Removed hard-coded pointers to references

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3934 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/BaseTest.java

@@ -42,9 +42,8 @@ public abstract class BaseTest {
     /** our log, which we want to capture anything from org.broadinstitute.sting */
     public static Logger logger = Logger.getRootLogger();
 
-    protected static String seqLocation = "/seq/";
-    protected static String oneKGLocation = "/broad/1KG/";
     protected static String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
+    protected static String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.fasta";
     protected static String b36KGReference = "/broad/1KG/reference/human_b36_both.fasta";
     protected static String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
     protected static String validationDataLocation = GATKDataLocation + "Validation_Data/";
@@ -76,60 +75,13 @@ public abstract class BaseTest {
             logger.setLevel(Level.WARN);
 
             // find our file sources
-            try {
+            if (!fileExist(hg18Reference) || !fileExist(hg19Reference) || !fileExist(b36KGReference)) {
-                findFileLocations();
+                logger.fatal("We can't locate the reference directories.  Aborting!");
-            } catch (IOException e) {
+                throw new RuntimeException("BaseTest setup failed: unable to locate the reference directories");
-                logger.fatal("We can't locate the base /seq and /broad/1KG directories, for the following reason: " + e.getMessage());
-                throw new RuntimeException("BaseTest setup failed: findFileLocations emited exception",e);
             }
         }
     }
 
-    public static void findFileLocations() throws IOException {
-        // if either doesn't exist
-        if (!fileExist(seqLocation) || !fileExist(oneKGLocation)) {
-
-            // get the working directory
-            String workDir = System.getProperty("user.dir");
-
-            if (!fileExist("test.conf")) {
-                throw new IOException("Unable to find both data directories or your test.conf, make sure it's placed in the base Sting directory");
-            }
-
-            BufferedReader inputStream = new BufferedReader(new FileReader("test.conf"));
-
-            String line = "";
-            while ((line = inputStream.readLine()) != null) {
-                String[] array = line.split("=");
-
-                // check the length
-                if (array.length != 2) {
-                    throw new IOException("Line : " + line + ", split != 2");
-                }
-                // clean up the right side
-                if (array[1].contains("\n")) {
-                    array[1] = array[1].substring(0, array[1].indexOf("\n") - 1);
-                }
-                // check to see if the right side exists
-                if (!fileExist(array[1])) {
-                    throw new IOException("Line : " + line + ", right side doesn't exist");
-                }
-                // check to see what type it is
-                if (array[0].equals("seq")) {
-                    seqLocation = array[1];
-                } else if (array[0].equals("1KG")) {
-                    oneKGLocation = array[1];
-                } else if (array[0].equals("validation")) {
-                    validationDataLocation = array[1];    
-                } else {
-                    throw new IOException("Line : " + line + ", unknown left side");
-                }
-            }
-
-        }
-
-    }
-
     /**
      * test if the file exists
      *
@@ -139,7 +91,6 @@ public abstract class BaseTest {
     public static boolean fileExist(String file) {
         File temp = new File(file);
         return temp.exists();
-
     }
     
     /**
@@ -192,14 +143,14 @@ public abstract class BaseTest {
         } catch (NoSuchAlgorithmException e) {
             throw new StingException("Unable to find MD5 digest");
         }
-        InputStream is = null;
+        InputStream is;
         try {
             is = new FileInputStream(file);
         } catch (FileNotFoundException e) {
             throw new StingException("Unable to open file " + file);
         }
         byte[] buffer = new byte[8192];
-        int read = 0;
+        int read;
         try {
             while ((read = is.read(buffer)) > 0) {
                 digest.update(buffer, 0, read);

java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java

@@ -10,7 +10,7 @@ import java.util.Arrays;
 
 public class VariantContextIntegrationTest extends WalkerTest {
     private static String cmdRoot = "-T TestVariantContext" +
-            " -R " + oneKGLocation + "reference/human_b36_both.fasta";
+            " -R " + b36KGReference;
 
     private static String root = cmdRoot +
             " -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +

java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java

@@ -29,7 +29,7 @@ public class VariantContextUnitTest extends BaseTest {
     @BeforeClass
     public static void init() throws FileNotFoundException {
         // sequence
-        seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(hg18Reference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }
     

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java

@@ -46,7 +46,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest {
     @BeforeClass
     public static void init() throws FileNotFoundException {
         // sequence
-        seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(hg18Reference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java

