Improved BQSR plotting and some new parameters

* Refactored CycleCovariate to be a fragment covariate instead of a per read covariate
   * Refactored the CycleCovariateUnitTest to test the pairing information
   * Updated BQSR Integration tests accordingly
   * Made quantization levels parameter not hidden anymore
   * Added hidden option to keep intermediate plotting files for debug purposes (they're automatically deleted)
   * Added hidden option not to generate the plots automatically (important for scatter/gathering)

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

@@ -66,18 +66,18 @@ public class CycleCovariate implements StandardCovariate {
 
         // Discrete cycle platforms
         if (DISCRETE_CYCLE_PLATFORMS.contains(ngsPlatform)) {
-            final short init;
+            final short readOrderFactor = read.getReadPairedFlag() && read.getSecondOfPairFlag() ? (short) -1 : 1;
             final short increment;
-            if (!read.getReadNegativeStrandFlag()) {
+            short cycle;
-                init = 1;
+            if (read.getReadNegativeStrandFlag()) {
-                increment = 1;
+                cycle = (short) (read.getReadLength() * readOrderFactor);
+                increment = (short) (-1 * readOrderFactor);
             }
             else {
-                init = (short) read.getReadLength();
+                cycle = readOrderFactor;
-                increment = -1;
+                increment = readOrderFactor;
             }
 
-            short cycle = init;
             for (int i = 0; i < read.getReadLength(); i++) {
                 cycles[i] = BitSetUtils.bitSetFrom(cycle);
                 cycle += increment;

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

@@ -143,9 +143,18 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "deletions_default_quality", shortName = "ddq", doc = "default quality for the base deletions covariate", required = false)
     public byte DELETIONS_DEFAULT_QUALITY = 45;
 
+    /**
+     * Reads with low quality bases on either tail (beginning or end) will not be considered in the context. This parameter defines the quality below which (inclusive) a tail is considered low quality
+     */
     @Argument(fullName = "low_quality_tail", shortName = "lqt", doc = "minimum quality for the bases in the tail of the reads to be considered", required = false)
     public byte LOW_QUAL_TAIL = 2;
 
+    /**
+     * BQSR generates a quantization table for quick quantization later by subsequent tools. BQSR does not quantize the base qualities, this is done by the engine with the -qq or -BQSR options.
+     * This parameter tells BQSR the number of levels of quantization to use to build the quantization table.
+     */
+    @Argument(fullName = "quantizing_levels", shortName = "ql", required = false, doc = "number of distinct quality scores in the quantized output")
+    public int QUANTIZING_LEVELS = 16;
 
 
     @Hidden
@@ -155,8 +164,11 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "force_platform", shortName = "fP", required = false, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
     public String FORCE_PLATFORM = null;
     @Hidden
-    @Argument(fullName = "quantizing_levels", shortName = "ql", required = false, doc = "number of distinct quality scores in the quantized output")
+    @Argument(fullName = "keep_intermediate_files", shortName = "k", required = false, doc ="does not remove the temporary csv file created to generate the plots")
-    public int QUANTIZING_LEVELS = 16;
+    public boolean KEEP_INTERMEDIATE_FILES = false;
+    @Hidden
+    @Argument(fullName = "no_plots", shortName = "np", required = false, doc = "does not generate any plots -- useful for queue scatter/gathering")
+    public boolean NO_PLOTS = false;
 
     public GATKReportTable generateReportTable() {
         GATKReportTable argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run");
@@ -176,6 +188,8 @@ public class RecalibrationArgumentCollection {
         argumentsTable.set("default_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM);
         argumentsTable.set("force_platform", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM);
         argumentsTable.set("quantizing_levels", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS);
+        argumentsTable.set("keep_intermediate_files", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, KEEP_INTERMEDIATE_FILES);
+        argumentsTable.set("no_plots", RecalDataManager.ARGUMENT_VALUE_COLUMN_NAME, NO_PLOTS);
         return argumentsTable;
     }
 

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

@@ -279,6 +279,12 @@ public class RecalibrationReport {
 
             else if (primaryKey.equals("quantizing_levels"))
                 RAC.QUANTIZING_LEVELS = Integer.parseInt((String) value);
+
+            else if (primaryKey.equals("keep_intermediate_files"))
+                RAC.KEEP_INTERMEDIATE_FILES = Boolean.parseBoolean((String) value);
+
+            else if (primaryKey.equals("no_plots"))
+                RAC.NO_PLOTS = Boolean.parseBoolean((String) value);
         }
 
         return RAC;

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

@@ -26,8 +26,9 @@ public class CycleCovariateUnitTest {
 
     @Test(enabled = true)
     public void testSimpleCycles() {
-        short readLength = 10;        
+        short readLength = 10;
         GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
+        read.setReadPairedFlag(true);
         read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
         read.getReadGroup().setPlatform("illumina");
 
@@ -38,6 +39,13 @@ public class CycleCovariateUnitTest {
         values = covariate.getValues(read);
         verifyCovariateArray(values.getMismatches(), readLength, (short) -1);
 
+        read.setSecondOfPairFlag(true);
+        values = covariate.getValues(read);
+        verifyCovariateArray(values.getMismatches(), (short) -readLength, (short) 1);
+
+        read.setReadNegativeStrandFlag(false);
+        values = covariate.getValues(read);
+        verifyCovariateArray(values.getMismatches(), (short) -1, (short) -1);
     }
 
     private void verifyCovariateArray(BitSet[] values, short init, short increment) {