Fix for ref 0 bases for Chris

-- Disturbingly, fixing this bug doesn't actually cause an test failures.
-- Wrote a new QCRefWalker to actually check in detail that the reference bases coming into the RefWalker are all correct when comparing against a clean uncached load of the contig bases directly.
-- However, I cannot run this tool due to some kind of weird BAM error -- sending this on to Matt

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java

@@ -0,0 +1,124 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.samtools.SAMSequenceRecord;
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RefWalker;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.StingException;
+
+import java.io.PrintStream;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Prints out counts of the number of reference ordered data objects encountered.
+ *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One reference file only.  And optionally -L intervals
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ *     If ok, nothing, else will throw an exception at the site where there's been a problem
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T QCRefWalker
+ * </pre>
+ *
+ */
+public class QCRefWalker extends RefWalker<Integer, Integer> {
+    @Output
+    public PrintStream out;
+
+    String contigName = "";
+    int contigStart, contigEnd;
+    IndexedFastaSequenceFile uncachedRef;
+    byte[] uncachedBases;
+
+    @Override
+    public void initialize() {
+        super.initialize();    //To change body of overridden methods use File | Settings | File Templates.
+        uncachedRef = getToolkit().getReferenceDataSource().getReference();
+    }
+
+    private final void throwError(ReferenceContext ref, String message) {
+        throw new StingException(String.format("Site %s failed: %s", ref, message));
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        final String locusContigName = ref.getLocus().getContig();
+        if ( ! locusContigName.equals(contigName) ) {
+            contigName = locusContigName;
+            ReferenceSequence refSeq = uncachedRef.getSequence(contigName);
+            contigStart = 1;
+            contigEnd = contigStart + refSeq.length();
+            uncachedBases = uncachedRef.getSubsequenceAt(contigName, contigStart, contigEnd).getBases();
+            logger.warn(String.format("Loading contig %s (%d-%d)", contigName, contigStart, contigEnd));
+        }
+
+        final byte refBase = ref.getBase();
+        if (! ( BaseUtils.isRegularBase(refBase) || BaseUtils.isNBase(refBase) ) )
+            throwError(ref, String.format("Refbase isn't a regular base (%d %c)", refBase, (char)refBase));
+
+        // check bases are equal
+        final int pos = (int)context.getPosition() - contigStart;
+        if ( pos > contigEnd )
+            throwError(ref, String.format("off contig (len=%d)", contigEnd));
+        final byte uncachedBase = uncachedBases[pos];
+
+        if ( uncachedBase != refBase )
+            throwError(ref, String.format("Provided refBase (%d %c) not equal to uncached one (%d %c)",
+                    refBase, (char)refBase, uncachedBase, (char)uncachedBase));
+
+        return 1;
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer one, Integer sum) {
+        return one + sum;
+    }
+}

public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java

@@ -167,7 +167,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
             if ( start < myCache.start || stop > myCache.stop || myCache.seq == null || myCache.seq.getContigIndex() != contigInfo.getSequenceIndex() ) {
                 cacheMisses++;
                 myCache.start = Math.max(start - cacheMissBackup, 0);
-                myCache.stop  = Math.min(myCache.start + cacheSize, contigInfo.getSequenceLength());
+                myCache.stop  = Math.min(start + cacheSize + cacheMissBackup, contigInfo.getSequenceLength());
                 myCache.seq   = super.getSubsequenceAt(contig, myCache.start, myCache.stop);
                 //System.out.printf("New cache at %s %d-%d%n", contig, cacheStart, cacheStop);
             } else {