@@ -42,7 +42,7 @@ public abstract class ReferenceViewTemplate extends BaseTest {
      */
     @BeforeClass
     public static void initialize() throws FileNotFoundException {
-        sequenceFile = new IndexedFastaSequenceFile( new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") );
+        sequenceFile = new IndexedFastaSequenceFile( new File(hg18Reference) );
         GenomeLocParser.setupRefContigOrdering(sequenceFile);
     }
 

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java

@@ -45,7 +45,7 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest {
 
     @BeforeClass
     public static void init() throws FileNotFoundException {
-        File sequenceFile = new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta");
+        File sequenceFile = new File(hg18Reference);
         GenomeLocParser.setupRefContigOrdering(new IndexedFastaSequenceFile(sequenceFile));
         TabularROD.setDelimiter(TabularROD.DEFAULT_DELIMITER, TabularROD.DEFAULT_DELIMITER_REGEX);
     }

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java

@@ -62,7 +62,7 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
         fl = new ArrayList<File>();
 
         // sequence
-        seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(hg18Reference));
         GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 

java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java

@@ -73,7 +73,7 @@ public class BoundedReadIteratorUnitTest extends BaseTest {
         fl = new ArrayList<File>();
 
         // sequence
-        seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(hg18Reference));
         GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 

java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodUnitTest.java

@@ -32,7 +32,7 @@ public class PlinkRodUnitTest extends BaseTest {
     @BeforeClass
     public static void beforeTests() {
         try {
-            seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
+            seq = new IndexedFastaSequenceFile(new File(b36KGReference));
         } catch (FileNotFoundException e) {
             throw new StingException("unable to load the sequence dictionary");
         }

java/test/org/broadinstitute/sting/gatk/refdata/TabularRODUnitTest.java

@@ -37,7 +37,7 @@ public class TabularRODUnitTest extends BaseTest {
     @BeforeClass
     public static void init() throws FileNotFoundException {
         // sequence
-        seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(hg18Reference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java

@@ -40,7 +40,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest {
 
     @BeforeClass
     public static void beforeClass() {
-        seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "/reference/human_b36_both.fasta")); // TODO: make human reference use BaseTest
+        seq = new IndexedFastaSequenceFile(new File(b36KGReference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java

@@ -36,7 +36,7 @@ public class VCF4UnitTest extends BaseTest {
     @BeforeClass
     public static void setupContig() {
         IndexedFastaSequenceFile seq;
-        seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(b36KGReference));
         GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 

java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java

@@ -34,7 +34,6 @@ import org.junit.Before;
 import org.junit.Test;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -100,7 +99,7 @@ public class RMDTrackManagerUnitTest extends BaseTest {
     // @Test used only to determine how fast queries are, don't uncomment! (unless you know what you're doing).
     public void testSpeedOfRealQuery() {
         IndexedFastaSequenceFile file = null;
-        file = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta"));
+        file = new IndexedFastaSequenceFile(new File(b36KGReference));
         final int intervalSize = 10000000;
         GenomeLocParser.setupRefContigOrdering(file.getSequenceDictionary());
         RMDTrackManager manager = new RMDTrackManager();

java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java

@@ -52,7 +52,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
     @Before
     public void setup() {
         builder = new TribbleRMDTrackBuilder();
-        IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
+        IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(b36KGReference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java

@@ -17,7 +17,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testGnarleyFHSPileup() {
         String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam "
-                 + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
+                 + "-R " + hg18Reference
                  +  " -L chr15:46,347,148 -o %s";
         String expected_md5 = "052187dd2bf2516a027578c8775856a8";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
@@ -27,7 +27,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
     @Test
     public void testExtendedEventPileup() {
         String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
-                 + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
+                 + "-R " + hg18Reference
                 + " -show_indels -o %s";
         String expected_md5="06eedc2e7927650961d99d703f4301a4";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));

java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java

@@ -23,7 +23,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
         md5.add("b4f98bee580508637c88c421064936fc");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                "-R " + b36KGReference +
                         " -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
                         " -T VariantsToVCF" +
                         " -L 1:10,000,000-11,000,000" +
@@ -40,7 +40,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
         md5.add("0f310612c8609cba3dcf9cc97b2c1195");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                "-R " + b36KGReference +
                         " -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
                         " -T VariantsToVCF" +
                         " -L 1:10,000,000-11,000,000" +
@@ -57,7 +57,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
         md5.add("28728ad3a6af20a1e1aaaf185ffbff2b");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                "-R " + b36KGReference +
                         " -B variant,HapMap," + validationDataLocation + "rawHapMap.yri.chr1.txt" +
                         " -T VariantsToVCF" +
                         " -L 1:1-1,000,000" +
@@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
         md5.add("19371e6cfea5f29fb75d5a2be7fccd34");
 
