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

public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R

@@ -12,7 +12,7 @@ if ( onCMDLine ) {
   inputFileName = args[1]
   outputPDF = args[2]
 } else {
-  inputFileName = "Q-8271@gsa2.jobreport.txt"
+  inputFileName = "Q-26618@gsa4.jobreport.txt"
   #inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/Q-25718@node1149.jobreport.txt"
   #inputFileName = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/rodPerformanceGoals/history/report.082711.txt"
   outputPDF = NA
@@ -129,9 +129,11 @@ plotGroup <- function(groupTable) {
   # as above, but averaging over all iterations
   groupAnnotationsNoIteration = setdiff(groupAnnotations, "iteration")
   if ( dim(sub)[1] > 1 ) {
-    sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
+    try({ # need a try here because we will fail to reduce when there's just a single iteration
-    textplot(as.data.frame(sum), show.rownames=F)
+      sum = cast(melt(sub, id.vars=groupAnnotationsNoIteration, measure.vars=c("runtime")), ... ~ ., fun.aggregate=c(mean, sd))
-    title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
+      textplot(as.data.frame(sum), show.rownames=F)
+      title(paste("Job summary for", name, "averaging over all iterations"), cex=3)
+    }, silent=T)
   }
 }
     
@@ -193,6 +195,7 @@ plotJobsGantt(gatkReportData, F, F)
 plotProgressByTime(gatkReportData)
 plotTimeByHost(gatkReportData)
 for ( group in gatkReportData ) {
+  print(group)
  plotGroup(group)
 }
   

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

@@ -100,11 +100,6 @@ public class SAMDataSource {
      */
     private final Map<SAMReaderID,GATKBAMFileSpan> readerPositions = new HashMap<SAMReaderID,GATKBAMFileSpan>();
 
-    /**
-     * Cached representation of the merged header used to generate a merging iterator.
-     */
-    private final SamFileHeaderMerger headerMerger;
-
     /**
      * The merged header.
      */
@@ -300,9 +295,8 @@ public class SAMDataSource {
 
         initializeReaderPositions(readers);
 
-        headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,readers.headers(),true);
+        mergedHeader = readers.getMergedHeader();
-        mergedHeader = headerMerger.getMergedHeader();
+        hasReadGroupCollisions = readers.hasReadGroupCollisions();
-        hasReadGroupCollisions = headerMerger.hasReadGroupCollisions();
 
         readProperties = new ReadProperties(
                 samFiles,
@@ -327,9 +321,9 @@ public class SAMDataSource {
 
             List<SAMReadGroupRecord> readGroups = reader.getFileHeader().getReadGroups();
             for(SAMReadGroupRecord readGroup: readGroups) {
-                if(headerMerger.hasReadGroupCollisions()) {
+                if(hasReadGroupCollisions) {
-                    mappingToMerged.put(readGroup.getReadGroupId(),headerMerger.getReadGroupId(reader,readGroup.getReadGroupId()));
+                    mappingToMerged.put(readGroup.getReadGroupId(),readers.getReadGroupId(id,readGroup.getReadGroupId()));
-                    mergedToOriginalReadGroupMappings.put(headerMerger.getReadGroupId(reader,readGroup.getReadGroupId()),readGroup.getReadGroupId());
+                    mergedToOriginalReadGroupMappings.put(readers.getReadGroupId(id,readGroup.getReadGroupId()),readGroup.getReadGroupId());
                 } else {
                     mappingToMerged.put(readGroup.getReadGroupId(),readGroup.getReadGroupId());
                     mergedToOriginalReadGroupMappings.put(readGroup.getReadGroupId(),readGroup.getReadGroupId());
@@ -562,7 +556,7 @@ public class SAMDataSource {
      */
     private StingSAMIterator getIterator(SAMReaders readers, Shard shard, boolean enableVerification) {
         // Set up merging to dynamically merge together multiple BAMs.
-        MergingSamRecordIterator mergingIterator = new MergingSamRecordIterator(headerMerger,readers.values(),true);
+        MergingSamRecordIterator mergingIterator = readers.createMergingIterator();
 
