Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java

@@ -60,24 +60,12 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
         if ( format.equals("") ) {
             this.format = "%s";
             this.dataType = GATKReportDataType.Unknown;
-            if ( defaultValue != null ) {
+            this.defaultValue = (defaultValue != null) ? defaultValue : "";
-                this.defaultValue = defaultValue;
-                //this.dataType = GATKReportDataType.fromObject(defaultValue);
-            }
-            else {
-                this.defaultValue = "";
-                //this.dataType = GATKReportDataType.Unknown;
-            }
         }
         else {
             this.format = format;
             this.dataType = GATKReportDataType.fromFormatString(format);
-            if ( defaultValue == null ) {
+            this.defaultValue = (defaultValue != null) ? defaultValue : dataType.getDefaultValue();
-                this.defaultValue = dataType.getDefaultValue();
-            }
-            else {
-                this.defaultValue = defaultValue;
-            }
         }
     }
 
@@ -225,8 +213,10 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
     public Object put(Object key, Object value) {
         if (value != null) {
             String formatted = formatValue(value);
-            updateMaxWidth(formatted);
+            if (!formatted.equals("")) {
-            updateFormat(formatted);
+                updateMaxWidth(formatted);
+                updateFormat(formatted);
+            }
         }
         return super.put(key, value);        
     }
@@ -236,7 +226,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
     }
 
     private void updateFormat(String formatted) {
-        if (!isRightAlign(formatted))
+        if (alignment == GATKReportColumnFormat.Alignment.RIGHT)
-            alignment = GATKReportColumnFormat.Alignment.LEFT;
+            alignment = isRightAlign(formatted) ? GATKReportColumnFormat.Alignment.RIGHT : GATKReportColumnFormat.Alignment.LEFT;
     }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDataManager.java

@@ -313,7 +313,7 @@ public class RecalDataManager {
      * @param read The read to adjust
      * @param RAC  The list of shared command line arguments
      */
-    public static void parseSAMRecord(final GATKSAMRecord read, final RecalibrationArgumentCollection RAC) {
+    public static void parsePlatformForRead(final GATKSAMRecord read, final RecalibrationArgumentCollection RAC) {
         GATKSAMReadGroupRecord readGroup = read.getReadGroup();
 
         if (RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) {
@@ -337,47 +337,47 @@ public class RecalDataManager {
     }
 
     /**
-     * Parse through the color space of the read and add a new tag to the SAMRecord that says which bases are inconsistent with the color space
+     * Parse through the color space of the read and add a new tag to the SAMRecord that says which bases are 
+     * inconsistent with the color space. If there is no call in the color space, this method returns true meaning
+     * this read should be skipped
      *
-     * @param read The SAMRecord to parse
+     * @param strategy the strategy used for SOLID no calls
+     * @param read     The SAMRecord to parse
+     * @return whether or not this read should be skipped   
      */
-    public static void parseColorSpace(final GATKSAMRecord read) {
+    public static boolean checkColorSpace(final SOLID_NOCALL_STRATEGY strategy, final GATKSAMRecord read) {
-
+        if (ReadUtils.isSOLiDRead(read)) {                                                                              // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
-        // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
+            if (read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null) {                            // Haven't calculated the inconsistency array yet for this read
-        if (ReadUtils.isSOLiDRead(read)) {
-            if (read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read
                 final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG);
                 if (attr != null) {
                     byte[] colorSpace;
-                    if (attr instanceof String) {
+                    if (attr instanceof String)
                         colorSpace = ((String) attr).getBytes();
-                    }
+                    else
-                    else {
                         throw new UserException.MalformedBAM(read, String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
-                    }
+                    
-
+                    byte[] readBases = read.getReadBases();                                                             // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read
-                    // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read
+                    if (read.getReadNegativeStrandFlag())
-                    byte[] readBases = read.getReadBases();
-                    if (read.getReadNegativeStrandFlag()) {
                         readBases = BaseUtils.simpleReverseComplement(read.getReadBases());
-                    }
+
                     final byte[] inconsistency = new byte[readBases.length];
-                    int iii;
+                    int i;
-                    byte prevBase = colorSpace[0]; // The sentinel
+                    byte prevBase = colorSpace[0];                                                                      // The sentinel
-                    for (iii = 0; iii < readBases.length; iii++) {
+                    for (i = 0; i < readBases.length; i++) {
-                        final byte thisBase = getNextBaseFromColor(read, prevBase, colorSpace[iii + 1]);
+                        final byte thisBase = getNextBaseFromColor(read, prevBase, colorSpace[i + 1]);
-                        inconsistency[iii] = (byte) (thisBase == readBases[iii] ? 0 : 1);
+                        inconsistency[i] = (byte) (thisBase == readBases[i] ? 0 : 1);
-                        prevBase = readBases[iii];
+                        prevBase = readBases[i];
                     }
                     read.setAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency);
+                }
+                else if (strategy == SOLID_NOCALL_STRATEGY.THROW_EXCEPTION)                                             // if the strategy calls for an exception, throw it
+                    throw new UserException.MalformedBAM(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() + " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias.");
 
-                }
+                else
-                else {
+                    return false;                                                                                       // otherwise, just skip the read
-                    throw new UserException.MalformedBAM(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() +
-                            " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias.");
-                }
             }
         }
+        return true;
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java

