Merge branch 'master' of github.com:broadinstitute/gsa-unstable

public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java

@@ -271,7 +271,18 @@ public class GATKReport {
      * @return a simplified GATK report
      */
     public static GATKReport newSimpleReport(final String tableName, final String... columns) {
-        GATKReportTable table = new GATKReportTable(tableName, "A simplified GATK table report", columns.length);
+        return newSimpleReportWithDescription(tableName, "A simplified GATK table report", columns);
+    }
+
+    /**
+     * @see #newSimpleReport(String, String...) but with a customized description
+     * @param tableName
+     * @param desc
+     * @param columns
+     * @return
+     */
+    public static GATKReport newSimpleReportWithDescription(final String tableName, final String desc, final String... columns) {
+        GATKReportTable table = new GATKReportTable(tableName, desc, columns.length);
 
         for (String column : columns) {
             table.addColumn(column, "");

public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java

@@ -315,6 +315,20 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, HasGenome
         return ( comparison == -1 || ( comparison == 0 && this.getStop() < that.getStart() ));        
     }
 
+    /**
+     * Tests whether this genome loc starts at the same position as that.
+     *
+     * i.e., do this and that have the same contig and the same start position
+     *
+     * @param that genome loc to compare to
+     * @return true if this and that have the same contig and the same start position
+     */
+    @Requires("that != null")
+    public final boolean startsAt( GenomeLoc that ) {
+        int comparison = this.compareContigs(that);
+        return comparison == 0 && this.getStart() == that.getStart();
+    }
+
     /**
      * Tests whether any portion of this contig is before that contig.
      * @param that Other contig to test.

public/java/src/org/broadinstitute/sting/utils/Utils.java

@@ -293,6 +293,10 @@ public class Utils {
         }
     }
 
+    public static <T> String join(final String separator, final T ... objects) {
+        return join(separator, Arrays.asList(objects));
+    }
+
     public static String dupString(char c, int nCopies) {
         char[] chars = new char[nCopies];
         Arrays.fill(chars, c);

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java

@@ -30,12 +30,17 @@ import net.sf.samtools.SAMSequenceRecord;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodecHeader;
+import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
 import java.util.*;
 
 /**
@@ -317,4 +322,33 @@ public class VCFUtils {
             assembly = "hg19";
         return assembly;
     }
+
+    /**
+     * Read all of the VCF records from source into memory, returning the header and the VariantContexts
+     *
+     * @param source the file to read, must be in VCF4 format
+     * @return
+     * @throws IOException
+     */
+    public static Pair<VCFHeader, List<VariantContext>> readVCF(final File source) throws IOException {
+        // read in the features
+        final List<VariantContext> vcs = new ArrayList<VariantContext>();
+        final VCFCodec codec = new VCFCodec();
+        PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
+        FeatureCodecHeader header = codec.readHeader(pbs);
+        pbs.close();
+
+        pbs = new PositionalBufferedStream(new FileInputStream(source));
+        pbs.skip(header.getHeaderEnd());
+
+        final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue();
+
+        while ( ! pbs.isDone() ) {
+            final VariantContext vc = codec.decode(pbs);
+            if ( vc != null )
+                vcs.add(vc);
+        }
+
+        return new Pair<VCFHeader, List<VariantContext>>(vcfHeader, vcs);
+    }
 }