         for(SAMReaderID id: getReaderIDs()) {
             CloseableIterator<SAMRecord> iterator = null;
@@ -707,6 +701,11 @@ public class SAMDataSource {
      * A collection of readers derived from a reads metadata structure.
      */
     private class SAMReaders implements Iterable<SAMFileReader> {
+        /**
+         * Cached representation of the merged header used to generate a merging iterator.
+         */
+        private final SamFileHeaderMerger headerMerger;
+
         /**
          * Internal storage for a map of id -> reader.
          */
@@ -798,6 +797,11 @@ public class SAMDataSource {
             }
 
             if ( totalNumberOfFiles > 0 ) logger.info(String.format("Done initializing BAM readers: total time %.2f", timer.getElapsedTime()));
+
+            Collection<SAMFileHeader> headers = new LinkedList<SAMFileHeader>();
+            for(SAMFileReader reader: readers.values())
+                headers.add(reader.getFileHeader());
+            headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,headers,true);
         }
 
         final private void printReaderPerformance(final int nExecutedTotal,
@@ -814,7 +818,37 @@ public class SAMDataSource {
                     nExecutedInTick, tickDurationInSec,
                     nExecutedTotal, totalNumberOfFiles, totalTimeInSeconds, totalTimeInSeconds / 60, nTasksPerSecond,
                     nRemaining, estTimeToComplete, estTimeToComplete / 60));
+        }
 
+        /**
+         * Return the header derived from the merging of these BAM files.
+         * @return the merged header.
+         */
+        public SAMFileHeader getMergedHeader() {
+            return headerMerger.getMergedHeader();
+        }
+
+        /**
+         * Do multiple read groups collide in this dataset?
+         * @return True if multiple read groups collide; false otherwis.
+         */
+        public boolean hasReadGroupCollisions() {
+            return headerMerger.hasReadGroupCollisions();
+        }
+
+        /**
+         * Get the newly mapped read group ID for the given read group.
+         * @param readerID Reader for which to discern the transformed ID.
+         * @param originalReadGroupID Original read group.
+         * @return Remapped read group.
+         */
+        public String getReadGroupId(final SAMReaderID readerID, final String originalReadGroupID) {
+            SAMFileHeader header = readers.get(readerID).getFileHeader();
+            return headerMerger.getReadGroupId(header,originalReadGroupID);
+        }
+
+        public MergingSamRecordIterator createMergingIterator() {
+            return new MergingSamRecordIterator(headerMerger,readers.values(),true);
         }
 
         /**
@@ -866,25 +900,6 @@ public class SAMDataSource {
         public boolean isEmpty() {
             return readers.isEmpty();
         }
-
-        /**
-         * Gets all the actual readers out of this data structure.
-         * @return A collection of the readers.
-         */
-        public Collection<SAMFileReader> values() {
-            return readers.values();
-        }
-
-        /**
-         * Gets all the actual readers out of this data structure.
-         * @return A collection of the readers.
-         */
-        public Collection<SAMFileHeader> headers() {
-            ArrayList<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(readers.size());
-            for (SAMFileReader reader : values())
-                headers.add(reader.getFileHeader());
-            return headers;
-        }
     }
 
     class ReaderInitializer implements Callable<ReaderInitializer> {

public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java

@@ -38,9 +38,9 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.clipreads.ClippingOp;
+import org.broadinstitute.sting.utils.clipping.ClippingOp;
-import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
+import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
-import org.broadinstitute.sting.utils.clipreads.ReadClipper;
+import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java

@@ -63,27 +63,26 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
     // Following derivation in http://en.wikipedia.org/wiki/Transmission_disequilibrium_test#A_modified_version_of_the_TDT
     private double calculateTDT( final VariantContext vc, final Set<Sample> triosToTest ) {
 
-        final double nABGivenABandBB = calculateNChildren(vc, triosToTest, HET, HET, HOM);
+        final double nABGivenABandBB = calculateNChildren(vc, triosToTest, HET, HET, HOM) + calculateNChildren(vc, triosToTest, HET, HOM, HET);
-        final double nBBGivenABandBB = calculateNChildren(vc, triosToTest, HOM, HET, HOM);
+        final double nBBGivenABandBB = calculateNChildren(vc, triosToTest, HOM, HET, HOM) + calculateNChildren(vc, triosToTest, HOM, HOM, HET);
         final double nAAGivenABandAB = calculateNChildren(vc, triosToTest, REF, HET, HET);
         final double nBBGivenABandAB = calculateNChildren(vc, triosToTest, HOM, HET, HET);
-        final double nAAGivenAAandAB = calculateNChildren(vc, triosToTest, REF, REF, HET);
+        final double nAAGivenAAandAB = calculateNChildren(vc, triosToTest, REF, REF, HET) + calculateNChildren(vc, triosToTest, REF, HET, REF);
-        final double nABGivenAAandAB = calculateNChildren(vc, triosToTest, HET, REF, HET);
+        final double nABGivenAAandAB = calculateNChildren(vc, triosToTest, HET, REF, HET) + calculateNChildren(vc, triosToTest, HET, HET, REF);
 
