style fixes, add SAMRecord converter to module

bigdatagenomics · May 13, 2019 · a19f440 · a19f440
1 parent c769cb7
commit a19f440
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Showing 6 changed files with 40 additions and 19 deletions.
diff --git a/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSAMRecord.java b/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSAMRecord.java
@@ -36,7 +36,7 @@
 /**
  * Convert AlignmentRecord to htsjdk SAMRecord.
  */
-public final class AlignmentRecordToSAMRecord extends AbstractConverter<AlignmentRecord, SAMRecord> {
+public final class AlignmentRecordToSamRecord extends AbstractConverter<AlignmentRecord, SAMRecord> {
 
     /** Regex to capture attributes. */
     private static final Pattern ATTRIBUTE = Pattern.compile("([^:]{2,4}):([AifZHB]):(.*)");
@@ -53,7 +53,7 @@ public final class AlignmentRecordToSAMRecord extends AbstractConverter<Alignmen
      *
      * @param header header, must not be null
      */
-    public AlignmentRecordToSAMRecord(final SAMFileHeader header) {
+    public AlignmentRecordToSamRecord(final SAMFileHeader header) {
         super(AlignmentRecord.class, SAMRecord.class);
 
         checkNotNull(header);

diff --git a/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/HtsjdkModule.java b/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/HtsjdkModule.java
@@ -17,6 +17,7 @@
  */
 package org.bdgenomics.convert.htsjdk;
 
+import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.ValidationStringency;
 
 import com.google.inject.AbstractModule;
@@ -26,6 +27,8 @@
 import org.bdgenomics.convert.Converter;
 import org.bdgenomics.convert.ConversionStringency;
 
+import org.bdgenomics.formats.avro.AlignmentRecord;
+
 /**
  * Guice module for the org.bdgenomics.convert.htsjdk package.
  */
@@ -44,4 +47,9 @@ Converter<ConversionStringency, ValidationStringency> createConversionStringency
     Converter<ValidationStringency, ConversionStringency> createValidationStringencyToConversionStringency() {
         return new ValidationStringencyToConversionStringency();
     }
+
+    @Provides @Singleton
+    Converter<SAMRecord, AlignmentRecord> createSamRecordToAlignmentRecord() {
+        return new SamRecordToAlignmentRecord();
+    }
 }
diff --git a/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/SAMRecordToAlignmentRecord.java b/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/SAMRecordToAlignmentRecord.java
@@ -39,7 +39,7 @@
 /**
  * Convert htsjdk SAMRecord to AlignmentRecord.
  */
-public final class SAMRecordToAlignmentRecord extends AbstractConverter<SAMRecord, AlignmentRecord> {
+public final class SamRecordToAlignmentRecord extends AbstractConverter<SAMRecord, AlignmentRecord> {
 
     /** Regex to capture the first cigar operation. */
     private static final Pattern FIRST_CIGAR_OPERATION = Pattern.compile("^([0-9]*)([A-Z]).*$");
@@ -54,7 +54,7 @@ public final class SAMRecordToAlignmentRecord extends AbstractConverter<SAMRecor
     /**
      * Create a new htsjdk SAMRecord to AlignmentRecord converter.
      */
-    public SAMRecordToAlignmentRecord() {
+    public SamRecordToAlignmentRecord() {
         super(SAMRecord.class, AlignmentRecord.class);
     }
 
@@ -175,7 +175,6 @@ public AlignmentRecord convert(final SAMRecord samRecord,
         }
 
         String attributes = encodeAttributes(getBinaryAttributes(samRecord));
-        //String attributes = encodeAttributes(samRecord.getBinaryAttributes());
         if (!attributes.isEmpty()) {
             builder.setAttributes(attributes);
         }
@@ -244,7 +243,6 @@ static SAMBinaryTagAndValue getBinaryAttributes(final SAMRecord samRecord) {
         catch (Exception e) {
             return null;
         }
-        //return (SAMBinaryTagAndValue) org.apache.commons.lang3.reflect.FieldUtils.readDeclaredField(samRecord, "mAttributes", true);
     }
 
     /**
@@ -263,17 +261,21 @@ static String encodeUnsignedArray(final String tag, final Object value) {
         catch (Exception e) {
             return null;
         }
-        // return (String) MethodUtils.invokeMethod(TAG_CODEC, true, "encodeUnsignedArray", new Object[] { tag, value }, new Class<?>[] { String.class, Object.class });
     }
 
+    /**
+     * Encode the specified attribute and its child attributes to a string.
+     *
+     * @param attribute attribute
+     * @return the specified attribute and its child attributes to a string
+     */
     static String encodeAttributes(SAMBinaryTagAndValue attribute) {
         StringBuilder sb = new StringBuilder();
         while (attribute != null) {
             if (!skipTag(attribute.tag)) {
                 final String encodedTag;
                 if (attribute.isUnsignedArray()) {
                     encodedTag = encodeUnsignedArray(SAMTag.makeStringTag(attribute.tag), attribute.value);
-                    // encodedTag = TAG_CODEC.encodeUnsignedArray(SAMTag.makeStringTag(attribute.tag), attribute.value);
                 }
                 else {
                     encodedTag = TAG_CODEC.encode(SAMTag.makeStringTag(attribute.tag), attribute.value);

diff --git a/...rt-htsjdk/src/test/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSAMRecordTest.java b/...rt-htsjdk/src/test/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSAMRecordTest.java
@@ -39,10 +39,10 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * Unit test for AlignmentRecordToSAMRecord.
+ * Unit test for AlignmentRecordToSamRecord.
  */
-public final class AlignmentRecordToSAMRecordTest {
-    private final Logger logger = LoggerFactory.getLogger(AlignmentRecordToSAMRecordTest.class);
+public final class AlignmentRecordToSamRecordTest {
+    private final Logger logger = LoggerFactory.getLogger(AlignmentRecordToSamRecordTest.class);
 
