Clean up CLI operation categories and names, and add documentation fo…

…r CLI.

* Removed CalculateDepth command.
* Clean up argument doc in TransformFeatures.
* Move OUTPUT to an option for Flagstat.
* Remove some output saving arguments in the View command that don't exactly
  make sense.
* Remove unused Vcf2ADAM/ADAM2Vcf -dict option and
  `org.bdgenomics.adam.cli.DictionaryCommand` trait.
* Remove WigFix2ADAM command.
* Move away from ParquetLoadSaveArgs.
* Move reads2coverage to actions.
* Reads2Coverage does not only write to Parquet, so clean up docs.
* Clean up fragments<->reads argument names.

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala

@@ -27,7 +27,11 @@ import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4JOption }
 
-class ADAM2FastaArgs extends ParquetLoadSaveArgs {
+class ADAM2FastaArgs extends Args4jBase {
+  @Argument(required = true, metaVar = "ADAM", usage = "The Parquet file to convert", index = 0)
+  var inputPath: String = null
+  @Argument(required = true, metaVar = "FASTA", usage = "Location to write the FASTA to", index = 1)
+  var outputPath: String = null
   @Args4JOption(required = false, name = "-coalesce", usage = "Choose the number of partitions to coalesce down to.")
   var coalesce: Int = -1
   @Args4JOption(required = false, name = "-force_shuffle_coalesce", usage = "Force shuffle while partitioning, default false.")

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala

@@ -27,7 +27,11 @@ import org.bdgenomics.formats.avro.AlignmentRecord
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.{ Argument, Option => Args4JOption }
 
-class ADAM2FastqArgs extends ParquetLoadSaveArgs {
+class ADAM2FastqArgs extends Args4jBase {
+  @Argument(required = true, metaVar = "INPUT", usage = "The read file to convert", index = 0)
+  var inputPath: String = null
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to write the FASTQ to", index = 1)
+  var outputPath: String = null
   @Argument(required = false, metaVar = "SECOND_OUTPUT", usage = "When writing FASTQ data, all second-in-pair reads will go here, if this argument is provided", index = 2)
   var outputPath2: String = null
 

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Vcf.scala

@@ -40,8 +40,6 @@ object ADAM2Vcf extends BDGCommandCompanion {
 }
 
 class ADAM2VcfArgs extends Args4jBase with ParquetArgs {
-  @Args4jOption(required = false, name = "-dict", usage = "Reference dictionary")
-  var dictionaryFile: File = _
 
   @Argument(required = true, metaVar = "ADAM", usage = "The ADAM variant files to convert", index = 0)
   var adamFile: String = _
@@ -64,17 +62,13 @@ class ADAM2VcfArgs extends Args4jBase with ParquetArgs {
   var single: Boolean = false
 }
 
-class ADAM2Vcf(val args: ADAM2VcfArgs) extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging {
+class ADAM2Vcf(val args: ADAM2VcfArgs) extends BDGSparkCommand[ADAM2VcfArgs] with Logging {
   val companion = ADAM2Vcf
 
   def run(sc: SparkContext) {
     require(!(args.sort && args.sortLexicographically),
       "Cannot set both -sort_on_save and -sort_lexicographically_on_save.")
 
-    var dictionary: Option[SequenceDictionary] = loadSequenceDictionary(args.dictionaryFile)
-    if (dictionary.isDefined)
-      log.info("Using contig translation")
-
     val adamGTs = sc.loadParquetGenotypes(args.adamFile)
 
     val coalesce = if (args.coalesce > 0) {

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala

@@ -32,13 +32,13 @@ object ADAMMain {
       CommandGroup(
         "ADAM ACTIONS",
         List(
-          CalculateDepth,
           CountReadKmers,
           CountContigKmers,
           Transform,
-          ADAM2Fastq,
+          TransformFeatures,
           Flatten,
-          MergeShards
+          MergeShards,
+          Reads2Coverage
         )
       ),
       CommandGroup(
@@ -49,20 +49,16 @@ object ADAMMain {
           VcfAnnotation2ADAM,
           Fasta2ADAM,
           ADAM2Fasta,
-          TransformFeatures,
-          WigFix2Bed,
+          ADAM2Fastq,
           Fragments2Reads,
-          Reads2Fragments,
-          Reads2Coverage
+          Reads2Fragments
         )
       ),
       CommandGroup(
         "PRINT",
         List(
           PrintADAM,
           FlagStat,
-          ListDict,
-          AlleleCount,
           View
         )
       )

adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountContigKmers.scala

@@ -28,7 +28,7 @@ import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 object CountContigKmers extends BDGCommandCompanion {
-  val commandName = "count_contig_kmers"
+  val commandName = "countContigKmers"
   val commandDescription = "Counts the k-mers/q-mers from a read dataset."
 
   def apply(cmdLine: Array[String]) = {

adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala

@@ -29,7 +29,7 @@ import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 object CountReadKmers extends BDGCommandCompanion {
-  val commandName = "count_kmers"
+  val commandName = "countKmers"
   val commandDescription = "Counts the k-mers/q-mers from a read dataset."
 
   def apply(cmdLine: Array[String]) = {

adam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala

@@ -36,10 +36,10 @@ object FlagStat extends BDGCommandCompanion {
   }
 }
 
-class FlagStatArgs extends Args4jBase with ParquetArgs {
+class FlagStatArgs extends Args4jBase {
   @Argument(required = true, metaVar = "INPUT", usage = "The ADAM data to return stats for", index = 0)
   val inputPath: String = null
-  @Argument(required = false, metaVar = "OUTPUT", usage = "Optionally write the stats to this file.", index = 1)
+  @Args4jOption(required = false, name = "-o", usage = "Optionally write the stats to this file.")
   val outputPath: String = null
   @Args4jOption(required = false, name = "-stringency", usage = "Set the parsing stringency: SILENT, LENIENT, STRICT.")
   val stringency: String = "SILENT"

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fragments2Reads.scala

@@ -35,9 +35,9 @@ object Fragments2Reads extends BDGCommandCompanion {
 }
 
 class Fragments2ReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
-  @Argument(required = true, metaVar = "INPUT", usage = "The Fragment file to apply the transforms to", index = 0)
+  @Argument(required = true, metaVar = "FRAGMENTS", usage = "The Fragment file to apply the transforms to", index = 0)
   var inputPath: String = null
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to write the transformed data in ADAM/Parquet format", index = 1)
+  @Argument(required = true, metaVar = "READS", usage = "Location to write the transformed data as reads", index = 1)
   var outputPath: String = null
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file")
   var asSingleFile: Boolean = false