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Working on reference ordered data; added build.xml for ant! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@14 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-01 18:27:32 +00:00
parent f64f3e2d90
commit 0ee2375292
3 changed files with 67 additions and 12 deletions
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38
java/build.xml 100644
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@ -0,0 +1,38 @@
<project name="AnalysisTK" default="dist" basedir=".">
<description>
simple build file
</description>
<!-- set global properties for this build -->
<property name="src" location="trunk/java/"/>
<property name="build" location="out/production/AnalysisTK"/>
<property name="dist" location="dist"/>
<target name="init">
<!-- Create the time stamp -->
<tstamp/>
<!-- Create the build directory structure used by compile -->
<mkdir dir="${build}"/>
</target>
<target name="compile" depends="init"
description="compile the source " >
<!-- Compile the java code from ${src} into ${build} -->
<javac srcdir="${src}" destdir="${build}"/>
</target>
<target name="dist" depends="compile"
description="generate the distribution" >
<!-- Create the distribution directory -->
<mkdir dir="${dist}/lib"/>
<!-- Put everything in ${build} into the MyProject-${DSTAMP}.jar file -->
<jar jarfile="${dist}/AnalysisTK-${DSTAMP}.jar" basedir="${build}"/>
</target>
<target name="clean"
description="clean up" >
<!-- Delete the ${build} and ${dist} directory trees -->
<delete dir="${build}"/>
<delete dir="${dist}"/>
</target>
</project>

6
java/src/edu/mit/broad/sting/atk/AnalysisTK.java
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@ -25,6 +25,7 @@ public class AnalysisTK extends CommandLineProgram {
@Option(shortName="B", doc="Debugging output", optional=true) public String DEBUGGING_STR = null;
@Option(shortName="L", doc="Genome region to operation on: from chr:start-end", optional=true) public String REGION_STR = null;
@Option(shortName="T", doc="Type of analysis to run") public String Analysis_Name = null;
@Option(shortName="DBSNP", doc="DBSNP file", optional=true) public String DBSNP_FILE = null;
public static HashMap<String, Object> MODULES = new HashMap<String,Object>();
public static void addModule(final String name, final Object walker) {
@ -60,6 +61,11 @@ public class AnalysisTK extends CommandLineProgram {
//dbsnp.testMe();
rods = new ReferenceOrderedData[] { dbsnp }; // { gff, dbsnp };
}
else if ( DBSNP_FILE != null ) {
ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class );
//dbsnp.testMe();
rods = new ReferenceOrderedData[] { dbsnp }; // { gff, dbsnp };
}
else {
rods = new ReferenceOrderedData[] {}; // { gff, dbsnp };
}

33
java/src/edu/mit/broad/sting/utils/ReferenceOrderedData.java
View File

@ -2,6 +2,7 @@ package edu.mit.broad.sting.utils;
import java.io.File;
import java.util.Iterator;
import edu.mit.broad.picard.util.TabbedTextFileParser;
/**
* Class for representing arbitrary reference ordered data sets
@ -30,9 +31,14 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
//
// ----------------------------------------------------------------------
public void testMe() {
ReferenceOrderedDatum last = null;
for ( ReferenceOrderedDatum rec : this ) {
System.out.println(rec.toString());
if ( last == null || ! last.getContig().equals(rec.getContig()) ) {
System.out.println(rec.toString());
}
last = rec;
}
System.exit(1);
}
// ----------------------------------------------------------------------
@ -41,10 +47,11 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
//
// ----------------------------------------------------------------------
private class SimpleRODIterator implements Iterator<ROD> {
private WhitespaceTextFileParser parser = null;
//private WhitespaceTextFileParser parser = null;
private TabbedTextFileParser parser = null;
public SimpleRODIterator() {
parser = new WhitespaceTextFileParser(true, file);
parser = new TabbedTextFileParser(true, file);
}
public boolean hasNext() {
@ -81,9 +88,11 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
// Otherwise we return the first object who's start is at pos
//
public ROD seekForward(final String contigName, final int pos) {
final boolean DEBUG = false;
ROD result = null;
//System.out.printf(" *** starting seek to %s %d %s%n", contigName, pos, prev);
if ( DEBUG ) System.out.printf(" *** starting seek to %s %d %s%n", contigName, pos, prev);
while ( hasNext() ) {
ROD current = next();
//System.out.printf(" -> Seeking to %s %d AT %s %d%n", contigName, pos, current.getContig(), current.getStart());
@ -102,18 +111,20 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
}
}
else if ( strCmp < 0 ) {
if ( DEBUG ) System.out.printf(" -> Jumping to contig %s%n", contigName);
// We've gone past the desired contig, break
break;
}
}
/*
if ( result == null )
;
//System.out.printf(" --- seek result to %s %d is NULL%n", contigName, pos);
else
System.out.printf(" ### Found %s %d%n", result.getContig(), result.getStart());
*/
if ( DEBUG ) {
if ( result == null )
;
//System.out.printf(" --- seek result to %s %d is NULL%n", contigName, pos);
else
System.out.printf(" ### Found %s %d%n", result.getContig(), result.getStart());
}
// we ran out of elements or found something
return result;