variants --> variant, etc.

.travis.yml

@@ -1,3 +1,3 @@
 language: java
 jdk:
-  - oraclejdk8
+  - openjdk8

CHANGES.md

@@ -1,5 +1,16 @@
 # convert Changelog #
 
+### Version 0.8.0 ###
+
+**Closed issues:**
+
+ - Bump bdg-formats dependency version to 0.14.0 [\#74](https://github.com/bigdatagenomics/convert/issues/74)
+
+**Merged and closed pull requests:**
+
+ - [CONVERT-74] Bump bdg-formats dependency version to 0.14.0 [\#75](https://github.com/bigdatagenomics/convert/pull/75) ([heuermh](https://github.com/heuermh))
+
+
 ### Version 0.6.0 ###
 
 **Closed issues:**

convert-ga4gh/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.bdgenomics.convert</groupId>
     <artifactId>convert-parent</artifactId>
-    <version>0.8.0-SNAPSHOT</version>
+    <version>0.9.0-SNAPSHOT</version>
   </parent>
 
   <packaging>jar</packaging>

convert-ga4gh/src/main/java/org/bdgenomics/convert/ga4gh/AlignmentRecordToReadAlignment.java

@@ -98,9 +98,9 @@ public ReadAlignment convert(final AlignmentRecord alignmentRecord,
             builder.setNextMatePosition(matePosition);
         }
 
-        if (isNotEmpty(alignmentRecord.getQuality())) {
-            List<Integer> alignedQuality = new ArrayList<Integer>(alignmentRecord.getQuality().length());
-            for (char c : alignmentRecord.getQuality().toCharArray()) {
+        if (isNotEmpty(alignmentRecord.getQualityScores())) {
+            List<Integer> alignedQuality = new ArrayList<Integer>(alignmentRecord.getQualityScores().length());
+            for (char c : alignmentRecord.getQualityScores().toCharArray()) {
                 alignedQuality.add(((int) c) - 33);
             }
             builder.addAllAlignedQuality(alignedQuality);

convert-ga4gh/src/test/java/org/bdgenomics/convert/ga4gh/AlignmentRecordToReadAlignmentTest.java

@@ -72,7 +72,7 @@ public void setUp() {
             .setReadMapped(true)
             .setCigar("10M")
             .setSequence("AAAAAAAAAA")
-            .setQuality("**********")
+            .setQualityScores("**********")
             .setReadNegativeStrand(false)
             .setMappingQuality(60)
             .setMismatchingPositions("10")
@@ -147,7 +147,7 @@ public void testConvertNoMapq() {
           .setReadMapped(true)
           .setCigar("10M")
           .setSequence("AAAAAAAAAA")
-          .setQuality("**********")
+          .setQualityScores("**********")
           .setReadNegativeStrand(false)
           .setMismatchingPositions("10")
           .setOriginalStart(12L)

convert-htsjdk/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.bdgenomics.convert</groupId>
     <artifactId>convert-parent</artifactId>
-    <version>0.8.0-SNAPSHOT</version>
+    <version>0.9.0-SNAPSHOT</version>
   </parent>
 
   <packaging>jar</packaging>

convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSamRecord.java

@@ -80,11 +80,11 @@ public SAMRecord convert(final AlignmentRecord alignmentRecord,
         builder.setReadName(alignmentRecord.getReadName());
         builder.setReadString(alignmentRecord.getSequence());
 
-        if (alignmentRecord.getQuality() == null) {
+        if (alignmentRecord.getQualityScores() == null) {
             builder.setBaseQualityString("*");
         }
         else {
-            builder.setBaseQualityString(alignmentRecord.getQuality());
+            builder.setBaseQualityString(alignmentRecord.getQualityScores());
         }
 
         String readGroupId = alignmentRecord.getReadGroupId();
@@ -178,8 +178,8 @@ public SAMRecord convert(final AlignmentRecord alignmentRecord,
         if (alignmentRecord.getMismatchingPositions() != null) {
             builder.setAttribute("MD", alignmentRecord.getMismatchingPositions());
         }
-        if (alignmentRecord.getOriginalQuality() != null) {
-            builder.setOriginalBaseQualities(SAMUtils.fastqToPhred(alignmentRecord.getOriginalQuality()));
+        if (alignmentRecord.getOriginalQualityScores() != null) {
+            builder.setOriginalBaseQualities(SAMUtils.fastqToPhred(alignmentRecord.getOriginalQualityScores()));
         }
         if (alignmentRecord.getOriginalCigar() != null) {
             builder.setAttribute("OC", alignmentRecord.getOriginalCigar());

convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/HtsjdkModule.java

@@ -29,6 +29,7 @@
 import htsjdk.variant.variantcontext.VariantContext;
 
 import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
 
 import com.google.inject.AbstractModule;
 import com.google.inject.Provides;
@@ -63,8 +64,8 @@ protected void configure() {
             .build(GenotypesToVariantContextFactory.class));
 
         install(new FactoryModuleBuilder()
-            .implement(new TypeLiteral<Converter<List<Variant>, VariantContext>>() {}, VariantsToVariantContext.class)
-            .build(VariantsToVariantContextFactory.class));
+            .implement(new TypeLiteral<Converter<Variant, VariantContext>>() {}, VariantToVariantContext.class)
+            .build(VariantToVariantContextFactory.class));
 
