Merge pull request #311 from samtools/yf_add_histogram_comp

Added function to compare metric file histograms (added test!)
samtools · Aug 25, 2015 · a84b5b7 · a84b5b7
2 parents 19eb038 + b1e41d7
commit a84b5b7
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diff --git a/src/java/htsjdk/samtools/metrics/MetricsFile.java b/src/java/htsjdk/samtools/metrics/MetricsFile.java
@@ -573,4 +573,21 @@ public static boolean areMetricsEqual(final File file1, final File file2) {
         }
 
     }
+
+    /**
+     * Compare the metrics and histograms in two files, ignoring headers.
+     */
+    public static boolean areMetricsAndHistogramsEqual(final File file1, final File file2) {
+        try {
+            final MetricsFile<MetricBase, Comparable<?>> mf1 = new MetricsFile<MetricBase, Comparable<?>>();
+            final MetricsFile<MetricBase, Comparable<?>> mf2 = new MetricsFile<MetricBase, Comparable<?>>();
+            mf1.read(new FileReader(file1));
+            mf2.read(new FileReader(file2));
+
+            return mf1.areMetricsEqual(mf2) && mf1.areHistogramsEqual(mf2);
+
+        } catch (FileNotFoundException e) {
+            throw new SAMException(e.getMessage(), e);
+        }
+    }
 }
diff --git a/src/tests/java/htsjdk/samtools/metrics/MetricsFileTest.java b/src/tests/java/htsjdk/samtools/metrics/MetricsFileTest.java
@@ -97,6 +97,8 @@ public void testFloatingPointEquality() throws IOException {
         MetricsFile<FloatingPointMetric,Integer> file2 = writeThenReadBack(file);
         Assert.assertEquals(file, file2);
 
+
+
     }
 
     @Test
@@ -178,6 +180,22 @@ public void testWriteMetricsFile() throws IOException, ClassNotFoundException {
         Assert.assertEquals(file, file3);
     }
 