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                "-R " + b36KGReference +
                         " -B variant,VCF," + validationDataLocation + "complexExample.vcf4" +
                         " -T VariantsToVCF" +
                         " -o %s",

java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -8,7 +8,7 @@ import java.util.Arrays;
 public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     public static String baseTestString() {
-        return "-T VariantAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta -o %s";
+        return "-T VariantAnnotator -R " + b36KGReference + " -o %s";
     }
 
     @Test

java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java

@@ -18,8 +18,6 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
 
     private boolean RUN_TESTS = true;
     private String root = "-T DepthOfCoverage ";
-    private String hg18 = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
-    private String b36 = "/broad/1KG/reference/human_b36_both.fasta";
 
     private String buildRootCmd(String ref, List<String> bams, List<String> intervals) {
         StringBuilder bamBuilder = new StringBuilder();
@@ -59,7 +57,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
         String[] intervals = {"1:10,000,000-10,002,000","1:10,003,000-10,004,000"};
         String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam"};
 
-        String cmd = buildRootCmd(b36,new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals))) + " --maxMappingQuality 0";
+        String cmd = buildRootCmd(b36KGReference,new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals))) + " --maxMappingQuality 0";
 
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());
 

java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java

@@ -18,8 +18,6 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
 
     private boolean RUN_TESTS = true;
     private String root = "-T DepthOfCoverage ";
-    private String hg18 = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
-    private String b36 = "/broad/1KG/reference/human_b36_both.fasta";
 
     private String buildRootCmd(String ref, List<String> bams, List<String> intervals) {
         StringBuilder bamBuilder = new StringBuilder();
@@ -53,7 +51,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
         String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};
 
-        String cmd = buildRootCmd(hg18,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25";
+        String cmd = buildRootCmd(hg18Reference,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25";
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
 
         // now add the expected files that get generated
@@ -88,7 +86,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
         String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};
 
-        String cmd = buildRootCmd(hg18,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv";
+        String cmd = buildRootCmd(hg18Reference,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv";
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
 
         spec.addAuxFile("d570c27d82a80ebd2852e9d34aff4e87",baseOutputFile);

java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java

@@ -10,13 +10,13 @@ public class BamToFastqIntegrationTest extends WalkerTest {
     public void testIntervals() {
 
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                "-T BamToFastq -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
+                "-T BamToFastq -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
                  1,
                  Arrays.asList("49431d567524d6fd32a569504b25f212"));
         executeTest("testBamToFasta", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                "-T BamToFastq -reverse -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
+                "-T BamToFastq -reverse -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
                  1,
                  Arrays.asList("f3a4a39d36270136c12bb1315fdb7dff"));
         executeTest("testBamToFastaReverse", spec2);

java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java

@@ -10,19 +10,19 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
     public void testIntervals() {
 
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
                  1,
                  Arrays.asList("328d2d52cedfdc52da7d1abff487633d"));
         executeTest("testFastaReference", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s",
                  1,
                  Arrays.asList("3a48986c3832a768b478c3e95f994b0f"));
         executeTest("testFastaAlternateReferenceIndels", spec2);
 
         WalkerTestSpec spec4 = new WalkerTestSpec(
-                "-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -B snps,GeliText," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
+                "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B snps,GeliText," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s",
                  1,
                  Arrays.asList("82705a88f6fc25880dd2331183531d9a"));
         executeTest("testFastaAlternateReferenceSnps", spec4);

java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -8,7 +8,7 @@ import java.util.Arrays;
 public class VariantFiltrationIntegrationTest extends WalkerTest {
 
     public static String baseTestString() {
-        return "-T VariantFiltration -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta";
+        return "-T VariantFiltration -o %s -R " + b36KGReference;
     }
 
 

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -21,7 +21,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 //    @Test
 //    public void testPooled1() {
 //        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-//                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
+//                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
 //                Arrays.asList("c91f44a198cd7222520118726ea806ca"));
 //        executeTest("testPooled1", spec);
 //    }
@@ -34,7 +34,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testMultiSamplePilot1Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000", 1,
                 Arrays.asList("3a402233264e21a84d421e3a4ea64768"));
         executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
     }
@@ -42,7 +42,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testMultiSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000", 1,
                 Arrays.asList("79736b3e955a16b30f827b2786fc08b1"));
         executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
     }
@@ -50,7 +50,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testSingleSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000", 1,
                 Arrays.asList("b8d93c6fcb4b17d454cdcbfc4b43f076"));
         executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
     }
@@ -66,17 +66,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         String md5 = "098802639cfab1b777c96d38376f118a";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1,
                 Arrays.asList(md5));
         executeTest("test parallelization (single thread)", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 2", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 2", 1,
                 Arrays.asList(md5));
         executeTest("test parallelization (2 threads)", spec2);
 