         final double numer = (nABGivenABandBB - nBBGivenABandBB) + 2.0 * (nAAGivenABandAB - nBBGivenABandAB) + (nAAGivenAAandAB - nABGivenAAandAB);
         final double denom = (nABGivenABandBB + nBBGivenABandBB) + 4.0 * (nAAGivenABandAB + nBBGivenABandAB) + (nAAGivenAAandAB + nABGivenAAandAB);
         return (numer * numer) / denom;
     }
 
-    private double calculateNChildren( final VariantContext vc, final Set<Sample> triosToTest, final int childIdx, final int momIdx, final int dadIdx ) {
+    private double calculateNChildren( final VariantContext vc, final Set<Sample> triosToTest, final int childIdx, final int parent1Idx, final int parent2Idx ) {
-        final double likelihoodVector[] = new double[triosToTest.size() * 2];
+        final double likelihoodVector[] = new double[triosToTest.size()];
         int iii = 0;
         for( final Sample child : triosToTest ) {
             final double[] momGL = vc.getGenotype(child.getMaternalID()).getLikelihoods().getAsVector();
             final double[] dadGL = vc.getGenotype(child.getPaternalID()).getLikelihoods().getAsVector();
             final double[] childGL = vc.getGenotype(child.getID()).getLikelihoods().getAsVector();
-            likelihoodVector[iii++] = momGL[momIdx] + dadGL[dadIdx] + childGL[childIdx];
+            likelihoodVector[iii++] = momGL[parent1Idx] + dadGL[parent2Idx] + childGL[childIdx];
-            likelihoodVector[iii++] = momGL[dadIdx] + dadGL[momIdx] + childGL[childIdx];
         }
 
         return MathUtils.sumLog10(likelihoodVector);

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java

@@ -34,10 +34,17 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
  */
 public class AlleleFrequencyCalculationResult {
 
-    // note that the cell at position zero in the likelihoods/posteriors array is actually probability of non-ref (since it's marginalized over all alleles)
+    // IMPORTANT NOTE:
+    // These 2 arrays are intended to contain the likelihoods/posterior probabilities for each alternate allele over each possible frequency (from 0 to 2N).
+    // For any given alternate allele and frequency, the likelihoods are marginalized over values for all other alternate alleles.  What this means is that
+    // the likelihoods at cell index zero (AF=0) in the array is actually that of the site's being polymorphic (because although this alternate allele may
+    // be at AF=0, it is marginalized over all other alternate alleles which are not necessarily at AF=0).
+    // In the bi-allelic case (where there are no other alternate alleles over which to marginalize),
+    // the value at cell index zero will be equal to AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED.
     final double[][] log10AlleleFrequencyLikelihoods;
     final double[][] log10AlleleFrequencyPosteriors;
 
+    // These 2 variables are intended to contain the likelihood/posterior probability for the site's being monomorphic (i.e. AF=0 for all alternate alleles)
     double log10LikelihoodOfAFzero = 0.0;
     double log10PosteriorOfAFzero = 0.0;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -493,12 +493,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             if (DISCORDANCE_ONLY) {
                 Collection<VariantContext> compVCs = tracker.getValues(discordanceTrack, context.getLocation());
                 if (!isDiscordant(vc, compVCs))
-                    return 0;
+                    continue;
             }
             if (CONCORDANCE_ONLY) {
                 Collection<VariantContext> compVCs = tracker.getValues(concordanceTrack, context.getLocation());
                 if (!isConcordant(vc, compVCs))
-                    return 0;
+                    continue;
             }
 
