complete refactoring

bigdatagenomics · Jun 18, 2019 · 0b3b45b · 0b3b45b
1 parent 0d44fc8
commit 0b3b45b
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Showing 7 changed files with 5 additions and 785 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala
@@ -41,7 +41,7 @@ private[adam] case class FastaDescriptionLine(
  */
 private[converters] object FastaConverters {
   // nucleotide + amino acid + ambiguity codes covers a-z
-  private val fastaRegex = "^[a-zA-Z]+$".r
+  private val fastaRegex = "^[a-zA-Z]+$".r // this should include '*' if indeed valid, per cleanSequence below
 
   /**
    * Return true if the specified line is a description line.
@@ -138,7 +138,7 @@ private[converters] object FastaConverters {
 /**
  * Convert FASTA format into Sequences.
  */
-private[adam] object FastaSequenceConverter4 {
+private[adam] object FastaSequenceConverter {
   import FastaConverters._
 
   /**
@@ -180,7 +180,7 @@ private[adam] object FastaSequenceConverter4 {
 /**
  * Convert FASTA format into Slices.
  */
-private[adam] object FastaSliceConverter4 {
+private[adam] object FastaSliceConverter {
   import FastaConverters._
 
   /**

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaSequenceConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaSequenceConverter.scala
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaSequenceConverter3.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaSequenceConverter3.scala