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 4", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 4", 1,
                 Arrays.asList(md5));
         executeTest("test parallelization (4 threads)", spec3);
     }
@@ -98,7 +98,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 " + entry.getKey(), 1,
+                    "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 " + entry.getKey(), 1,
                     Arrays.asList(entry.getValue()));
             executeTest(String.format("testParameter[%s]", entry.getKey()), spec);
         }
@@ -107,12 +107,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
                 Arrays.asList("4937bab94b0bae1aa61cdf3a06cb49e8"));
         executeTest("testConfidence1", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
                 Arrays.asList("f8b722dad5c4868a4bba246eef83f96d"));
         executeTest("testConfidence2", spec2);
     }
@@ -131,7 +131,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -vf " + entry.getKey(), 1,
+                    "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -vf " + entry.getKey(), 1,
                     Arrays.asList(entry.getValue()));
             executeTest(String.format("testOtherFormat[%s]", entry.getKey()), spec);
         }
@@ -154,7 +154,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         for ( Map.Entry<Double, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-T UnifiedGenotyper -vf GELI -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 --heterozygosity " + entry.getKey(), 1,
+                    "-T UnifiedGenotyper -vf GELI -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 --heterozygosity " + entry.getKey(), 1,
                     Arrays.asList(entry.getValue()));
             executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec);
         }
@@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-T UnifiedGenotyper -vf GELI -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm " + entry.getKey(), 1,
+                    "-T UnifiedGenotyper -vf GELI -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm " + entry.getKey(), 1,
                     Arrays.asList(entry.getValue()));
             executeTest(String.format("testOtherBaseCallModel[%s]", entry.getKey()), spec);
         }
@@ -189,7 +189,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiTechnologies() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper" +
-                        " -R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        " -R " + b36KGReference +
                         " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
                         " -varout %s" +
                         " -L 1:10,000,000-10,100,000" +

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java

@@ -10,7 +10,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
     @Test
     public void testUnifiedGenotyperWholeGenome() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T UnifiedGenotyper" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
@@ -24,7 +24,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
     @Test
     public void testUnifiedGenotyperWholeExome() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T UnifiedGenotyper" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
@@ -38,7 +38,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
     @Test
     public void testUnifiedGenotyperWGParallel() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T UnifiedGenotyper" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +

java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java

@@ -11,7 +11,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testRealignerLod5() {
         String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "18fca887d1eb7dc300e717ae03b9da62"};
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
+                "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
                  Arrays.asList(md5s));
         executeTest("test realigner lod5", spec);
@@ -21,7 +21,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testRealignerLod50() {
         String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "9537e4f195ce5840136f60fb61201369"};
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
+                "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
                  Arrays.asList(md5s));
         executeTest("test realigner lod50", spec);
@@ -31,7 +31,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testRealignerKnownsOnly() {
         String[] md5s = {"7084d4e543bc756730ab306768028530", "1091436c40d5ba557d85662999cc0c1d"};
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf4 -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
+                "-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf4 -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
                  2,
                  Arrays.asList(md5s));
         executeTest("test realigner known indels only", spec);

java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java

@@ -10,7 +10,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
     public void testRealigner() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
 
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T IndelRealigner" +
                         " -LOD 5" +
                         " -maxConsensuses 100" +
@@ -25,7 +25,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
         executeTest("testIndelRealignerWholeGenome", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T IndelRealigner" +
                         " -LOD 5" +
                         " -maxConsensuses 100" +

java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java

@@ -11,19 +11,19 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
     public void testIntervals() {
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates",
+                "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates",
                  1,
                  Arrays.asList("d21e83a8b0d3f63acd9ca3b0b636e515"));
         executeTest("test standard", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates",
+                "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates",
                  1,
                  Arrays.asList("bfccfa50f62d10ee2fe8cfa68fb70002"));
         executeTest("test dbsnp", spec2);
 