             if (alleleRestriction.equals(NumberAlleleRestriction.BIALLELIC) && !vc.isBiallelic())
@@ -512,16 +512,20 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
             VariantContext sub = subsetRecord(vc, samples);
             if ( (sub.isPolymorphicInSamples() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {
+                boolean failedJexlMatch = false;
                 for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
                     if ( !VariantContextUtils.match(sub, jexl) ) {
-                        return 0;
+                        failedJexlMatch = true;
+                        break;
                     }
                 }
-                if (SELECT_RANDOM_NUMBER) {
+                if ( !failedJexlMatch ) {
-                    randomlyAddVariant(++variantNumber, sub);
+                    if (SELECT_RANDOM_NUMBER) {
-                }
+                        randomlyAddVariant(++variantNumber, sub);
-                else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
+                    }
-                    vcfWriter.add(sub);
+                    else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
+                        vcfWriter.add(sub);
+                    }
                 }
             }
         }

public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import com.google.java.contract.Requires;
 import net.sf.samtools.Cigar;

public/java/src/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 /**
  * How should we represent a clipped bases in a read?

public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import com.google.java.contract.Requires;
 import net.sf.samtools.CigarElement;

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

@@ -171,7 +171,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testTDTAnnotation() {
-        final String MD5 = "9fe37b61aab695ad47ce3c587148e91f";
+        final String MD5 = "204e67536a17af7eaa6bf0a910818997";
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf" +
                         " -L " + validationDataLocation + "ug.random50000.subset300bp.chr1.family.vcf -NO_HEADER -ped " + validationDataLocation + "ug.random50000.family.ped -o %s", 1,

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -116,6 +116,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testUsingDbsnpName--" + testFile, spec);
     }
 
+    @Test
+    public void testMultipleRecordsAtOnePosition() {
+        String testFile = validationDataLocation + "selectVariants.onePosition.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s -NO_HEADER",
+                1,
+                Arrays.asList("20b52c96f5c48258494d072752b53693")
+        );
+
+        executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec);
+    }
+
     @Test
     public void testParallelization() {
         String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";

public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
@@ -8,7 +8,9 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 
-import java.util.*;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Stack;
 
 /**
  * Created by IntelliJ IDEA.
@@ -17,7 +19,7 @@ import java.util.*;
  * Time: 6:45 AM
  * To change this template use File | Settings | File Templates.
  */
-public class ClipReadsTestUtils {
+public class ReadClipperTestUtils {
     //Should contain all the utils needed for tests to mass produce
     //reads, cigars, and other needed classes
 

public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java

@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
@@ -50,13 +50,13 @@ public class ReadClipperUnitTest extends BaseTest {
 
     @BeforeClass
     public void init() {
-        cigarList = ClipReadsTestUtils.generateCigarList(maximumCigarSize);
+        cigarList = ReadClipperTestUtils.generateCigarList(maximumCigarSize);
     }
 
     @Test(enabled = true)
     public void testHardClipBothEndsByReferenceCoordinates() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             int readLength = alnStart - alnEnd;
@@ -71,7 +71,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReadCoordinates() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int readLength = read.getReadLength();
             for (int i=0; i<readLength; i++) {
                 GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReadCoordinates(0, i);
@@ -86,7 +86,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReferenceCoordinates() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             for (int i=alnStart; i<=alnEnd; i++) {
@@ -108,7 +108,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReferenceCoordinatesLeftTail() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             if (ReadUtils.getRefCoordSoftUnclippedStart(read) == alnStart) {                                // we can't test left clipping if the read has hanging soft clips on the left side
@@ -124,7 +124,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReferenceCoordinatesRightTail() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             if (ReadUtils.getRefCoordSoftUnclippedEnd(read) == alnEnd) {                                        // we can't test right clipping if the read has hanging soft clips on the right side
@@ -144,7 +144,7 @@ public class ReadClipperUnitTest extends BaseTest {
 
         // create a read for every cigar permutation
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int readLength = read.getReadLength();
             byte [] quals = new byte[readLength];
 
@@ -216,7 +216,7 @@ public class ReadClipperUnitTest extends BaseTest {
         GATKSAMRecord expected = ArtificialSAMUtils.createArtificialRead(CLIPPED_BASES, CLIPPED_QUALS, CLIPPED_CIGAR);
 
