The user can now set the maximum allowable cycle on the command-line with --maximum_cycle_value. This value is (now) enforced in the Cycle covariate and a User Error is thrown if the maximum value is passed (with a helpful error message). Added unit tests to cover this new functionality.

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

@@ -102,13 +102,10 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "no_standard_covs", shortName = "noStandard", doc = "Do not use the standard set of covariates, but rather just the ones listed using the -cov argument", required = false)
     public boolean DO_NOT_USE_STANDARD_COVARIATES = false;
 
-    /////////////////////////////
-    // Debugging-only Arguments
-    /////////////////////////////
     /**
      * This calculation is critically dependent on being able to skip over known polymorphic sites. Please be sure that you know what you are doing if you use this option.
      */
-    @Hidden
+    @Advanced
     @Argument(fullName = "run_without_dbsnp_potentially_ruining_quality", shortName = "run_without_dbsnp_potentially_ruining_quality", required = false, doc = "If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only.")
     public boolean RUN_WITHOUT_DBSNP = false;
 
@@ -139,6 +136,13 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "indels_context_size", shortName = "ics", doc = "size of the k-mer context to be used for base insertions and deletions", required = false)
     public int INDELS_CONTEXT_SIZE = 3;
 
+    /**
+     * The cycle covariate will generate an error if it encounters a cycle greater than this value.
+     * This argument is ignored if the Cycle covariate is not used.
+     */
+    @Argument(fullName = "maximum_cycle_value", shortName = "maxCycle", doc = "the maximum cycle value permitted for the Cycle covariate", required = false)
+    public int MAXIMUM_CYCLE_VALUE = 500;
+
     /**
      * A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off (default is off)
      */
@@ -176,9 +180,15 @@ public class RecalibrationArgumentCollection {
     @Argument(fullName = "binary_tag_name", shortName = "bintag", required = false, doc = "the binary tag covariate name if using it")
     public String BINARY_TAG_NAME = null;
 
+
+    /////////////////////////////
+    // Debugging-only Arguments
+    /////////////////////////////
+
     @Hidden
     @Argument(fullName = "default_platform", shortName = "dP", required = false, doc = "If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.")
     public String DEFAULT_PLATFORM = null;
+
     @Hidden
     @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;

public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java

@@ -49,7 +49,7 @@ import java.util.EnumSet;
 
 public class CycleCovariate implements StandardCovariate {
 
-    private static final int MAXIMUM_CYCLE_VALUE = 1000;
+    private int MAXIMUM_CYCLE_VALUE;
     private static final int CUSHION_FOR_INDELS = 4;
     private String default_platform = null;
 
@@ -59,6 +59,8 @@ public class CycleCovariate implements StandardCovariate {
     // Initialize any member variables using the command-line arguments passed to the walkers
     @Override
     public void initialize(final RecalibrationArgumentCollection RAC) {
+        this.MAXIMUM_CYCLE_VALUE = RAC.MAXIMUM_CYCLE_VALUE;
+
         if (RAC.DEFAULT_PLATFORM != null && !NGSPlatform.isKnown(RAC.DEFAULT_PLATFORM))
             throw new UserException.CommandLineException("The requested default platform (" + RAC.DEFAULT_PLATFORM + ") is not a recognized platform.");
 
@@ -88,6 +90,9 @@ public class CycleCovariate implements StandardCovariate {
 
             final int MAX_CYCLE_FOR_INDELS = readLength - CUSHION_FOR_INDELS - 1;
             for (int i = 0; i < readLength; i++) {
+                if ( cycle > MAXIMUM_CYCLE_VALUE )
+                    throw new UserException("The maximum allowed value for the cycle is " + MAXIMUM_CYCLE_VALUE + ", but a larger cycle was detected in read " + read.getReadName() + ".  Please use the --maximum_cycle_value argument to increase this value (at the expense of requiring more memory to run)");
+
                 final int substitutionKey = keyFromCycle(cycle);
                 final int indelKey = (i < CUSHION_FOR_INDELS || i > MAX_CYCLE_FOR_INDELS) ? -1 : substitutionKey;
                 values.addCovariate(substitutionKey, indelKey, indelKey, i);

public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.recalibration;
 
 import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.recalibration.covariates.CycleCovariate;
 import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -53,9 +54,31 @@ public class CycleCovariateUnitTest {
         for (short i = 0; i < values.length; i++) {
             short actual = Short.decode(covariate.formatKey(values[i][0]));
             int expected = init + (increment * i);
-            //            System.out.println(String.format("%d: %d, %d", i, actual, expected));
             Assert.assertEquals(actual, expected);
         }
     }
 
+    @Test(enabled = true, expectedExceptions={UserException.class})
+    public void testMoreThanMaxCycleFails() {
+        int readLength = RAC.MAXIMUM_CYCLE_VALUE + 1;
+        GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
+        read.setReadPairedFlag(true);
+        read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
+        read.getReadGroup().setPlatform("illumina");
+
+        ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
+        covariate.recordValues(read, readCovariates);
+    }
+
+    @Test(enabled = true)
+    public void testMaxCyclePasses() {
+        int readLength = RAC.MAXIMUM_CYCLE_VALUE;
+        GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
+        read.setReadPairedFlag(true);
+        read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
+        read.getReadGroup().setPlatform("illumina");
+
+        ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
+        covariate.recordValues(read, readCovariates);
+    }
 }