[ADAM-1372] Increase visibility for DefaultHeaderLines.allHeaderLines

adam-core/src/main/scala/org/bdgenomics/adam/converters/SupportedHeaderLines.scala → adam-core/src/main/scala/org/bdgenomics/adam/converters/DefaultHeaderLines.scala

@@ -27,9 +27,9 @@ import htsjdk.variant.vcf.{
 }
 
 /**
- * All header lines for VCF INFO and GT format fields that are supported in ADAM.
+ * Default set of VCF header lines for INFO and GT format fields supported in ADAM.
  */
-private[adam] object SupportedHeaderLines {
+object DefaultHeaderLines {
 
   lazy val ancestralAllele = new VCFInfoHeaderLine("AA",
     1,
@@ -89,7 +89,7 @@ private[adam] object SupportedHeaderLines {
     "Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'")
 
   /**
-   * All info keys in VCF format.
+   * Default set of VCF header lines for INFO fields supported in ADAM.
    */
   lazy val infoHeaderLines = Seq(
     ancestralAllele,
@@ -167,7 +167,7 @@ private[adam] object SupportedHeaderLines {
     "Total number of reads with mapping quality=0")
 
   /**
-   * All format lines in VCF format.
+   * Default set of VCF header lines for GT format fields supported in ADAM.
    */
   lazy val formatHeaderLines = Seq(
     genotype,
@@ -186,7 +186,7 @@ private[adam] object SupportedHeaderLines {
   )
 
   /**
-   * All supported header lines in VCF format.
+   * Default set of VCF header lines for INFO and GT format fields supported in ADAM.
    */
   lazy val allHeaderLines = infoHeaderLines ++ formatHeaderLines
 }

adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala

@@ -1394,7 +1394,7 @@ private[adam] class VariantContextConverter(
           val key = il.getID
 
           // filter out the lines that we already support
-          if (SupportedHeaderLines.infoHeaderLines
+          if (DefaultHeaderLines.infoHeaderLines
             .find(_.getID == key)
             .isEmpty) {
 
@@ -1467,7 +1467,7 @@ private[adam] class VariantContextConverter(
           val key = fl.getID
 
           // filter out the lines that we already support
-          if (SupportedHeaderLines.formatHeaderLines
+          if (DefaultHeaderLines.formatHeaderLines
             .find(_.getID == key)
             .isEmpty) {
 
@@ -1818,7 +1818,7 @@ private[adam] class VariantContextConverter(
           val key = il.getID
 
           // filter out the lines that we already support
-          if (SupportedHeaderLines.infoHeaderLines
+          if (DefaultHeaderLines.infoHeaderLines
             .find(_.getID == key)
             .isDefined) {
 
@@ -1891,7 +1891,7 @@ private[adam] class VariantContextConverter(
           val key = fl.getID
 
           // filter out the lines that we already support
-          if (SupportedHeaderLines.formatHeaderLines
+          if (DefaultHeaderLines.formatHeaderLines
             .find(_.getID == key)
             .isDefined) {
 

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

@@ -239,7 +239,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
     deduped.flatMap(line => line match {
       case fl: VCFFormatHeaderLine => {
         val key = fl.getID
-        SupportedHeaderLines.formatHeaderLines
+        DefaultHeaderLines.formatHeaderLines
           .find(_.getID == key)
           .fold(Some(fl).asInstanceOf[Option[VCFCompoundHeaderLine]])(defaultLine => {
             auditLine(fl, defaultLine, (newId, oldLine) => {
@@ -252,7 +252,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
       }
       case il: VCFInfoHeaderLine => {
         val key = il.getID
-        SupportedHeaderLines.infoHeaderLines
+        DefaultHeaderLines.infoHeaderLines
           .find(_.getID == key)
           .fold(Some(il).asInstanceOf[Option[VCFCompoundHeaderLine]])(defaultLine => {
             auditLine(il, defaultLine, (newId, oldLine) => {
@@ -266,7 +266,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
       case l => {
         Some(l)
       }
-    }) ++ SupportedHeaderLines.allHeaderLines
+    }) ++ DefaultHeaderLines.allHeaderLines
   }
 
   private def headerLines(header: VCFHeader): Seq[VCFHeaderLine] = {

adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/ADAMVCFOutputFormat.scala