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
-                "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
+                "-T RealignerTargetCreator -R " + b36KGReference + " -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s",
                  1,
                  Arrays.asList("1a11cfc9cc713617c82bdec503ebe02a"));
         //TODO -- Guillermo, re-enable this when the VCF->VC conversion works with indels

java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java

@@ -10,7 +10,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest {
     public void testRealignerTargetCreator() {
 
         WalkerTestSpec spec1 = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T RealignerTargetCreator" +
                         " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
@@ -21,7 +21,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest {
         executeTest("testRealignerTargetCreatorWholeGenome", spec1);
 
         WalkerTestSpec spec2 = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T RealignerTargetCreator" +
                         " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +

java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java

@@ -28,7 +28,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
                 String md5 = entry.getValue();
 
                 WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                                 " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
                                 " -T CountCovariates" +
                                 " -I " + bam +
@@ -64,7 +64,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
             if ( paramsFile != null ) {
                 WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                                 " -T TableRecalibration" +
                                 " -I " + bam +
                                 ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
@@ -90,7 +90,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             String md5 = entry.getValue();
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                    "-R " + b36KGReference +
                             " -T CountCovariates" +
                             " -I " + bam +
                             " -L 1:1-1,000" +
@@ -115,7 +115,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
             if ( paramsFile != null ) {
                 WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                                 " -T TableRecalibration" +
                                 " -I " + bam +
                                 ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" )
@@ -144,7 +144,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             String md5 = entry.getValue();
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                    "-R " + b36KGReference +
                             " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
                             " -T CountCovariates" +
                             " -I " + bam +
@@ -172,7 +172,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
             if ( paramsFile != null ) {
                 WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                                 " -T TableRecalibration" +
                                 " -I " + bam +
                                 " -outputBam %s" +
@@ -201,7 +201,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             String md5 = entry.getValue();
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                    "-R " + b36KGReference +
                             " -B dbsnp,VCF," + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
@@ -225,7 +225,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             String md5 = entry.getValue();
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                    "-R " + b36KGReference +
                             " -B anyNameABCD,VCF," + validationDataLocation + "vcfexample3.vcf" +
                             " -T CountCovariates" +
                             " -I " + bam +
@@ -253,7 +253,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             String md5 = entry.getValue();
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                    "-R " + b36KGReference +
                             " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
                             " -T CountCovariates" +
                             " -I " + bam +
@@ -285,7 +285,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
             if ( paramsFile != null ) {
                 WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                                 " -T TableRecalibration" +
                                 " -I " + bam +
                                 " -L 1:10,100,000-10,300,000" +
@@ -312,7 +312,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             String md5 = entry.getValue();
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                    "-R " + b36KGReference +
                             " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
                             " -T CountCovariates" +
                             " -I " + bam +
@@ -340,7 +340,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
             System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
             if ( paramsFile != null ) {
                 WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                                 " -T TableRecalibration" +
                                 " -I " + bam +
                                 " -outputBam %s" +

java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java

@@ -10,7 +10,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
 
     private void testCountCovariatesWholeGenomeRunner(String moreArgs) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T CountCovariates" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
@@ -24,7 +24,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
 
     private  void testCountCovariatesWholeExomeRunner(String moreArgs) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T CountCovariates" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
@@ -49,7 +49,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
     @Test
     public void testTableRecalibratorWholeGenome() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T TableRecalibration" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
@@ -64,7 +64,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
     @Test
     public void testTableRecalibratorWholeExome() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T TableRecalibration" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +

java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java

@@ -9,7 +9,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
     @Test
     public void testProbes() {
         String testVCF = validationDataLocation + "complexExample.vcf4";
-        String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B input,VCF,"+testVCF+" -o %s";
+        String testArgs = "-R " + b36KGReference + " -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B input,VCF,"+testVCF+" -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("71e717e1813791575231f884b51c0aa3"));
         executeTest("Test probes", spec);
@@ -19,7 +19,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
     public void testProbesUsingDbSNPMask() {
         String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf";
         String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R "
-                + oneKGLocation + "reference/human_b36_both.fasta -omitWindow -nameConvention "
+                + b36KGReference + " -omitWindow -nameConvention "
                 + "-project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation +
                 "pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
@@ -33,7 +33,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
     public void testProbesUsingDbSNPMaskWithNMW1() {
     String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf";
         String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R "
-                + oneKGLocation + "reference/human_b36_both.fasta -omitWindow -nameConvention "
+                + b36KGReference + " -omitWindow -nameConvention "
                 + "-nmw 1 -project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation +
 	    "pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s";
         WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,

