From 6cd3a416174ae1f60685e328cace30a5f8c5dd3a Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 4 Nov 2015 15:41:37 -0600 Subject: [PATCH] separate command line argument words by underscores --- .../src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala | 2 +- .../src/main/scala/org/bdgenomics/adam/cli/Adam2Fastq.scala | 6 +++--- .../scala/org/bdgenomics/adam/cli/CountContigKmers.scala | 2 +- .../main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala | 2 +- .../src/main/scala/org/bdgenomics/adam/cli/Vcf2ADAM.scala | 6 +++--- .../scala/org/bdgenomics/adam/cli/VcfAnnotation2ADAM.scala | 2 +- 6 files changed, 10 insertions(+), 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 index e9685229b1..900e3c092e 100644 --- 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 index e3e8d4bdd6..b12276a931 100644 --- 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 index b0e957f215..3cfeceadd4 100644 --- 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 index a56eb44e2c..234f094b35 100644 --- 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 index 31b6c95dd2..8932639f00 100644 --- 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 index 072430aceb..15908374c4 100644 --- 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 }