@@ -20,7 +20,6 @@ package org.bdgenomics.adam.rdd.variant
 import htsjdk.variant.vcf.{ VCFHeaderLine, VCFHeader }
 import org.apache.hadoop.fs.{ FileSystem, Path }
 import org.apache.hadoop.mapreduce.{ RecordWriter, TaskAttemptContext }
-import org.bdgenomics.adam.converters.SupportedHeaderLines
 import org.bdgenomics.adam.models.SequenceDictionary
 import org.seqdoop.hadoop_bam.{
   KeyIgnoringVCFOutputFormat,

adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDD.scala

@@ -20,7 +20,7 @@ package org.bdgenomics.adam.rdd.variant
 import htsjdk.samtools.ValidationStringency
 import htsjdk.variant.vcf.VCFHeaderLine
 import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.converters.SupportedHeaderLines
+import org.bdgenomics.adam.converters.DefaultHeaderLines
 import org.bdgenomics.adam.models.{
   ReferencePosition,
   ReferenceRegion,
@@ -73,7 +73,7 @@ private[adam] class GenotypeArraySerializer extends IntervalArraySerializer[Refe
 case class GenotypeRDD(rdd: RDD[Genotype],
                        sequences: SequenceDictionary,
                        @transient samples: Seq[Sample],
-                       @transient headerLines: Seq[VCFHeaderLine] = SupportedHeaderLines.allHeaderLines) extends MultisampleAvroGenomicRDD[Genotype, GenotypeRDD] {
+                       @transient headerLines: Seq[VCFHeaderLine] = DefaultHeaderLines.allHeaderLines) extends MultisampleAvroGenomicRDD[Genotype, GenotypeRDD] {
 
   protected def buildTree(rdd: RDD[(ReferenceRegion, Genotype)])(
     implicit tTag: ClassTag[Genotype]): IntervalArray[ReferenceRegion, Genotype] = {

adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextRDD.scala

@@ -24,7 +24,7 @@ import org.apache.hadoop.io.LongWritable
 import org.apache.hadoop.fs.Path
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.converters.{
-  SupportedHeaderLines,
+  DefaultHeaderLines,
   VariantContextConverter
 }
 import org.bdgenomics.adam.models.{
@@ -86,7 +86,7 @@ private[adam] class VariantContextArraySerializer extends IntervalArraySerialize
 case class VariantContextRDD(rdd: RDD[VariantContext],
                              sequences: SequenceDictionary,
                              @transient samples: Seq[Sample],
-                             @transient headerLines: Seq[VCFHeaderLine] = SupportedHeaderLines.allHeaderLines) extends MultisampleGenomicRDD[VariantContext, VariantContextRDD]
+                             @transient headerLines: Seq[VCFHeaderLine] = DefaultHeaderLines.allHeaderLines) extends MultisampleGenomicRDD[VariantContext, VariantContextRDD]
     with Logging {
 
   protected def buildTree(rdd: RDD[(ReferenceRegion, VariantContext)])(

adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantRDD.scala

@@ -21,7 +21,7 @@ import htsjdk.samtools.ValidationStringency
 import htsjdk.variant.vcf.{ VCFHeader, VCFHeaderLine }
 import org.apache.hadoop.fs.Path
 import org.apache.spark.rdd.RDD
-import org.bdgenomics.adam.converters.SupportedHeaderLines
+import org.bdgenomics.adam.converters.DefaultHeaderLines
 import org.bdgenomics.adam.models.{
   ReferenceRegion,
   ReferenceRegionSerializer,
@@ -78,7 +78,7 @@ private[adam] class VariantArraySerializer extends IntervalArraySerializer[Refer
  */
 case class VariantRDD(rdd: RDD[Variant],
                       sequences: SequenceDictionary,
-                      @transient headerLines: Seq[VCFHeaderLine] = SupportedHeaderLines.allHeaderLines) extends AvroGenomicRDD[Variant, VariantRDD] {
+                      @transient headerLines: Seq[VCFHeaderLine] = DefaultHeaderLines.allHeaderLines) extends AvroGenomicRDD[Variant, VariantRDD] {
 
   protected def buildTree(rdd: RDD[(ReferenceRegion, Variant)])(
     implicit tTag: ClassTag[Variant]): IntervalArray[ReferenceRegion, Variant] = {