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Simple improvements to allele caller 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@254 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-02 14:09:14 +00:00
parent d952790258
commit 2cd9a1597f
2 changed files with 19 additions and 3 deletions
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16
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
View File

@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate; import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.apache.log4j.Logger;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import java.util.List; import java.util.List;
@ -18,7 +19,11 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
{ {
@Argument public int N; @Argument public int N;
@Argument public int DOWNSAMPLE; @Argument public int DOWNSAMPLE;
@Argument public String GFF_OUTPUT_FILE; @Argument(required=false,defaultValue="")
public String GFF_OUTPUT_FILE;
protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class);
Random random; Random random;
PrintStream output; PrintStream output;
@ -29,6 +34,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
String bases = getBases(context); String bases = getBases(context);
double quals[][] = getOneBaseQuals(context); double quals[][] = getOneBaseQuals(context);
logger.debug(String.format("In alleleFrequnecy walker: N=%d, d=%d", N, DOWNSAMPLE));
if ((DOWNSAMPLE != 0) && (DOWNSAMPLE < bases.length())) if ((DOWNSAMPLE != 0) && (DOWNSAMPLE < bases.length()))
{ {
String downsampled_bases = ""; String downsampled_bases = "";
@ -88,6 +95,9 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
} }
} }
} }
logger.debug(String.format(" => result is %s", alleleFreq));
return alleleFreq; return alleleFreq;
} }
@ -447,6 +457,9 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
try try
{ {
this.random = new java.util.Random(0); this.random = new java.util.Random(0);
if ( GFF_OUTPUT_FILE == null )
this.output = out;
else
this.output = new PrintStream(GFF_OUTPUT_FILE); this.output = new PrintStream(GFF_OUTPUT_FILE);
} }
catch (Exception e) catch (Exception e)
@ -467,6 +480,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
try try
{ {
this.output.flush(); this.output.flush();
if ( GFF_OUTPUT_FILE != null )
this.output.close(); this.output.close();
} }
catch (Exception e) catch (Exception e)

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

@ -56,6 +56,8 @@ public class AlleleFrequencyEstimate {
notes); notes);
} }
public String toString() { return asTabularString(); }
public String asString() { public String asString() {
// Print out the called bases // Print out the called bases
// Notes: switched from qhat to qstar because qhat doesn't work at n=1 (1 observed base) where having a single non-ref // Notes: switched from qhat to qstar because qhat doesn't work at n=1 (1 observed base) where having a single non-ref