ExperimentalReadShardBalancerUnitTest was being skipped; fixed

TestNG skips tests when an exception occurs in a data provider,
which is what was happening here.

This was due to an AWFUL AWFUL use of a non-final static for
ReadShard.MAX_READS. This is fine if you assume only one instance
of SAMDataSource, but with multiple tests creating multiple SAMDataSources,
and each one overwriting ReadShard.MAX_READS, you have a recipe for
problems. As a result of this the test ran fine individually, but not as
part of the unit test suite.

Quick fix for now to get the tests running -- this "mutable static"
interface should really be refactored away though, when I have time.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java

@@ -34,10 +34,21 @@ import java.util.*;
  * @version 0.1
  */
 public class ReadShard extends Shard {
+
+    /**
+     * Default read shard buffer size
+     */
+    public static final int DEFAULT_MAX_READS = 10000;
+
     /**
      * What is the maximum number of reads per BAM file which should go into a read shard.
+     *
+     * TODO: this non-final static variable should either be made final or turned into an
+     * TODO: instance variable somewhere -- as both static and mutable it wreaks havoc
+     * TODO: with tests that use multiple instances of SAMDataSource (since SAMDataSource
+     * TODO: changes this value)
      */
-    public static int MAX_READS = 10000;
+    public static int MAX_READS = DEFAULT_MAX_READS;
 
     /**
      * The reads making up this shard.
@@ -51,6 +62,9 @@ public class ReadShard extends Shard {
     /**
      * Sets the maximum number of reads buffered in a read shard.  Implemented as a weirdly static interface
      * until we know what effect tuning this parameter has.
+     *
+     * TODO: this mutable static interface is awful and breaks tests -- need to refactor
+     *
      * @param bufferSize New maximum number
      */
     static void setReadBufferSize(final int bufferSize) {

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -252,7 +252,7 @@ public class SAMDataSource {
         validationStringency = strictness;
         this.removeProgramRecords = removeProgramRecords;
         if(readBufferSize != null)
-            ReadShard.setReadBufferSize(readBufferSize);
+            ReadShard.setReadBufferSize(readBufferSize);   // TODO: use of non-final static variable here is just awful, especially for parallel tests
         else {
             // Choose a sensible default for the read buffer size.  For the moment, we're picking 1000 reads per BAM per shard (which effectively
             // will mean per-thread once ReadWalkers are parallelized) with a max cap of 250K reads in memory at once.

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/ExperimentalReadShardBalancerUnitTest.java

@@ -90,7 +90,7 @@ public class ExperimentalReadShardBalancerUnitTest extends BaseTest {
                                                          new GenomeLocParser(header.getSequenceDictionary()),
                                                          false,
                                                          SAMFileReader.ValidationStringency.SILENT,
-                                                         null,
+                                                         ReadShard.DEFAULT_MAX_READS,  // reset ReadShard.MAX_READS to ReadShard.DEFAULT_MAX_READS for each test
                                                          downsamplingMethod,
                                                          new ValidationExclusion(),
                                                          new ArrayList<ReadFilter>(),
@@ -180,10 +180,10 @@ public class ExperimentalReadShardBalancerUnitTest extends BaseTest {
         for ( int numContigs = 1; numContigs <= 3; numContigs++ ) {
             for ( int numStacksPerContig : Arrays.asList(1, 2, 4) ) {
                 // Use crucial read shard boundary values as the stack sizes
-                for ( int stackSize : Arrays.asList(ReadShard.MAX_READS / 2, ReadShard.MAX_READS / 2 + 10, ReadShard.MAX_READS, ReadShard.MAX_READS - 1, ReadShard.MAX_READS + 1, ReadShard.MAX_READS * 2) ) {
+                for ( int stackSize : Arrays.asList(ReadShard.DEFAULT_MAX_READS / 2, ReadShard.DEFAULT_MAX_READS / 2 + 10, ReadShard.DEFAULT_MAX_READS, ReadShard.DEFAULT_MAX_READS - 1, ReadShard.DEFAULT_MAX_READS + 1, ReadShard.DEFAULT_MAX_READS * 2) ) {
-                    for ( int numUnmappedReads : Arrays.asList(0, ReadShard.MAX_READS / 2, ReadShard.MAX_READS * 2) ) {
+                    for ( int numUnmappedReads : Arrays.asList(0, ReadShard.DEFAULT_MAX_READS / 2, ReadShard.DEFAULT_MAX_READS * 2) ) {
                         // The first value will result in no downsampling at all, the others in some downsampling
-                        for ( int downsamplingTargetCoverage : Arrays.asList(ReadShard.MAX_READS * 10, ReadShard.MAX_READS, ReadShard.MAX_READS / 2) ) {
+                        for ( int downsamplingTargetCoverage : Arrays.asList(ReadShard.DEFAULT_MAX_READS * 10, ReadShard.DEFAULT_MAX_READS, ReadShard.DEFAULT_MAX_READS / 2) ) {
                             new ExperimentalReadShardBalancerTest(numContigs, numStacksPerContig, stackSize, numUnmappedReads, downsamplingTargetCoverage);
                         }
                     }