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Added NullWalker module (do nothing). 

Added SingleSampleGenotyper module (old-school single sample genotyping).

Added Utils.SortPermutation (return the permutaton that would sort the input array).
Added Utils.PermuteArray (apply a permutation to an array).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@29 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-10 21:26:07 +00:00
parent 6b8650b0c0
commit 716af47dd5
4 changed files with 284 additions and 0 deletions
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2
java/src/edu/mit/broad/sting/atk/AnalysisTK.java
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@ -37,6 +37,8 @@ public class AnalysisTK extends CommandLineProgram {
addModule("CountReads", new CountReadsWalker()); addModule("CountReads", new CountReadsWalker());
addModule("PrintReads", new PrintReadsWalker()); addModule("PrintReads", new PrintReadsWalker());
addModule("Base_Quality_Histogram", new BaseQualityHistoWalker()); addModule("Base_Quality_Histogram", new BaseQualityHistoWalker());
addModule("SingleSampleGenotyper", new SingleSampleGenotyper());
addModule("Null", new NullWalker());
} }
private TraversalEngine engine = null; private TraversalEngine engine = null;

44
java/src/edu/mit/broad/sting/atk/modules/NullWalker.java 100644
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@ -0,0 +1,44 @@
package edu.mit.broad.sting.atk.modules;
import edu.mit.broad.sting.atk.LocusWalker;
import edu.mit.broad.sting.atk.LocusIterator;
import edu.mit.broad.sting.utils.ReferenceOrderedDatum;
import edu.mit.broad.sting.utils.rodDbSNP;
import edu.mit.broad.sting.utils.Utils;
import net.sf.samtools.SAMRecord;
import java.util.List;
// Null traversal. For ATK performance measuring.
// j.maguire 3-7-2009
public class NullWalker implements LocusWalker<Integer, Integer> {
public void initialize() {
}
public String walkerType() { return "ByLocus"; }
// Do we actually want to operate on the context?
public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
return true; // We are keeping all the reads
}
// Map over the edu.mit.broad.sting.atk.LocusContext
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context)
{
return 1;
}
// Given result of map function
public Integer reduceInit()
{
return 0;
}
public Integer reduce(Integer value, Integer sum)
{
return 0;
}
public void onTraveralDone() {
}
}

149
java/src/edu/mit/broad/sting/atk/modules/SingleSampleGenotyper.java 100644
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@ -0,0 +1,149 @@
package edu.mit.broad.sting.atk.modules;
import edu.mit.broad.sting.atk.LocusWalker;
import edu.mit.broad.sting.atk.LocusIterator;
import edu.mit.broad.sting.utils.ReferenceOrderedDatum;
import edu.mit.broad.sting.utils.rodDbSNP;
import edu.mit.broad.sting.utils.Utils;
import net.sf.samtools.SAMRecord;
import java.util.List;
// Draft single sample genotyper
// j.maguire 3-7-2009
public class SingleSampleGenotyper implements LocusWalker<Integer, Integer> {
public void initialize() {
}
public String walkerType() { return "ByLocus"; }
// Do we actually want to operate on the context?
public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
return true; // We are keeping all the reads
}
protected class GenotypeLikelihoods
{
public double[] likelihoods;
public String[] genotypes;
GenotypeLikelihoods()
{
likelihoods = new double[10];
genotypes = new String[10];
genotypes[0] = "AA";
genotypes[1] = "AC";
genotypes[2] = "AG";
genotypes[3] = "AT";
genotypes[4] = "CC";
genotypes[5] = "CG";
genotypes[6] = "CT";
genotypes[7] = "GG";
genotypes[8] = "GT";
genotypes[9] = "TT";
}
void add(char ref, char read, byte qual)
{
double p_error = Math.pow(10.0, (double)qual / -10);
for (int i = 0; i < genotypes.length; i++)
{
likelihoods[i] += AlleleLikelihood(ref, read, genotypes[i], p_error);
}
}
double AlleleLikelihood(char ref, char read, String genotype, double p_error)
{
char h1 = genotype.charAt(0);
char h2 = genotype.charAt(1);
double p_base;
if ((h1 == h2) && (h1 == read)) { p_base = Math.log10(1-p_error); }
else if ((h1 != h2) && (h1 == read) || (h2 == read)) { p_base = Math.log10(0.5 - (p_error/2.0)); }
else { p_base = Math.log10(p_error); }
return p_base;
}
public String toString()
{
Integer[] permutation = Utils.SortPermutation(likelihoods);
String[] sorted_genotypes = Utils.PermuteArray(genotypes, permutation);
double[] sorted_likelihoods = Utils.PermuteArray(likelihoods, permutation);
String s = "";
for (int i = sorted_genotypes.length-1; i >= 0; i--)
{
if (i != sorted_genotypes.length-1) { s = s + " "; }
s = s + sorted_genotypes[i] + ":" + sorted_likelihoods[i];
}
return s;
}
}
// Map over the edu.mit.broad.sting.atk.LocusContext
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
//System.out.printf("Reads %s:%d %d%n", context.getContig(), context.getPosition(), context.getReads().size());
//for ( SAMRecord read : context.getReads() ) {
// System.out.println(" -> " + read.getReadName());
//}
List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets();
String bases = "";
String quals = "";
//String offsetString = "";
// Look up hapmap and dbsnp priors
String rodString = "";
for ( ReferenceOrderedDatum datum : rodData )
{
if ( datum != null )
{
if ( datum instanceof rodDbSNP)
{
rodDbSNP dbsnp = (rodDbSNP)datum;
rodString += dbsnp.toMediumString();
}
else
{
rodString += datum.toSimpleString();
}
}
}
if ( rodString != "" )
rodString = "[ROD: " + rodString + "]";
// Accumulate genotype likelihoods
GenotypeLikelihoods G = new GenotypeLikelihoods();
for ( int i = 0; i < reads.size(); i++ )
{
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
bases += read.getReadString().charAt(offset);
quals += read.getBaseQualityString().charAt(offset);
G.add(ref, read.getReadString().charAt(offset), read.getBaseQualities()[offset]);
}
if ( context.getLocation().getStart() % 1 == 0 ) {
//System.out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString);
System.out.printf("%s %s %s %s\n", ref, bases, G.toString(), rodString);
}
return 1;
}
// Given result of map function
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) {
return value + sum;
}
public void onTraveralDone() {
}
}

