separate command line argument words by underscores

bigdatagenomics · Nov 4, 2015 · 6cd3a41 · 6cd3a41
1 parent b91188b
commit 6cd3a41
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Showing 6 changed files with 10 additions and 10 deletions.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala
@@ -31,7 +31,7 @@ class ADAM2FastaArgs extends ParquetLoadSaveArgs {
   var coalesce: Int = -1
   @Args4JOption(required = false, name = "-force_shuffle_coalesce", usage = "Force shuffle while partitioning, default false.")
   var forceShuffle: Boolean = false
-  @Args4JOption(required = false, name = "-line-width", usage = "Hard wrap FASTA formatted sequence at line width, default 60")
+  @Args4JOption(required = false, name = "-line_width", usage = "Hard wrap FASTA formatted sequence at line width, default 60")
   var lineWidth: Int = 60
 }
 

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Adam2Fastq.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Adam2Fastq.scala
@@ -34,11 +34,11 @@ class Adam2FastqArgs extends ParquetLoadSaveArgs {
   var validationStringency = ValidationStringency.LENIENT
   @Args4JOption(required = false, name = "-repartition", usage = "Set the number of partitions to map data to")
   var repartition: Int = -1
-  @Args4JOption(required = false, name = "-persist-level", usage = "Persist() intermediate RDDs")
+  @Args4JOption(required = false, name = "-persist_level", usage = "Persist() intermediate RDDs")
   var persistLevel: String = null
-  @Args4JOption(required = false, name = "-no-projection", usage = "Disable projection on records. No great reason to do this, but useful for testing / comparison.")
+  @Args4JOption(required = false, name = "-no_projection", usage = "Disable projection on records. No great reason to do this, but useful for testing / comparison.")
   var disableProjection: Boolean = false
-  @Args4JOption(required = false, name = "-output-oq", usage = "Output the original sequencing quality scores")
+  @Args4JOption(required = false, name = "-output_oq", usage = "Output the original sequencing quality scores")
   var outputOriginalBaseQualities = false
 }
 

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountContigKmers.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountContigKmers.scala
@@ -43,7 +43,7 @@ class CountContigKmersArgs extends Args4jBase with ParquetArgs {
   var outputPath: String = null
   @Argument(required = true, metaVar = "KMER_LENGTH", usage = "Length of k-mers", index = 2)
   var kmerLength: Int = 0
-  @Args4jOption(required = false, name = "-printHistogram", usage = "Prints a histogram of counts.")
+  @Args4jOption(required = false, name = "-print_histogram", usage = "Prints a histogram of counts.")
   var printHistogram: Boolean = false
 }
 

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala
@@ -44,7 +44,7 @@ class CountReadKmersArgs extends Args4jBase with ParquetArgs {
   var outputPath: String = null
   @Argument(required = true, metaVar = "KMER_LENGTH", usage = "Length of k-mers", index = 2)
   var kmerLength: Int = 0
-  @Args4jOption(required = false, name = "-printHistogram", usage = "Prints a histogram of counts.")
+  @Args4jOption(required = false, name = "-print_histogram", usage = "Prints a histogram of counts.")
   var printHistogram: Boolean = false
   @Args4jOption(required = false, name = "-repartition", usage = "Set the number of partitions to map data to")
   var repartition: Int = -1

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Vcf2ADAM.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Vcf2ADAM.scala
@@ -51,8 +51,8 @@ class Vcf2ADAMArgs extends Args4jBase with ParquetSaveArgs {
   @Args4jOption(required = false, name = "-force_shuffle_coalesce", usage = "Even if the repartitioned RDD has fewer partitions, force a shuffle.")
   var forceShuffle: Boolean = false
 
-  @Args4jOption(required = false, name = "-onlyvariants", usage = "Output Variant objects instead of Genotypes")
-  var onlyvariants: Boolean = false
+  @Args4jOption(required = false, name = "-only_variants", usage = "Output Variant objects instead of Genotypes")
+  var onlyVariants: Boolean = false
 }
 
 class Vcf2ADAM(val args: Vcf2ADAMArgs) extends BDGSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging {
@@ -73,7 +73,7 @@ class Vcf2ADAM(val args: Vcf2ADAMArgs) extends BDGSparkCommand[Vcf2ADAMArgs] wit
       }
     }
 
-    if (args.onlyvariants) {
+    if (args.onlyVariants) {
       adamVariants
         .map(v => v.variant.variant)
         .adamParquetSave(args)

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VcfAnnotation2ADAM.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/VcfAnnotation2ADAM.scala
@@ -43,7 +43,7 @@ class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs {
   var vcfFile: String = _
   @Argument(required = true, metaVar = "ADAM", usage = "Location to write ADAM Variant annotations data", index = 1)
   var outputPath: String = null
-  @Args4jOption(required = false, name = "-current-db", usage = "Location of existing ADAM Variant annotations data")
+  @Args4jOption(required = false, name = "-current_db", usage = "Location of existing ADAM Variant annotations data")
   var currentAnnotations: String = null
 }