         install(new FactoryModuleBuilder()
             .implement(new TypeLiteral<Converter<VariantContext, List<Genotype>>>() {}, VariantContextToGenotypes.class)
@@ -129,4 +130,9 @@ Converter<VCFHeader, List<Reference>> createVcfHeaderToReferences(final Converte
     Converter<VCFHeader, List<Sample>> createVcfHeaderToSamples() {
         return new VcfHeaderToSamples();
     }
+
+    @Provides @Singleton
+    Converter<VCFHeader, List<VCFHeaderLine>> createVcfHeaderToVcfHeaderLines() {
+        return new VcfHeaderToVcfHeaderLines();
+    }
 }

convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/SamRecordToAlignmentRecord.java

@@ -81,10 +81,10 @@ public AlignmentRecord convert(final SAMRecord samRecord,
         }
 
         if (samRecord.getBaseQualityString() != "*") {
-            builder.setQuality(samRecord.getBaseQualityString());
+            builder.setQualityScores(samRecord.getBaseQualityString());
         }
         if (samRecord.getOriginalBaseQualities() != null) {
-            builder.setOriginalQuality(SAMUtils.phredToFastq(samRecord.getOriginalBaseQualities()));
+            builder.setOriginalQualityScores(SAMUtils.phredToFastq(samRecord.getOriginalBaseQualities()));
         }
 
         int readReference = samRecord.getReferenceIndex();

convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/VariantToVariantContext.java

@@ -0,0 +1,71 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.convert.htsjdk;
+
+import com.google.inject.Inject;
+
+import com.google.inject.assistedinject.Assisted;
+
+import htsjdk.variant.variantcontext.VariantContext;
+
+import htsjdk.variant.vcf.VCFHeader;
+
+import org.bdgenomics.convert.AbstractConverter;
+import org.bdgenomics.convert.ConversionException;
+import org.bdgenomics.convert.ConversionStringency;
+
+import org.bdgenomics.formats.avro.Variant;
+
+import org.slf4j.Logger;
+
+/**
+ * Convert a Variant to a VariantContext.
+ */
+public final class VariantToVariantContext extends AbstractConverter<Variant, VariantContext> {
+
+    /** Header. */
+    private final VCFHeader header;
+
+
+    /**
+     * Create a new Variant to VariantContext converter with the specified header.
+     *
+     * @param header header, must not be null
+     */
+    @Inject
+    public VariantToVariantContext(@Assisted final VCFHeader header) {
+        super(Variant.class, VariantContext.class);
+
+        checkNotNull(header);
+        this.header = header;
+    }
+
+
+    @Override
+    public VariantContext convert(final Variant variant,
+                                  final ConversionStringency stringency,
+                                  final Logger logger) throws ConversionException {
+
+        if (variant == null) {
+            warnOrThrow(variant, "must not be null", null, stringency, logger);
+            return null;
+        }
+
+        return null;
+    }
+}

convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/VariantToVariantContextFactory.java

@@ -0,0 +1,40 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.convert.htsjdk;
+
+import htsjdk.variant.variantcontext.VariantContext;
+
+import htsjdk.variant.vcf.VCFHeader;
+
+import org.bdgenomics.convert.Converter;
+
+import org.bdgenomics.formats.avro.Variant;
+
+/**
+ * Factory for creating Variant to VariantContext converters, which
+ * require late binding for a VCFHeader.
+ */
+public interface VariantToVariantContextFactory {
+
+    /**
+     * Create a new Variant to VariantContext converter with the specified header.
+     *
+     * @param header header, must not be null
+     */
+    Converter<Variant, VariantContext> create(VCFHeader header);
+}

convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/VcfHeaderToVcfHeaderLines.java

@@ -0,0 +1,62 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.convert.htsjdk;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
+
+import org.bdgenomics.convert.AbstractConverter;
+import org.bdgenomics.convert.ConversionException;
+import org.bdgenomics.convert.ConversionStringency;
+
+import org.slf4j.Logger;
+
+/**
+ * Convert a VCFHeader to a list of VCFHeaderLines.
+ */
+public final class VcfHeaderToVcfHeaderLines extends AbstractConverter<VCFHeader, List<VCFHeaderLine>> {
+
+    /**
+     * Create a new VCFHeader to a list of VCFHeaderLines converter.
+     */
+    public VcfHeaderToVcfHeaderLines() {
+        super(VCFHeader.class, VCFHeaderLine.class);
+    }
+
+
+    @Override
+    public List<VCFHeaderLine> convert(final VCFHeader header,
+                                       final ConversionStringency stringency,
+                                       final Logger logger) throws ConversionException {
+
+        if (header == null) {
+            warnOrThrow(header, "must not be null", null, stringency, logger);
+            return null;
+        }
+
+        List<VCFHeaderLine> headerLines = new ArrayList<VCFHeaderLine>();
+        headerLines.addAll(header.getFilterLines());
+        headerLines.addAll(header.getFormatHeaderLines());
+        headerLines.addAll(header.getInfoHeaderLines());
+        headerLines.addAll(header.getOtherHeaderLines());
+        return headerLines;
+    }
+}