Merge branch 'incoming'

public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java

@@ -32,9 +32,14 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 
+import java.io.File;
 import java.io.PrintStream;
+import java.util.Collection;
+import java.util.Set;
+import java.util.TreeSet;
 
 /**
  * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear
@@ -54,6 +59,13 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
     String platform = null; // E.g. ILLUMINA, 454
     @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
     int nReadsToPrint = -1;
+    @Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line). Can be specified multiple times", required=false)
+    public Set<File> sampleFiles;
+    @Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
+    public Set<String> sampleNames;
+
+    private TreeSet<String> samplesToChoose = new TreeSet<String>();
+    private boolean NO_SAMPLES_SPECIFIED = false;
 
     /**
      * The initialize function.
@@ -61,6 +73,17 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
     public void initialize() {
         if  ( platform != null )
             platform = platform.toUpperCase();
+
+        Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
+        samplesToChoose.addAll(samplesFromFile);
+
+        if (sampleNames != null)
+            samplesToChoose.addAll(sampleNames);
+
+        if(samplesToChoose.isEmpty()) {
+            NO_SAMPLES_SPECIFIED = true;
+        }
+
     }
 
     /**
@@ -87,6 +110,22 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
             if ( readPlatformAttr == null || !readPlatformAttr.toString().toUpperCase().contains(platform))
                 return false;
         }
+        if (!NO_SAMPLES_SPECIFIED )  {
+            // user specified samples to select
+            String readSample = read.getReadGroup().getSample();
+            boolean  found = false;
+            for (String sampleSelected : samplesToChoose) {
+                if (readSample.equalsIgnoreCase(sampleSelected)) {
+                    found = true;
+                    break;
+                }
+
+            }
+
+            if (!found)
+                return false;
+        }
+
 
         // check if we've reached the output limit
         if ( nReadsToPrint == 0 ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java

@@ -24,12 +24,28 @@ public class IndelType implements InfoFieldAnnotation, ExperimentalAnnotation {
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
          int run;
-        if ( vc.isIndel() && vc.isBiallelic() ) {
+        if (vc.isMixed()) {
+            Map<String, Object> map = new HashMap<String, Object>();
+            map.put(getKeyNames().get(0), String.format("%s", "MIXED"));
+            return map;
+
+        }
+        else if ( vc.isIndel() ) {
             String type="";
+            if (!vc.isBiallelic())
+                type = "MULTIALLELIC_INDEL";
+            else {
+                if (vc.isInsertion())
+                    type = "INS.";
+                else if (vc.isDeletion())
+                    type = "DEL.";
+                else
+                    type = "OTHER.";
                 ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
                 for (int k : inds) {
                     type = type+ IndelUtils.getIndelClassificationName(k)+".";
                 }
+            }
             Map<String, Object> map = new HashMap<String, Object>();
             map.put(getKeyNames().get(0), String.format("%s", type));
             return map;

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -96,8 +96,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
     private boolean KEEP_AF_SPECTRUM = false;
 
+    @Hidden
     @Argument(fullName="afFile", shortName="afFile", doc="The output recal file used by ApplyRecalibration", required=false)
-    private File AF_FILE = null;
+    private File AF_FILE = new File("");
 
     @Argument(fullName="family_structure", shortName="family", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
     private String FAMILY_STRUCTURE = "";
@@ -240,7 +241,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + fractionRandom + "% of the variants at random from the variant track");
 
 
-        if (AF_FILE != null) {
+        if (KEEP_AF_SPECTRUM) {
             try {
                 afBreakpoints = new ArrayList<Double>();
                 afBoosts = new ArrayList<Double>();
@@ -328,7 +329,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                     if (SELECT_RANDOM_FRACTION && KEEP_AF_SPECTRUM ) {
                         // ok we have a comp VC and we need to match the AF spectrum of inputAFRodName.
                         // We then pick a variant with probablity AF*desiredFraction
-
                          if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )  {
                             String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY);
 
@@ -354,21 +354,23 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                             // now boost af by table read from file if desired
                             //double bkpt = 0.0;
                             int bkidx = 0;
-                            if (AF_FILE != null) {
+                            if (!afBreakpoints.isEmpty()) {
                                 for ( Double bkpt : afBreakpoints) {
                                     if (af < bkpt + bkDelta)
                                         break;
                                     else bkidx++;
                                 }
-                                afBoost = afBreakpoints.get(bkidx);
+                                if (bkidx >=afBoosts.size())
-                                System.out.format("af:%f bkidx:%d afboost:%f\n",af,bkidx,afBoost);
+                                    bkidx = afBoosts.size()-1;
+                                afBoost = afBoosts.get(bkidx);
+                                //System.out.formatPrin("af:%f bkidx:%d afboost:%f\n",af,bkidx,afBoost);
 
 
 
                             }
 
                             //System.out.format("%s .. %4.4f\n",afo.toString(), af);
-                            if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * af * afBoost)
+                            if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * afBoost *   afBoost)
                                 vcfWriter.add(sub, ref.getBase());
                         }