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

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

@@ -177,11 +177,8 @@ public class GATKReport {
      */
     public void print(PrintStream out) {
         out.println(GATKREPORT_HEADER_PREFIX + getVersion().toString() + SEPARATOR + getTables().size());
-        for (GATKReportTable table : tables.values()) {
+        for (GATKReportTable table : tables.values())
-            if (table.getNumRows() > 0) {
+            table.write(out);
-                table.write(out);
-            }
-        }
     }
 
     public Collection<GATKReportTable> getTables() {

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

@@ -48,9 +48,9 @@ public enum GATKReportDataType {
     Boolean("%[Bb]"),
 
     /**
-     * Used for byte and char value. Will display as a char so use printable values!
+     * Used for char values. Will display as a char so use printable values!
      */
-    Byte("%[Cc]"),
+    Character("%[Cc]"),
 
     /**
      * Used for float and double values. Will output a decimal with format %.8f unless otherwise specified.
@@ -58,7 +58,7 @@ public enum GATKReportDataType {
     Decimal("%.*[EeFf]"),
 
     /**
-     * Used for int, and long values. Will display the full number by default.
+     * Used for int, byte, short, and long values. Will display the full number by default.
      */
     Integer("%[Dd]"),
 
@@ -97,17 +97,26 @@ public enum GATKReportDataType {
         GATKReportDataType value;
         if (object instanceof Boolean) {
             value = GATKReportDataType.Boolean;
-        } else if (object instanceof Byte || object instanceof Character) {
+
-            value = GATKReportDataType.Byte;
+        } else if (object instanceof Character) {
-        } else if (object instanceof Float || object instanceof Double) {
+            value = GATKReportDataType.Character;
+
+        } else if (object instanceof Float ||
+                object instanceof Double) {
             value = GATKReportDataType.Decimal;
-        } else if (object instanceof Integer || object instanceof Long) {
+
+        } else if (object instanceof Integer ||
+                object instanceof Long ||
+                object instanceof Short ||
+                object instanceof Byte ) {
             value = GATKReportDataType.Integer;
+
         } else if (object instanceof String) {
             value = GATKReportDataType.String;
+
         } else {
             value = GATKReportDataType.Unknown;
-            //throw new ReviewedStingException("GATKReport could not convert the data object into a GATKReportDataType. Acceptable data objects are found in the documentation.");
+            //throw new UserException("GATKReport could not convert the data object into a GATKReportDataType. Acceptable data objects are found in the documentation.");
         }
         return value;
     }
@@ -140,8 +149,8 @@ public enum GATKReportDataType {
                 return 0.0D;
             case Boolean:
                 return false;
-            case Byte:
+            case Character:
-                return (byte) 0;
+                return '0';
             case Integer:
                 return 0L;
             case String:
@@ -166,16 +175,7 @@ public enum GATKReportDataType {
             case Boolean:
             case Integer:
                 return a.toString().equals(b.toString());
-            case Byte:
+            case Character:
-                // A mess that checks if the bytes and characters contain the same value
-                if ((a instanceof Character && b instanceof Character) ||
-                        (a instanceof Byte && b instanceof Byte))
-                    return a.toString().equals(b.toString());
-                else if (a instanceof Character && b instanceof Byte) {
-                    return ((Character) a).charValue() == ((Byte) b).byteValue();
-                } else if (a instanceof Byte && b instanceof Character) {
-                    return ((Byte) a).byteValue() == ((Character) b).charValue();
-                }
             case String:
             default:
                 return a.equals(b);
@@ -201,8 +201,8 @@ public enum GATKReportDataType {
                     return Long.parseLong(str);
                 case String:
                     return str;
-                case Byte:
+                case Character:
-                    return (byte) str.toCharArray()[0];
+                    return str.toCharArray()[0];
                 default:
                     return str;
             }
@@ -225,7 +225,7 @@ public enum GATKReportDataType {
                 return "%d";
             case String:
                 return "%s";
-            case Byte:
+            case Character:
                 return "%c";
             case Null:
             default:

