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Simple tool for picking sequenom probes for SNPs. Can be extended to indels if necessary. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1780 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-10-07 23:46:41 +00:00
parent 1905b5defa
commit 02d2492d68
1 changed files with 108 additions and 0 deletions
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108
java/src/org/broadinstitute/sting/playground/gatk/walkers/PickSequenomProbes.java 100755
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package org.broadinstitute.sting.playground.gatk.walkers;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.io.*;
import java.util.*;
@WalkerName("PickSequenomProbes")
@Requires(value={DataSource.REFERENCE})
@Reference(window=@Window(start=-200,stop=200))
public class PickSequenomProbes extends RefWalker<String, String>
{
@Argument(required=false, shortName="snp_mask", doc="positions to be masked with N's") public String SNP_MASK = null;
ArrayList<GenomeLoc> mask = null;
Object[] mask_array = null;
public void initialize()
{
System.out.printf("Loading SNP mask... ");
if (SNP_MASK != null)
{
mask = new ArrayList<GenomeLoc>();
mask.addAll(GenomeLocParser.intervalFileToList(SNP_MASK));
Object[] temp_array = mask.toArray();
mask_array = new GenomeLoc[temp_array.length];
for (int i = 0; i < temp_array.length; i++) { mask_array[i] = (GenomeLoc)temp_array[i]; }
Arrays.sort(mask_array);
}
System.out.printf("Done.\n");
}
private boolean in_mask(GenomeLoc loc)
{
return (Arrays.binarySearch(mask_array, loc) >= 0);
}
public String map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context)
{
String refBase = String.valueOf(ref.getBase());
System.out.printf("Probing " + ref.getLocus() + " " + ref.getWindow() + "\n");
Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
Variation snp = null;
while (rods.hasNext())
{
ReferenceOrderedDatum rod = rods.next();
if (!(rod instanceof Variation))
continue;
Variation variant = (Variation) rod;
if (variant.isSNP())
{
snp = variant;
}
}
String contig = context.getLocation().getContig();
long offset = context.getLocation().getStart();
char[] context_bases = ref.getBases();
long true_offset = offset - 400;
for (long i = 0; i < 401; i++)
{
GenomeLoc loc = GenomeLocParser.parseGenomeLoc(context.getLocation().getContig() + ":" + true_offset + "-" + true_offset);
if (in_mask(loc)) { context_bases[(int)i] = 'N'; }
true_offset += 1;
}
char[] leading_bases = Arrays.copyOfRange(context_bases, 0, 200);
char[] trailing_bases = Arrays.copyOfRange(context_bases, 201, 401);
if (snp != null)
{
String snp_string = new String(leading_bases) + new String("[" + refBase + "/" + snp.getAlternativeBaseForSNP() + "]") + new String(trailing_bases);
String fasta_string = new String(">" + context.getLocation().toString() + "_" + ref.getWindow().toString());
return fasta_string + "\n" + snp_string + "\n";
}
else
{
return "";
}
}
public String reduceInit()
{
return "";
}
public String reduce(String data, String sum)
{
out.print(data);
return "";
}
public void onTraversalDone(String sum)
{
}
}