First working version of VariantContextBenchmark

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java

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+/*
+ * Copyright (c) 2011, 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.utils.variantcontext;
+
+import com.google.caliper.Param;
+import com.google.caliper.SimpleBenchmark;
+import com.google.caliper.runner.CaliperMain;
+import org.broad.tribble.readers.AsciiLineReader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * Caliper microbenchmark of parsing a VCF file
+ */
+public class VariantContextBenchmark extends SimpleBenchmark {
+    @Param({"/Users/depristo/Desktop/broadLocal/localData/ALL.chr20.merged_beagle_mach.20101123.snps_indels_svs.genotypes.vcf"})
+    String vcfFile;
+
+    @Param({"1000"})
+    int linesToRead; // set automatically by framework
+
+    @Param({"100"})
+    int nSamplesToTake; // set automatically by framework
+
+    private String INPUT_STRING;
+
+    private enum Operation {
+        READ,
+        READ_SUBSET
+    }
+
+    @Override protected void setUp() {
+        // read it into a String so that we don't try to benchmark IO issues
+        try {
+            FileInputStream s = new FileInputStream(new File(vcfFile));
+            AsciiLineReader lineReader = new AsciiLineReader(s);
+            int counter = 0;
+            StringBuffer sb = new StringBuffer();
+            while (counter++ < linesToRead ) {
+                String line = lineReader.readLine();
+                if ( line == null )
+                    break;
+                sb.append(line + "\n");
+            }
+            s.close();
+            INPUT_STRING = sb.toString();
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    private void parseGenotypes(VCFCodec codec, Operation op) {
+        try {
+            InputStream is = new ByteArrayInputStream(INPUT_STRING.getBytes());
+            AsciiLineReader lineReader = new AsciiLineReader(is);
+            codec.readHeader(lineReader);
+
+            int counter = 0;
+            List<String> samples = null;
+            while (counter++ < linesToRead ) {
+                String line = lineReader.readLine();
+                if ( line == null )
+                    break;
+
+                VariantContext vc = (VariantContext)codec.decode(line);
+                if ( samples == null ) {
+                    samples = new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake);
+                }
+
+                if ( op == Operation.READ_SUBSET)
+                    processOneVC(vc, samples);
+            }
+        } catch (Exception e) {
+            System.out.println("Benchmarking run failure because of " + e.getMessage());
+        }
+    }
+
+    public void timeOriginalRead(int rep) {
+        for ( int i = 0; i < rep; i++ )
+            parseGenotypes(new VCFCodec(), Operation.READ);
+    }
+
+    public void timeOriginalReadSubset(int rep) {
+        for ( int i = 0; i < rep; i++ )
+            parseGenotypes(new VCFCodec(), Operation.READ_SUBSET);
+    }
+
+    public static void main(String[] args) {
+        CaliperMain.main(VariantContextBenchmark.class, args);
+    }
+
+    private static final void processOneVC(VariantContext vc, List<String> samples) {
+        VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values(), vc.getAlleles());
+        sub.getNSamples();
+    }
+
+}