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

Genotype is Comparable via sampleName

This commit is contained in:
Mark DePristo 2011-11-20 18:26:27 -05:00
parent f9e25081ab
commit 9445326c6c
2 changed files with 13 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
build.xml
View File

@ -927,8 +927,8 @@
<jvmarg value="-Dpipeline.run=${pipeline.run}" /> <jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" /> <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<jvmarg line="${cofoja.jvm.args}"/> <jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> --> <jvmarg value="-Xdebug"/>
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> --> <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/>
<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/> <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false"> <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">

12
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
View File

@ -12,7 +12,7 @@ import java.util.*;
* *
* @author Mark DePristo * @author Mark DePristo
*/ */
public class Genotype { public class Genotype implements Comparable<Genotype> {
public final static String PHASED_ALLELE_SEPARATOR = "|"; public final static String PHASED_ALLELE_SEPARATOR = "|";
public final static String UNPHASED_ALLELE_SEPARATOR = "/"; public final static String UNPHASED_ALLELE_SEPARATOR = "/";
@ -351,4 +351,14 @@ public class Genotype {
public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); } public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); }
public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); } public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); }
public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); } public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
/**
* comparable genotypes -> compareTo on the sample names
* @param genotype
* @return
*/
@Override
public int compareTo(final Genotype genotype) {
return getSampleName().compareTo(genotype.getSampleName());
}
} }