java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java

@@ -9,7 +9,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest {
     @Test
     public void testSNPs() {
         String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
-        String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s";
+        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s";
         WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("2dab4630f40b76c0762de83fcbb60d09"));
         executeTest("Test SNPs", spec);
@@ -19,7 +19,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest {
     // TODO- need to be reenabled when PED reader tracks gets updated to read indels correctly
     public void testIndels() {
         String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
-        String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s";
+        String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s";
         WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
                 Arrays.asList("fad2dd71550dec064d458c4aa83e4de9"));
         executeTest("Test Indels", spec);

java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -10,7 +10,7 @@ import java.util.Map;
 public class
         VariantEvalIntegrationTest extends WalkerTest {
     private static String cmdRoot = "-T VariantEval" +
-            " -R " + oneKGLocation + "reference/human_b36_both.fasta";
+            " -R " + b36KGReference;
 
     private static String root = cmdRoot +
             " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
@@ -99,13 +99,13 @@ public class
 
     @Test
     public void testVEGenomicallyAnnotated() {
-        String vecmd = "-T VariantEval " +
+        String vecmd = "-T VariantEval" +
-                       "-R " + oneKGLocation + "reference/human_b36_both.fasta " +
+                       " -R " + b36KGReference +
-                       "-L 21 " +
+                       " -L 21" +
-                       "-D " + GATKDataLocation + "dbsnp_129_b36.rod " +
+                       " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
-                       "-E CountFunctionalClasses -noStandard " +
+                       " -E CountFunctionalClasses -noStandard" +
-                       "-B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf " +
+                       " -B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf" +
-                       "-o %s";
+                       " -o %s";
         String md5 = "d41d8cd98f00b204e9800998ecf8427e";
 
         WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5));

java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -19,7 +19,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
             String md5 = entry.getValue();
 
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                    "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                    "-R " + b36KGReference +
                             " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
                             " -T GenerateVariantClusters" +
                             " -B input,VCF," + vcf +
@@ -47,7 +47,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
             if ( paramsFile != null ) {
                 File file = createTempFile("cluster",".vcf");
                 WalkerTestSpec spec = new WalkerTestSpec(
-                        "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                                 " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
                                 " -T VariantRecalibrator" +
                                 " -B input,VCF," + vcf +

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java

@@ -36,7 +36,7 @@ import java.util.Arrays;
 public class CombineVariantsIntegrationTest extends WalkerTest {
 
     public static String baseTestString(String args) {
-        return "-T CombineVariants -L 1:1-50,000,000 -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta" + args;
+        return "-T CombineVariants -L 1:1-50,000,000 -o %s -R " + b36KGReference + args;
     }
 
     public void test1InOut(String file, String md5) {

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java

@@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
     @Test
     public void testb36Tohg19() {
          WalkerTestSpec spec = new WalkerTestSpec(
-                 "-T LiftoverVariants -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta -B variant,vcf," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict " + oneKGLocation + "reference/human_g1k_v37.dict",
+                 "-T LiftoverVariants -o %s -R " + b36KGReference + " -B variant,vcf," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
                  1,
                  Arrays.asList("1637877892a019061e74eb3d9a9d100f"));
          executeTest("test b36 to hg19", spec);

java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java

@@ -36,7 +36,7 @@ public class BeagleIntegrationTest extends WalkerTest {
     @Test
     public void testBeagleOutput() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T BeagleOutputToVCF -R " + oneKGLocation + "reference/human_g1k_v37.fasta " +
+                "-T BeagleOutputToVCF -R " + hg19Reference + " " +
                         "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
                         "-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " +
                         "-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " +
@@ -48,7 +48,7 @@ public class BeagleIntegrationTest extends WalkerTest {
     @Test
     public void testBeagleInput() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T ProduceBeagleInput -R " + oneKGLocation + "reference/human_g1k_v37.fasta " +
+                "-T ProduceBeagleInput -R " + hg19Reference + " " +
                         "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
                          "-beagle %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e"));
         executeTest("test BeagleInput", spec);

java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java

@@ -10,8 +10,8 @@ import java.util.List;
 public class ClipReadsWalkersIntegrationTest extends WalkerTest {
     public void testClipper(String name, String args, String md51, String md52) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " +
+                "-R " + hg18Reference +
-                        "-T ClipReads " +
+                        " -T ClipReads " +
                         "-I " + validationDataLocation + "clippingReadsTest.bam " +
                         "-o %s " +
                         "-ob %s " + args,
@@ -43,7 +43,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testUseOriginalQuals() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" +
+                "-R " + hg18Reference +
                         " -T ClipReads" +
                         " -I " + validationDataLocation + "originalQuals.chr1.1-1K.bam" +
                         " -L chr1:1-1,000" +