         ReadClipper lowQualClipper = new ReadClipper(read);
-        ClipReadsTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
+        ReadClipperTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
     }
 
     @Test(enabled = true)
@@ -224,7 +224,7 @@ public class ReadClipperUnitTest extends BaseTest {
 
         // Generate a list of cigars to test
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             ReadClipper readClipper = new ReadClipper(read);
             GATKSAMRecord clippedRead = readClipper.hardClipSoftClippedBases();
 
@@ -276,12 +276,12 @@ public class ReadClipperUnitTest extends BaseTest {
     public void testHardClipLeadingInsertions() {
         for (Cigar cigar : cigarList) {
             if (startsWithInsertion(cigar)) {
-                GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+                GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
                 GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipLeadingInsertions();
 
                 int expectedLength = read.getReadLength() - leadingInsertionLength(read.getCigar());
                 if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
-                    expectedLength -= leadingInsertionLength(ClipReadsTestUtils.invertCigar(read.getCigar()));
+                    expectedLength -= leadingInsertionLength(ReadClipperTestUtils.invertCigar(read.getCigar()));
 
                 if (! clippedRead.isEmpty()) {
                     Assert.assertEquals(expectedLength, clippedRead.getReadLength(), String.format("%s -> %s", read.getCigarString(), clippedRead.getCigarString()));  // check that everything else is still there

public/java/test/org/broadinstitute/sting/utils/clipreads/ClippingOpUnitTest.java

@@ -1,67 +0,0 @@
-package org.broadinstitute.sting.utils.clipreads;
-
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-
-/**
- * Created by IntelliJ IDEA.
- * User: roger
- * Date: 11/27/11
- * Time: 5:17 AM
- * To change this template use File | Settings | File Templates.
- */
-public class ClippingOpUnitTest extends BaseTest {
-
-    ClippingOp clippingOp;
-    GATKSAMRecord read;
-
-    @BeforeTest
-    public void init() {
-        read = ClipReadsTestUtils.makeRead();
-    }
-
-    @Test
-    private void testHardClip() {
-//        List<TestParameter> testList = new LinkedList<TestParameter>();
-//        testList.add(new TestParameter(0, 0, 1, 4, "1H3M"));//clip 1 base at start
-//        testList.add(new TestParameter(3, 3, 0, 3, "3M1H"));//clip 1 base at end
-//        testList.add(new TestParameter(0, 1, 2, 4, "2H2M"));//clip 2 bases at start
-//        testList.add(new TestParameter(2, 3, 0, 2, "2M2H"));//clip 2 bases at end
-//        testList.add(new TestParameter(0, 2, 3, 4, "3H1M"));//clip 3 bases at start
-//        testList.add(new TestParameter(1, 3, 0, 1, "1M3H"));//clip 3 bases at end
-//
-//        for (TestParameter p : testList) {
-//            init();
-//            clippingOp = new ClippingOp(p.inputStart, p.inputStop);
-//            logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.substringStart + "," + p.substringStop + "," + p.cigar);
-//            ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.HARDCLIP_BASES, read),
-//                    ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
-//                    ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
-//                    p.cigar);
-//        }
-
-    }
-
-    @Test
-    private void testSoftClip() {
-//        List<TestParameter> testList = new LinkedList<TestParameter>();
-//        testList.add(new TestParameter(0, 0, -1, -1, "1S3M"));//clip 1 base at start
-//        testList.add(new TestParameter(3, 3, -1, -1, "3M1S"));//clip 1 base at end
-//        testList.add(new TestParameter(0, 1, -1, -1, "2S2M"));//clip 2 bases at start
-//        testList.add(new TestParameter(2, 3, -1, -1, "2M2S"));//clip 2 bases at end
-//        testList.add(new TestParameter(0, 2, -1, -1, "3S1M"));//clip 3 bases at start
-//        testList.add(new TestParameter(1, 3, -1, -1, "1M3S"));//clip 3 bases at end
-//
-//        for (TestParameter p : testList) {
-//            init();
-//            clippingOp = new ClippingOp(p.inputStart, p.inputStop);
-//            logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.cigar);
-//            ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.SOFTCLIP_BASES, read),
-//                    ClipReadsTestUtils.BASES.getBytes(), ClipReadsTestUtils.QUALS.getBytes(), p.cigar);
-//        }
-
-    }
-}