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

@@ -254,7 +254,7 @@ public class GATKReportTable {
      * @param dottedColumnValues Period concatenated values.
      * @return The first primary key matching the column values or throws an exception.
      */
-    public Object getPrimaryKey(String dottedColumnValues) {
+    public Object getPrimaryKeyByData(String dottedColumnValues) {
         Object key = findPrimaryKey(dottedColumnValues);
         if (key == null)
             throw new ReviewedStingException("Attempted to get non-existent GATKReportTable key for values: " + dottedColumnValues);
@@ -411,9 +411,8 @@ public class GATKReportTable {
         if (value == null)
             value = "null";
 
-        // This code is bs. Why am do I have to conform to bad code
+        // This code below is bs. Why am do I have to conform to bad code
-        // Below is some ode to convert a string into its appropriate type.
+        // Below is some code to convert a string into its appropriate type.
-        // This is just Roger ranting
 
         // If we got a string but the column is not a String type
         Object newValue = null;
@@ -431,7 +430,7 @@ public class GATKReportTable {
                 } catch (Exception e) {
                 }
             }
-            if (column.getDataType().equals(GATKReportDataType.Byte) && ((String) value).length() == 1) {
+            if (column.getDataType().equals(GATKReportDataType.Character) && ((String) value).length() == 1) {
                 newValue = ((String) value).charAt(0);
 
             }
@@ -816,7 +815,7 @@ public class GATKReportTable {
             out.println();
         }
 
-        out.println();
+         out.println();
     }
 
     public int getNumRows() {
@@ -877,8 +876,6 @@ public class GATKReportTable {
                     this.set(rowKey, columnKey, toAdd.get(rowKey));
                     //System.out.printf("Putting row with PK: %s \n", rowKey);
                 } else {
-
-                    // TODO we should be able to handle combining data by adding, averaging, etc.
                     this.set(rowKey, columnKey, toAdd.get(rowKey));
 
                     System.out.printf("OVERWRITING Row with PK: %s \n", rowKey);

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

@@ -94,8 +94,11 @@ public class RecalibrationReport {
                 BitSet key = entry.getKey();
                 RecalDatum otherDatum = entry.getValue();
                 RecalDatum thisDatum = thisTable.get(key);
-                thisDatum.increment(otherDatum);                                                                          // add the two datum objects into 'this'
+                if (thisDatum == null)
-                thisDatum.resetCalculatedQualities();                                                                      // reset the empirical quality to make sure the user doesn't forget to recalculate it
+                    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.resetCalculatedQualities();                                                                   // reset the empirical quality to make sure the user doesn't forget to recalculate it
             }            
         }
     }

public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java

@@ -34,21 +34,22 @@ import java.io.IOException;
 import java.io.PrintStream;
 
 public class GATKReportUnitTest extends BaseTest {
-    @Test(enabled = false)
+    @Test
     public void testParse() throws Exception {
         String reportPath = validationDataLocation + "exampleGATKReportv1.tbl";
         GATKReport report = new GATKReport(reportPath);
+        Assert.assertEquals(report.getVersion(), GATKReportVersion.V1_0);
+        Assert.assertEquals(report.getTables().size(), 5);
 
         GATKReportTable countVariants = report.getTable("CountVariants");
-        //Assert.assertEquals(countVariants.getVersion(), GATKReportVersion.V0_1);
+        Object countVariantsPK = countVariants.getPrimaryKeyByData("dbsnp.eval.none.all");
-        Object countVariantsPK = countVariants.getPrimaryKey("none.eval.none.all");
+        Assert.assertEquals(countVariants.get(countVariantsPK, "nProcessedLoci"), "63025520");
-        Assert.assertEquals(countVariants.get(countVariantsPK, "nProcessedLoci"), "100000");
+        Assert.assertEquals(countVariants.get(countVariantsPK, "nNoCalls"), "0");
-        Assert.assertEquals(countVariants.get(countVariantsPK, "nNoCalls"), "99872");
+        Assert.assertEquals(countVariants.get(countVariantsPK, "heterozygosity"), 4.73e-06);
 