java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java

@@ -38,7 +38,7 @@ public class HLACallerIntegrationTest extends WalkerTest {
     @Test
     public void testFindClosestHLA() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T FindClosestHLA -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -PolymorphicSites " + validationDataLocation + "HLA_POLYMORPHIC_SITES.txt -o %s", 1,
+                "-T FindClosestHLA -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + b36KGReference + " -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -PolymorphicSites " + validationDataLocation + "HLA_POLYMORPHIC_SITES.txt -o %s", 1,
                 Arrays.asList("a49b6f54a4585d1dd958c55a5523427d"));
         executeTest("test FindClosestHLA", spec);
     }
@@ -46,7 +46,7 @@ public class HLACallerIntegrationTest extends WalkerTest {
     @Test
     public void testCalculateBaseLikelihoods() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T CalculateBaseLikelihoods -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 0 -o %s", 1,
+                "-T CalculateBaseLikelihoods -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + b36KGReference + " -L " + intervals + " -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 0 -o %s", 1,
                 Arrays.asList("98e64882f93bf7550457bee4182caab6"));
         executeTest("test CalculateBaseLikelihoods", spec);
     }
@@ -54,7 +54,7 @@ public class HLACallerIntegrationTest extends WalkerTest {
     @Test
     public void testHLACaller() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T HLACaller -noVerbose -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 5 -HLAfrequencies " + validationDataLocation + "HLA_FREQUENCIES.txt -bl " + validationDataLocation + "HLA_HISEQ.baselikelihoods -o %s", 1,
+                "-T HLACaller -noVerbose -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + b36KGReference + " -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 5 -HLAfrequencies " + validationDataLocation + "HLA_FREQUENCIES.txt -bl " + validationDataLocation + "HLA_HISEQ.baselikelihoods -o %s", 1,
                 Arrays.asList("f9931b378bde213e71fca6ecaa24b48b"));
         executeTest("test HLACaller", spec);
     }

java/test/org/broadinstitute/sting/playground/gatk/walkers/HapmapPoolAllelicInfoIntegrationTest.java

@@ -1,58 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.junit.Test;
-
-import java.util.Arrays;
-
-/**
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: Nov 18, 2009
- * Time: 9:29:31 AM
- * To change this template use File | Settings | File Templates.
- *
-public class HapmapPoolAllelicInfoIntegrationTest extends WalkerTest {
-
-   @Test
-    public void testFHSPool3() {
-        String test_args = "-T HapmapPoolAllelicInfo -samples /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_samples.txt "
-                + "-B /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_sample_paths.txt "
-                + "-B calls,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli "
-                + "-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_test.bam "
-                + "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -of %s "
-                + "-ps 40 -L /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_test_intervals.interval_list -q 0";
-        String md5ForThisTest = "da1222d7514f247eae066134d8e3cde3";
-        WalkerTestSpec spec = new WalkerTestSpec(test_args, 1, Arrays.asList(md5ForThisTest));
-        executeTest("Pool 3 of FHS Pilot on testbed intervals", spec);
-    }
-
-    @Test
-    public void testFHSPool3NoIntervals() {
-       String test_args = "-T HapmapPoolAllelicInfo -samples /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_samples.txt "
-                + "-B /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_sample_paths.txt "
-                + "-B calls,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli "
-                + "-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_test.bam "
-                + "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -of %s "
-                + "-ps 40 -q 0";
-        String md5ForThisTest = "9ee3f390657c32c9c4fbe654bcd3cdf9";
-        WalkerTestSpec spec = new WalkerTestSpec(test_args, 1, Arrays.asList(md5ForThisTest));
-        executeTest("Testing hapmap sites without reads at them (no testbed intervals)", spec);
-    }
-
-    @Test
-    public void testSmallPool() {
-
-        String test_args = "-T HapmapPoolAllelicInfo -samples /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878_NA12891_samples.txt "
-                +"-B NA12878,GFF,/humgen/gsa-scr1/andrewk/hapmap_1kg/gffs/NA12878.gff "
-                +"-B NA12891,GFF,/humgen/gsa-scr1/andrewk/hapmap_1kg/gffs/NA12891.gff "
-                +"-I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12891.a2b.recal.annotation_subset.bam "
-                +"-L chr1:14000000-18000000 -B calls,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12891.a2b.ssg1b.geli.calls "
-                +"-of %s -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -ps 2 -q 0";
-        String md5ForThisTest = "cc81a9d8279e7b6ad50f9dc1f19a7419";
-        WalkerTestSpec spec = new WalkerTestSpec(test_args, 1, Arrays.asList(md5ForThisTest));
-        executeTest("Test on pool of two individuals -- CEU father+daughter chips against subset of the father's calls; power at lod 3", spec);
-
-    }
-}
-*/