@@ -109,7 +109,6 @@ public class RecalDatum extends RecalDatumOptimized {
 
     public final void resetCalculatedQualities() {
         empiricalQuality = 0.0;
-        estimatedQReported = 0.0;
     }
 
     private double calcExpectedErrors() {

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReport.java

@@ -24,7 +24,7 @@ public class RecalibrationReport {
     GATKReportTable argumentTable;                                                                                      // keep the argument table untouched just for output purposes
     RecalibrationArgumentCollection RAC;                                                                                // necessary for quantizing qualities with the same parameter | todo -- this should be a new parameter, not necessarily coming from the original table parameter list
     
-    private static String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check that needs propagate through the code";
+    private static String UNRECOGNIZED_REPORT_TABLE_EXCEPTION = "Unrecognized table. Did you add an extra required covariate? This is a hard check.";
 
     public RecalibrationReport(final File RECAL_FILE) {
         GATKReport report = new GATKReport(RECAL_FILE);
@@ -77,10 +77,11 @@ public class RecalibrationReport {
     /**
      * Combines two recalibration reports by adding all observations and errors
      * 
-     * Note: This method DOES NOT recalculate the empirical qualities and quantized qualities. You have to recalculate them
+     * Note: This method DOES NOT recalculate the empirical qualities and quantized qualities. You have to recalculate
-     * after combining. The reason for not calculating it is because this function is inteded for combining a series of 
+     * them after combining. The reason for not calculating it is because this function is inteded for combining a
-     * recalibration reports, and it only makes sense to calculate the empirical qualities and quantized qualities after all 
+     * series of recalibration reports, and it only makes sense to calculate the empirical qualities and quantized
-     * the recalibration reports have been combined. Having the user recalculate when appropriate, makes this method faster
+     * qualities after all the recalibration reports have been combined. Having the user recalculate when appropriate,
+     * makes this method faster
      *
      * Note2: The empirical quality reported, however, is recalculated given its simplicity.
      * 
@@ -97,7 +98,7 @@ public class RecalibrationReport {
                 if (thisDatum == null)
                     thisDatum = otherDatum;                                                                             // sometimes the datum in other won't be present in 'this'. So just assign it!
                 else
-                    thisDatum.increment(otherDatum);                                                                    // add the two datum objects into 'this'
+                    thisDatum.combine(otherDatum);                                                                      // add the two datum objects into 'this'
                 thisDatum.resetCalculatedQualities();                                                                   // reset the empirical quality to make sure the user doesn't forget to recalculate it
             }            
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -222,7 +222,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
             verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tMLE\tMAP");
 
         annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
-        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, 2*samples.size());
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, UnifiedGenotyperEngine.DEFAULT_PLOIDY);
 
         // initialize the header
         Set<VCFHeaderLine> headerInfo = getHeaderInfo();

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -51,6 +51,8 @@ import java.util.*;
 
 public class UnifiedGenotyperEngine {
     public static final String LOW_QUAL_FILTER_NAME = "LowQual";
+    
+    public static final int DEFAULT_PLOIDY = 2;
 
     public enum OUTPUT_MODE {
         /** produces calls only at variant sites */
@@ -95,7 +97,8 @@ public class UnifiedGenotyperEngine {
     private final Logger logger;
     private final PrintStream verboseWriter;
 
-    // number of chromosomes (2 * samples) in input
+    // number of chromosomes (ploidy * samples) in input
+    private final int ploidy;
     private final int N;
 
     // the standard filter to use for calls below the confidence threshold but above the emit threshold
@@ -112,11 +115,11 @@ public class UnifiedGenotyperEngine {
     // ---------------------------------------------------------------------------------------------------------
     @Requires({"toolkit != null", "UAC != null"})
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), 2*(SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()).size()));
+        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), DEFAULT_PLOIDY*(SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()).size()));
     }
 
-    @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0","N>0"})
+    @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0","ploidy>0"})
-    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples, int N) {
+    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples, int ploidy) {
         this.BAQEnabledOnCMDLine = toolkit.getArguments().BAQMode != BAQ.CalculationMode.OFF;
         genomeLocParser = toolkit.getGenomeLocParser();
         this.samples = new TreeSet<String>(samples);
@@ -127,7 +130,8 @@ public class UnifiedGenotyperEngine {
         this.verboseWriter = verboseWriter;
         this.annotationEngine = engine;
 
-        this.N = N;
+        this.ploidy = ploidy;
+        this.N = samples.size() * ploidy;
         log10AlleleFrequencyPriorsSNPs = new double[N+1];
         log10AlleleFrequencyPriorsIndels = new double[N+1];
         computeAlleleFrequencyPriors(N, log10AlleleFrequencyPriorsSNPs, UAC.heterozygosity);

public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java

@@ -60,7 +60,7 @@ public class BQSRGathererUnitTest {
      * @param factor 1 to test for equality, any other value to multiply the original value and match with the calculated
      */
     private void testTablesWithColumnsAndFactor(GATKReportTable original, GATKReportTable calculated, List<String> columnsToTest, int factor) {
-        for (Object primaryKey : original.getPrimaryKeys()) {                                                  // tables don't necessarily have the same primary keys
+        for (Object primaryKey : original.getPrimaryKeys()) {                                                           // tables don't necessarily have the same primary keys
             for (String column : columnsToTest) {
                 Object actual = calculated.get(primaryKey, column);
                 Object expected = original.get(primaryKey, column);