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- take command line arguments 

- output GFF lines to a file (specified by a command line argument)
- improve the GFF output string


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@240 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-31 18:43:00 +00:00
parent 8d601a6a42
commit ede52f7359
3 changed files with 48 additions and 22 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
View File

@ -172,13 +172,8 @@ public class AlleleFrequencyMetricsWalker extends LocusWalker<AlleleFrequencyEst
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{
// Print RESULT data for confident calls
//if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asTabularString()); }
//out.print(alleleFreq.asTabularString());
if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asGFFString()); }
if (this.num_loci_total % 1000 == 0) { printMetrics(); }
return "null";
}

63
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
View File

@ -5,16 +5,23 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import net.sf.samtools.SAMRecord;
import java.util.List;
import java.util.Arrays;
import java.util.Random;
import java.io.PrintStream;
public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, Integer> {
public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String>
{
int N=2;
int DOWNSAMPLE = 0;
java.util.Random random;
@Argument public int N;
@Argument public int DOWNSAMPLE;
@Argument public String GFF_OUTPUT_FILE;
Random random;
PrintStream output;
public AlleleFrequencyEstimate map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context)
{
@ -347,14 +354,17 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
return result;
}
private String confident_interval_start = "";
private double confident_interval_min_LOD = 0;
private double confident_interval_max_LOD = 0;
private boolean inside_confident_interval = false;
public Integer reduceInit() { return 0; }
public Integer reduce(AlleleFrequencyEstimate alleleFreq, Integer sum)
public String reduceInit() { return ""; }
public String reduce(AlleleFrequencyEstimate alleleFreq, String sum)
{
// Print RESULT data for confident calls
if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { System.out.print(alleleFreq.asGFFString()); }
return 0;
if ((alleleFreq.lodVsRef >= 5) || (alleleFreq.lodVsRef <= -5)) { this.output.print(alleleFreq.asGFFString()); }
return "";
}
static int nuc2num[];
@ -376,16 +386,37 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
num2nuc[2] = 'T';
num2nuc[3] = 'G';
this.random = new java.util.Random(0);
try
{
this.random = new java.util.Random(0);
this.output = new PrintStream(GFF_OUTPUT_FILE);
}
catch (Exception e)
{
e.printStackTrace();
System.exit(-1);
}
if (System.getenv("N") != null) { this.N = (new Integer(System.getenv("N"))).intValue(); }
else { this.N = 2; }
if (System.getenv("DOWNSAMPLE") != null) { this.DOWNSAMPLE = (new Integer(System.getenv("DOWNSAMPLE"))).intValue(); }
else { this.DOWNSAMPLE = 0; }
//if (System.getenv("N") != null) { this.N = (new Integer(System.getenv("N"))).intValue(); }
//else { this.N = 2; }
//
//if (System.getenv("DOWNSAMPLE") != null) { this.DOWNSAMPLE = (new Integer(System.getenv("DOWNSAMPLE"))).intValue(); }
//else { this.DOWNSAMPLE = 0; }
}
public void onTraversalDone(String result)
{
try
{
this.output.flush();
this.output.close();
}
catch (Exception e)
{
e.printStackTrace();
System.exit(-1);
}
}
static void print_base_qual_matrix(double [][]quals) {
// Print quals for debugging

2
java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
View File

@ -33,7 +33,7 @@ public class AlleleFrequencyEstimate {
{
String[] tokens;
tokens = location.split(":");
return String.format("%s\tCALLER\tVARIANT\t%s\t%s\t%f\t.\t.\tREF \"%c\"\t;\tALT \"%c\"\t;\tFREQ %f\n",
return String.format("%s\tCALLER\tVARIANT\t%s\t%s\t%f\t.\t.\tREF %c\t;\tALT %c\t;\tFREQ %f\n",
tokens[0],
tokens[1],
tokens[1],