java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java

@@ -14,7 +14,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
         TODO put this test back in once it gets faster.
         String[] md5 = {"d19d6d1eb52fb09e7493653dc645d92a"};
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " +
+                "-T GenomicAnnotator -R " + b36KGReference + " " +
                 "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " +
                 "-B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " +
                 "-m " + //generate many records from one input record if necessary
@@ -28,13 +28,13 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
 
         String[] md5WithDashSArg = {"94edacdaee0dd58508d35d4d6040e31b"};
         WalkerTestSpec specWithSArg = new WalkerTestSpec(
-                "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " +
+                "-T GenomicAnnotator -R " + b36KGReference +
-                "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " +
+                " -B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" +
-                "-B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " +
+                " -B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt" +
-                "-m " + //generate many records from one input record if necessary
+                " -m" + //generate many records from one input record if necessary
-                "-vcf %s " +
+                " -vcf %s" +
-                "-BTI variant " +
+                " -BTI variant" +
-                "-s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet",
+                " -s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet",
                  1,
                  Arrays.asList(md5WithDashSArg));
         executeTest("test with dbSNP and -s arg", specWithSArg);

java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java

@@ -10,10 +10,10 @@ import java.util.List;
 public class DuplicatesWalkersIntegrationTest extends WalkerTest {
     public void testCounter(String name, String args, String md5) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T CountDuplicates " +
+                "-T CountDuplicates" +
-                        "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " +
+                        " -R " + hg18Reference +
-                        "-I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam " +
+                        " -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam" +
-                        "-o %s " + args,
+                        " -o %s " + args,
                 1, // just one output file
                 Arrays.asList("tmp"),
                 Arrays.asList(md5));
@@ -25,10 +25,10 @@ public class DuplicatesWalkersIntegrationTest extends WalkerTest {
 
     public void testCombiner(String name, String args, String md51, String md52) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T CombineDuplicates " +
+                "-T CombineDuplicates" +
-                        "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " +
+                        " -R " + hg18Reference +
-                        "-I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam " +
+                        " -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam" +
-                        "-o %s --outputBAM %s " + args,
+                        " -o %s --outputBAM %s " + args,
                 2, // just one output file
                 Arrays.asList("tmp", "bam"),
                 Arrays.asList(md51, md52));

java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java

@@ -11,7 +11,7 @@ import java.util.Arrays;
 public class RodSystemValidationIntegrationTest extends WalkerTest {
 
     public static String baseTestString1KG() {
-            return "-T RodSystemValidation -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta";
+            return "-T RodSystemValidation -o %s -R " + b36KGReference;
         }
 
 

java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java

@@ -33,7 +33,7 @@ import java.util.Arrays;
 public class VariantSelectIntegrationTest extends WalkerTest {
 
     public static String baseTestString() {
-        return "-T VariantSelect -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta";
+        return "-T VariantSelect -o %s -R " + b36KGReference;
     }
 
 

java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java

@@ -24,7 +24,7 @@ public class GenomeLocUnitTest extends BaseTest {
     @BeforeClass
     public static void init() throws FileNotFoundException {
         // sequence
-        seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(hg18Reference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java

@@ -23,7 +23,7 @@ public class BedParserUnitTest extends BaseTest {
 
     @BeforeClass
     public static void beforeTests() {
-        seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(b36KGReference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }
 

java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java

@@ -66,7 +66,7 @@ public class GLFWriterUnitTest extends BaseTest {
     @BeforeClass
     public static void beforeTests() {
         IndexedFastaSequenceFile seq;
-        seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
+        seq = new IndexedFastaSequenceFile(new File(b36KGReference));
         GenomeLocParser.setupRefContigOrdering(seq);
 
     }

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java

@@ -37,7 +37,7 @@ public class VCFWriterUnitTest extends BaseTest {
 
     @BeforeClass
     public static void beforeTests() {
-        IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(hg18Reference));
         GenomeLocParser.setupRefContigOrdering(seq);
     }