         GATKReportTable validationReport = report.getTable("ValidationReport");
-        //Assert.assertEquals(validationReport.getVersion(), GATKReportVersion.V0_1);
+        Object validationReportPK = countVariants.getPrimaryKeyByData("dbsnp.eval.none.novel");
-        Object validationReportPK = countVariants.getPrimaryKey("none.eval.none.known");
+        Assert.assertEquals(validationReport.get(validationReportPK, "PPV"), Double.NaN);
-        Assert.assertEquals(validationReport.get(validationReportPK, "sensitivity"), "NaN");
     }
 
     @DataProvider(name = "rightAlignValues")
@@ -117,15 +118,15 @@ public class GATKReportUnitTest extends BaseTest {
         report1.addTable("TableName", "Description");
         report1.getTable("TableName").addPrimaryKey("id", displayPK);
         report1.getTable("TableName").addColumn("colA", GATKReportDataType.String.getDefaultValue(), "%s");
-        report1.getTable("TableName").addColumn("colB", GATKReportDataType.Byte.getDefaultValue(), "%c");
+        report1.getTable("TableName").addColumn("colB", GATKReportDataType.Character.getDefaultValue(), "%c");
         report1.getTable("TableName").set(1, "colA", "NotNum");
-        report1.getTable("TableName").set(1, "colB", (byte) 64);
+        report1.getTable("TableName").set(1, "colB", (char) 64);
 
         report2 = new GATKReport();
         report2.addTable("TableName", "Description");
         report2.getTable("TableName").addPrimaryKey("id", displayPK);
         report2.getTable("TableName").addColumn("colA", GATKReportDataType.String.getDefaultValue(), "%s");
-        report2.getTable("TableName").addColumn("colB", GATKReportDataType.Byte.getDefaultValue(), "%c");
+        report2.getTable("TableName").addColumn("colB", GATKReportDataType.Character.getDefaultValue(), "%c");
         report2.getTable("TableName").set(2, "colA", "df3");
         report2.getTable("TableName").set(2, "colB", 'A');
 
@@ -133,7 +134,7 @@ public class GATKReportUnitTest extends BaseTest {
         report3.addTable("TableName", "Description");
         report3.getTable("TableName").addPrimaryKey("id", displayPK);
         report3.getTable("TableName").addColumn("colA", GATKReportDataType.String.getDefaultValue(), "%s");
-        report3.getTable("TableName").addColumn("colB", GATKReportDataType.Byte.getDefaultValue(), "%c");
+        report3.getTable("TableName").addColumn("colB", GATKReportDataType.Character.getDefaultValue(), "%c");
         report3.getTable("TableName").set(3, "colA", "df5f");
         report3.getTable("TableName").set(3, "colB", 'c');
 
@@ -146,13 +147,13 @@ public class GATKReportUnitTest extends BaseTest {
         table.addColumn("SomeInt", GATKReportDataType.Integer.getDefaultValue(), true, "%d");
         table.addColumn("SomeFloat", GATKReportDataType.Decimal.getDefaultValue(), true, "%.16E");
         table.addColumn("TrueFalse", false, true, "%B");
-        table.set("12df", "SomeInt", 34);
+        table.set("12df", "SomeInt", Byte.MAX_VALUE);
         table.set("12df", "SomeFloat", 34.0);
         table.set("12df", "TrueFalse", true);
-        table.set("5f", "SomeInt", -1);
+        table.set("5f", "SomeInt", Short.MAX_VALUE);
-        table.set("5f", "SomeFloat", 0.000003);
+        table.set("5f", "SomeFloat", Double.MAX_VALUE);
         table.set("5f", "TrueFalse", false);
-        table.set("RZ", "SomeInt", 904948230958203958L);
+        table.set("RZ", "SomeInt", Long.MAX_VALUE);
         table.set("RZ", "SomeFloat", 535646345.657453464576);
         table.set("RZ", "TrueFalse", true);
 

public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala

@@ -136,7 +136,7 @@ object PipelineTest extends BaseTest with Logging {
     println("    value (min,target,max) table key metric")
     for (validation <- evalSpec.validations) {
       val table = report.getTable(validation.table)
-      val key = table.getPrimaryKey(validation.key)
+      val key = table.getPrimaryKeyByData(validation.key)
       val value = String.valueOf(table.get(key, validation.metric))
       val inRange = if (value == null) false else validation.inRange(value)
       val flag = if (!inRange) "*" else " "