89
java/src/edu/mit/broad/sting/utils/Utils.java
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@ -108,4 +108,93 @@ public class Utils {
GenomeLoc.setContigOrdering(refContigOrdering); GenomeLoc.setContigOrdering(refContigOrdering);
} }
// Java Generics can't do primitive types, so I had to do this the simplistic way
public static Integer[] SortPermutation(final int[] A)
{
class comparator implements Comparator
{
public int compare(Object a, Object b)
{
if (A[(Integer)a] < A[(Integer)b]) { return -1; }
if (A[(Integer)a] == A[(Integer)b]) { return 0; }
if (A[(Integer)a] > A[(Integer)b]) { return 1; }
return 0;
}
}
Integer[] permutation = new Integer[A.length];
for (int i = 0; i < A.length; i++)
{
permutation[i] = i;
}
Arrays.sort(permutation, new comparator());
return permutation;
}
public static Integer[] SortPermutation(final double[] A)
{
class comparator implements Comparator
{
public int compare(Object a, Object b)
{
if (A[(Integer)a] < A[(Integer)b]) { return -1; }
if (A[(Integer)a] == A[(Integer)b]) { return 0; }
if (A[(Integer)a] > A[(Integer)b]) { return 1; }
return 0;
}
}
Integer[] permutation = new Integer[A.length];
for (int i = 0; i < A.length; i++)
{
permutation[i] = i;
}
Arrays.sort(permutation, new comparator());
return permutation;
}
public static int[] PermuteArray(int[] array, Integer[] permutation)
{
int[] output = new int[array.length];
for (int i = 0; i < output.length; i++)
{
output[i] = array[permutation[i]];
}
return output;
}
public static double[] PermuteArray(double[] array, Integer[] permutation)
{
double[] output = new double[array.length];
for (int i = 0; i < output.length; i++)
{
output[i] = array[permutation[i]];
}
return output;
}
public static Object[] PermuteArray(Object[] array, Integer[] permutation)
{
Object[] output = new Object[array.length];
for (int i = 0; i < output.length; i++)
{
output[i] = array[permutation[i]];
}
return output;
}
public static String[] PermuteArray(String[] array, Integer[] permutation)
{
String[] output = new String[array.length];
for (int i = 0; i < output.length; i++)
{
output[i] = array[permutation[i]];
}
return output;
}
} }