     SAMFileHeader header;
     Converter<AlignmentRecord, SAMRecord> converter;
@@ -53,7 +53,7 @@ public void setUp() {
         SAMSequenceRecord sequenceRecord = new SAMSequenceRecord("1", 3000000);
         header.getSequenceDictionary().addSequence(sequenceRecord);
 
-        converter = new AlignmentRecordToSAMRecord(header);
+        converter = new AlignmentRecordToSamRecord(header);
     }
 
     @Test
@@ -63,7 +63,7 @@ public void testConstructor() {
 
     @Test(expected=NullPointerException.class)
     public void testConstructorNullHeader() {
-        new AlignmentRecordToSAMRecord(null);
+        new AlignmentRecordToSamRecord(null);
     }
 
     @Test(expected=ConversionException.class)

diff --git a/convert-htsjdk/src/test/java/org/bdgenomics/convert/htsjdk/HtsjdkModuleTest.java b/convert-htsjdk/src/test/java/org/bdgenomics/convert/htsjdk/HtsjdkModuleTest.java
@@ -24,6 +24,7 @@
 import com.google.inject.Injector;
 import com.google.inject.Guice;
 
+import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.ValidationStringency;
 
 import org.junit.Before;
@@ -32,6 +33,8 @@
 import org.bdgenomics.convert.Converter;
 import org.bdgenomics.convert.ConversionStringency;
 
+import org.bdgenomics.formats.avro.AlignmentRecord;
+
 /**
  * Unit test for HtsjdkModule.
  */
@@ -54,6 +57,7 @@ public void testHtsjdkModule() {
         Target target = injector.getInstance(Target.class);
         assertNotNull(target.getConversionStringencyToValidationStringency());
         assertNotNull(target.getValidationStringencyToConversionStringency());
+        assertNotNull(target.getSamRecordToAlignmentRecord());
     }
 
     /**
@@ -62,13 +66,16 @@ public void testHtsjdkModule() {
     static class Target {
         final Converter<ConversionStringency, ValidationStringency> conversionStringencyToValidationStringency;
         final Converter<ValidationStringency, ConversionStringency> validationStringencyToConversionStringency;
+        final Converter<SAMRecord, AlignmentRecord> samRecordToAlignmentRecord;
 
         @Inject
         Target(final Converter<ConversionStringency, ValidationStringency> conversionStringencyToValidationStringency,
-               final Converter<ValidationStringency, ConversionStringency> validationStringencyToConversionStringency) {
+               final Converter<ValidationStringency, ConversionStringency> validationStringencyToConversionStringency,
+               final Converter<SAMRecord, AlignmentRecord> samRecordToAlignmentRecord) {
+
             this.conversionStringencyToValidationStringency = conversionStringencyToValidationStringency;
             this.validationStringencyToConversionStringency = validationStringencyToConversionStringency;
-
+            this.samRecordToAlignmentRecord = samRecordToAlignmentRecord;
         }
 
         Converter<ConversionStringency, ValidationStringency> getConversionStringencyToValidationStringency() {
@@ -78,6 +85,10 @@ Converter<ConversionStringency, ValidationStringency> getConversionStringencyToV
         Converter<ValidationStringency, ConversionStringency> getValidationStringencyToConversionStringency() {
             return validationStringencyToConversionStringency;
         }
+
+        Converter<SAMRecord, AlignmentRecord> getSamRecordToAlignmentRecord() {
+            return samRecordToAlignmentRecord;
+        }
     }
 
     /**

diff --git a/...rt-htsjdk/src/test/java/org/bdgenomics/convert/htsjdk/SAMRecordToAlignmentRecordTest.java b/...rt-htsjdk/src/test/java/org/bdgenomics/convert/htsjdk/SAMRecordToAlignmentRecordTest.java
@@ -40,10 +40,10 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * Unit test for SAMRecordToAlignmentRecord.
+ * Unit test for SamRecordToAlignmentRecord.
  */
-public final class SAMRecordToAlignmentRecordTest {
-    private final Logger logger = LoggerFactory.getLogger(SAMRecordToAlignmentRecordTest.class);
+public final class SamRecordToAlignmentRecordTest {
+    private final Logger logger = LoggerFactory.getLogger(SamRecordToAlignmentRecordTest.class);
 
     Converter<SAMRecord, AlignmentRecord> converter;
     SAMFileHeader header;
@@ -54,7 +54,7 @@ public void setUp() {
         SAMSequenceRecord sequenceRecord = new SAMSequenceRecord("1", 3000000);
         header.getSequenceDictionary().addSequence(sequenceRecord);
 
-        converter = new SAMRecordToAlignmentRecord();
+        converter = new SamRecordToAlignmentRecord();
     }
 
     @Test