+    @Test
+    public void areMetricsFilesEqualTest(){
+        final File TEST_DIR = new File("testdata/htsjdk/samtools/metrics/");
+        final File file1 = new File(TEST_DIR,"metricsOne.metrics");
+        final File file2 = new File(TEST_DIR,"metricsOneCopy.metrics");
+        final File fileModifiedHist = new File(TEST_DIR,"metricsOneModifiedHistogram.metrics");
+        final File fileModifiedMet = new File(TEST_DIR,"metricsOneModifiedMetrics.metrics");
+
+        Assert.assertTrue(MetricsFile.areMetricsEqual(file1, file2));
+        Assert.assertTrue(MetricsFile.areMetricsEqual(file1, fileModifiedHist));
+
+        Assert.assertFalse(MetricsFile.areMetricsAndHistogramsEqual(file1, fileModifiedHist));
+        Assert.assertFalse(MetricsFile.areMetricsEqual(file1, fileModifiedMet));
+        Assert.assertFalse(MetricsFile.areMetricsAndHistogramsEqual(file1, fileModifiedMet));
+    }
+
     /** Helper method to persist metrics to file and read them back again. */
     private <METRIC extends MetricBase> MetricsFile<METRIC, Integer> writeThenReadBack(MetricsFile<METRIC,Integer> in) throws IOException {
         File f = File.createTempFile("test", ".metrics");
@@ -189,4 +207,7 @@ private <METRIC extends MetricBase> MetricsFile<METRIC, Integer> writeThenReadBa
         retval.read(new FileReader(f));
         return retval;
     }
+
+
+
 }
diff --git a/testdata/htsjdk/samtools/metrics/metricsOne.metrics b/testdata/htsjdk/samtools/metrics/metricsOne.metrics
@@ -0,0 +1,13 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.illumina.MarkIlluminaAdapters INPUT=testdata/picard/illumina/MarkIlluminaAdaptersTest/unevenReads.sam OUTPUT=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven5946421709712534555.sam METRICS=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven4591996041776878558.metrics    MIN_MATCH_BASES_SE=12 MIN_MATCH_BASES_PE=6 MAX_ERROR_RATE_SE=0.1 MAX_ERROR_RATE_PE=0.1 ADAPTERS=[INDEXED, DUAL_INDEXED, PAIRED_END] ADAPTER_TRUNCATION_LENGTH=30 PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN=100 NUM_ADAPTERS_TO_KEEP=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Aug 24 13:31:51 EDT 2015
+
+## METRICS CLASS	htsjdk.samtools.metrics.MetricsFileTest$TestMetric
+STRING_PROP	DATE_PROP	SHORT_PROP	INTEGER_PROP	LONG_PROP	FLOAT_PROP	DOUBLE_PROP	ENUM_PROP	BOOLEAN_PROP	CHARACTER_PROP	SHORT_PRIMITIVE	INT_PRIMITIVE	LONG_PRIMITIVE	FLOAT_PRIMITIVE	DOUBLE_PRIMITIVE	BOOLEAN_PRIMITIVE	CHAR_PRIMITIVE
+Hello World	2008-12-31	123		9223372036854775807	456.789001	0.713487	Two	N	A	123	919834781	9223372034707292160	0.55694	0.229233	Y	B
+
+## HISTOGRAM	java.lang.Integer
+clipped_bases	read_count
+6	1
+7	1
diff --git a/testdata/htsjdk/samtools/metrics/metricsOneCopy.metrics b/testdata/htsjdk/samtools/metrics/metricsOneCopy.metrics
@@ -0,0 +1,13 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.illumina.MarkIlluminaAdapters INPUT=testdata/picard/illumina/MarkIlluminaAdaptersTest/unevenReads.sam OUTPUT=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven5946421709712534555.sam METRICS=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven4591996041776878558.metrics    MIN_MATCH_BASES_SE=12 MIN_MATCH_BASES_PE=6 MAX_ERROR_RATE_SE=0.1 MAX_ERROR_RATE_PE=0.1 ADAPTERS=[INDEXED, DUAL_INDEXED, PAIRED_END] ADAPTER_TRUNCATION_LENGTH=30 PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN=100 NUM_ADAPTERS_TO_KEEP=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Aug 24 13:31:51 EDT 2015
+
+## METRICS CLASS	htsjdk.samtools.metrics.MetricsFileTest$TestMetric
+STRING_PROP	DATE_PROP	SHORT_PROP	INTEGER_PROP	LONG_PROP	FLOAT_PROP	DOUBLE_PROP	ENUM_PROP	BOOLEAN_PROP	CHARACTER_PROP	SHORT_PRIMITIVE	INT_PRIMITIVE	LONG_PRIMITIVE	FLOAT_PRIMITIVE	DOUBLE_PRIMITIVE	BOOLEAN_PRIMITIVE	CHAR_PRIMITIVE
+Hello World	2008-12-31	123		9223372036854775807	456.789001	0.713487	Two	N	A	123	919834781	9223372034707292160	0.55694	0.229233	Y	B
+
+## HISTOGRAM	java.lang.Integer
+clipped_bases	read_count
+6	1
+7	1
diff --git a/testdata/htsjdk/samtools/metrics/metricsOneModifiedHistogram.metrics b/testdata/htsjdk/samtools/metrics/metricsOneModifiedHistogram.metrics
@@ -0,0 +1,14 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.illumina.MarkIlluminaAdapters INPUT=testdata/picard/illumina/MarkIlluminaAdaptersTest/unevenReads.sam OUTPUT=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven5946421709712534555.sam METRICS=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven4591996041776878558.metrics    MIN_MATCH_BASES_SE=12 MIN_MATCH_BASES_PE=6 MAX_ERROR_RATE_SE=0.1 MAX_ERROR_RATE_PE=0.1 ADAPTERS=[INDEXED, DUAL_INDEXED, PAIRED_END] ADAPTER_TRUNCATION_LENGTH=30 PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN=100 NUM_ADAPTERS_TO_KEEP=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Aug 24 13:31:51 EDT 2015
+
+## METRICS CLASS	htsjdk.samtools.metrics.MetricsFileTest$TestMetric
+STRING_PROP	DATE_PROP	SHORT_PROP	INTEGER_PROP	LONG_PROP	FLOAT_PROP	DOUBLE_PROP	ENUM_PROP	BOOLEAN_PROP	CHARACTER_PROP	SHORT_PRIMITIVE	INT_PRIMITIVE	LONG_PRIMITIVE	FLOAT_PRIMITIVE	DOUBLE_PRIMITIVE	BOOLEAN_PRIMITIVE	CHAR_PRIMITIVE
+Hello World	2008-12-31	123		9223372036854775807	456.789001	0.713487	Two	N	A	123	919834781	9223372034707292160	0.55694	0.229233	Y	B
+
+## HISTOGRAM	java.lang.Integer
+clipped_bases	read_count
+6	1
+7	1
+8	1
diff --git a/testdata/htsjdk/samtools/metrics/metricsOneModifiedMetrics.metrics b/testdata/htsjdk/samtools/metrics/metricsOneModifiedMetrics.metrics
@@ -0,0 +1,13 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.illumina.MarkIlluminaAdapters INPUT=testdata/picard/illumina/MarkIlluminaAdaptersTest/unevenReads.sam OUTPUT=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven5946421709712534555.sam METRICS=/var/folders/tc/hy9lszxd1dg9cf4bky51mrrd9k3s6g/T/uneven4591996041776878558.metrics    MIN_MATCH_BASES_SE=12 MIN_MATCH_BASES_PE=6 MAX_ERROR_RATE_SE=0.1 MAX_ERROR_RATE_PE=0.1 ADAPTERS=[INDEXED, DUAL_INDEXED, PAIRED_END] ADAPTER_TRUNCATION_LENGTH=30 PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN=100 NUM_ADAPTERS_TO_KEEP=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon Aug 24 13:31:51 EDT 2015
+
+## METRICS CLASS	htsjdk.samtools.metrics.MetricsFileTest$TestMetric
+STRING_PROP	DATE_PROP	SHORT_PROP	INTEGER_PROP	LONG_PROP	FLOAT_PROP	DOUBLE_PROP	ENUM_PROP	BOOLEAN_PROP	CHARACTER_PROP	SHORT_PRIMITIVE	INT_PRIMITIVE	LONG_PRIMITIVE	FLOAT_PRIMITIVE	DOUBLE_PRIMITIVE	BOOLEAN_PRIMITIVE	CHAR_PRIMITIVE
+Hello World	2008-12-31	122		9223372036854775807	456.789001	0.713487	Two	N	A	123	919834781	9223372034707292160	0.55694	0.229233	Y	B
+
+## HISTOGRAM	java.lang.Integer
+clipped_bases	read_count
+6	1
+7	1