff, dbsnp }; rods.add(hapmap); // { gff, dbsnp };
} }

3
java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java
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@ -35,6 +35,9 @@ public class HapMapAlleleFrequenciesROD extends ReferenceOrderedDatum {
public Integer varCounts; // maybe we don't need these? public Integer varCounts; // maybe we don't need these?
public Integer totalCounts; // maybe we don't need these? public Integer totalCounts; // maybe we don't need these?
public HapMapAlleleFrequenciesROD(String name) {
super(name);
}
public GenomeLoc getLocation() { return loc; } public GenomeLoc getLocation() { return loc; }

16
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
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@ -7,6 +7,8 @@ import java.io.FileNotFoundException;
import java.util.Iterator; import java.util.Iterator;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import edu.mit.broad.picard.util.TabbedTextFileParser; import edu.mit.broad.picard.util.TabbedTextFileParser;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
@ -23,12 +25,14 @@ import org.broadinstitute.sting.utils.Utils;
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements Iterable<ROD> { public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements Iterable<ROD> {
private String name;
private File file = null; private File file = null;
private Class<ROD> type = null; // runtime type information for object construction private Class<ROD> type = null; // runtime type information for object construction
public ReferenceOrderedData(File file, Class<ROD> type ) { public ReferenceOrderedData(final String name, File file, Class<ROD> type ) {
this.file = file; this.file = file;
this.type = type; this.type = type;
this.name = name;
} }
public RODIterator iterator() { public RODIterator iterator() {
@ -232,7 +236,9 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
ROD parseLine(final String[] parts) { ROD parseLine(final String[] parts) {
//System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts)); //System.out.printf("Parsing GFFLine %s%n", Utils.join(" ", parts));
try { try {
ROD obj = type.newInstance(); //ROD obj = type.newInstance();
Constructor c = type.getConstructor(String.class);
ROD obj = (ROD)c.newInstance(name);
obj.parseLine(parts); obj.parseLine(parts);
return obj; return obj;
} catch ( java.lang.InstantiationException e ) { } catch ( java.lang.InstantiationException e ) {
@ -241,6 +247,12 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
} catch ( java.lang.IllegalAccessException e ) { } catch ( java.lang.IllegalAccessException e ) {
System.out.println(e); System.out.println(e);
return null; // wow, unsafe! return null; // wow, unsafe!
} catch ( java.lang.NoSuchMethodException e ) {
System.out.println(e);
return null; // wow, unsafe!
} catch ( InvocationTargetException e ) {
System.out.println(e);
return null; // wow, unsafe!
} }
} }
} }

7
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java
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@ -10,8 +10,13 @@ import org.broadinstitute.sting.utils.GenomeLoc;
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
public abstract class ReferenceOrderedDatum implements Comparable<ReferenceOrderedDatum> { public abstract class ReferenceOrderedDatum implements Comparable<ReferenceOrderedDatum> {
protected String name;
public ReferenceOrderedDatum() { } public ReferenceOrderedDatum(String name) {
this.name = name;
}
public String getName() { return this.name; }
public abstract void parseLine(final String[] parts); public abstract void parseLine(final String[] parts);

4
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
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@ -52,7 +52,9 @@ public class rodDbSNP extends ReferenceOrderedDatum implements AllelicVariant {
// Constructors // Constructors
// //
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
public rodDbSNP() {} public rodDbSNP(final String name) {
super(name);
}
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
// //

4
java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
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@ -29,8 +29,8 @@ public class rodGFF extends ReferenceOrderedDatum {
// Constructors // Constructors
// //
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
public rodGFF() { public rodGFF(final String name) {
super(name);
} }
public void setValues(final String contig, final String source, final String feature, public void setValues(final String contig, final String source, final String feature,

4
java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
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@ -49,7 +49,7 @@ public class PrepareROD extends CommandLineProgram {
Class<? extends ReferenceOrderedDatum> rodClass = Types.get(ROD_TYPE.toLowerCase()); Class<? extends ReferenceOrderedDatum> rodClass = Types.get(ROD_TYPE.toLowerCase());
ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = new ReferenceOrderedData(new File(ROD_FILE), rodClass ); ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = new ReferenceOrderedData("ROD", new File(ROD_FILE), rodClass );
try { try {
rod.validateFile(); rod.validateFile();
} catch ( Exception e ) { } catch ( Exception e ) {
@ -68,7 +68,7 @@ public class PrepareROD extends CommandLineProgram {
} }
System.out.printf("Validating output file %s%n", rodData.size(), OUTPUT_FILE); System.out.printf("Validating output file %s%n", rodData.size(), OUTPUT_FILE);
ReferenceOrderedData outputRod = new ReferenceOrderedData(new File(OUTPUT_FILE), rodClass ); ReferenceOrderedData outputRod = new ReferenceOrderedData("ROD", new File(OUTPUT_FILE), rodClass );
try { try {
outputRod.validateFile(); outputRod.validateFile();
//outputRod.hasSameContents(ROD_FILE); //outputRod.hasSameContents(ROD_FILE);