[CANNOLI-183] Support VariantContext as Parquet in cli package.

cli/src/main/scala/org/bdgenomics/cannoli/cli/BcftoolsMpileup.scala

@@ -46,7 +46,7 @@ class BcftoolsMpileupArgs extends BcftoolsMpileupFnArgs with ADAMSaveAnyArgs wit
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe alignment records from (e.g. .bam, .cram, .sam). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe genotypes to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe variant contexts to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
@@ -73,8 +73,6 @@ class BcftoolsMpileup(protected val args: BcftoolsMpileupArgs) extends BDGSparkC
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
-    warn("inputPath " + args.inputPath + " outputPath " + args.outputPath)
-
     val alignments = sc.loadAlignments(args.inputPath, stringency = stringency)
     val variantContexts = new BcftoolsMpileupFn(args, stringency, sc).apply(alignments)
 
@@ -87,7 +85,7 @@ class BcftoolsMpileup(protected val args: BcftoolsMpileupArgs) extends BDGSparkC
         stringency
       )
     } else {
-      variantContexts.toGenotypes.saveAsParquet(args)
+      variantContexts.saveAsParquet(args)
     }
   }
 }

cli/src/main/scala/org/bdgenomics/cannoli/cli/BcftoolsNorm.scala

@@ -22,6 +22,7 @@ import htsjdk.samtools.ValidationStringency
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.util.FileExtensions._
 import org.bdgenomics.cannoli.{
   BcftoolsNorm => BcftoolsNormFn,
   BcftoolsNormArgs => BcftoolsNormFnArgs
@@ -42,10 +43,10 @@ object BcftoolsNorm extends BDGCommandCompanion {
  * Bcftools norm command line arguments.
  */
 class BcftoolsNormArgs extends BcftoolsNormFnArgs with ADAMSaveAnyArgs with ParquetArgs {
-  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in VCF format.", index = 0)
+  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe variant contexts from (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe to, in VCF format.", index = 1)
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe variant contexts to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
@@ -72,8 +73,19 @@ class BcftoolsNorm(protected val args: BcftoolsNormArgs) extends BDGSparkCommand
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
-    val variantContexts = sc.loadVcf(args.inputPath, stringency = stringency)
+    val variantContexts = sc.loadVariantContexts(args.inputPath)
     val pipedVariantContexts = new BcftoolsNormFn(args, stringency, sc).apply(variantContexts)
-    pipedVariantContexts.saveAsVcf(args, stringency)
+
+    if (isVcfExt(args.outputPath)) {
+      pipedVariantContexts.saveAsVcf(
+        args.outputPath,
+        asSingleFile = args.asSingleFile,
+        deferMerging = args.deferMerging,
+        disableFastConcat = args.disableFastConcat,
+        stringency
+      )
+    } else {
+      pipedVariantContexts.saveAsParquet(args)
+    }
   }
 }

cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala

@@ -43,7 +43,7 @@ class FreebayesArgs extends FreebayesFnArgs with ADAMSaveAnyArgs with ParquetArg
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe alignment records from (e.g. .bam, .cram, .sam). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe genotypes to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe variant contexts to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
@@ -82,7 +82,7 @@ class Freebayes(protected val args: FreebayesArgs) extends BDGSparkCommand[Freeb
         stringency
       )
     } else {
-      variantContexts.toGenotypes.saveAsParquet(args)
+      variantContexts.saveAsParquet(args)
     }
   }
 }

cli/src/main/scala/org/bdgenomics/cannoli/cli/SamtoolsMpileup.scala

@@ -46,7 +46,7 @@ class SamtoolsMpileupArgs extends SamtoolsMpileupFnArgs with ADAMSaveAnyArgs wit
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe alignment records from (e.g. .bam, .cram, .sam). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe genotypes to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe variant contexts to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
@@ -85,7 +85,7 @@ class SamtoolsMpileup(protected val args: SamtoolsMpileupArgs) extends BDGSparkC
         stringency
       )
     } else {
-      variantContexts.toGenotypes.saveAsParquet(args)
+      variantContexts.saveAsParquet(args)
     }
   }
 }

cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala

@@ -22,6 +22,7 @@ import htsjdk.samtools.ValidationStringency
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.util.FileExtensions._
 import org.bdgenomics.cannoli.{ SnpEff => SnpEffFn, SnpEffArgs => SnpEffFnArgs }
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
@@ -39,10 +40,10 @@ object SnpEff extends BDGCommandCompanion {
  * SnpEff command line arguments.
  */
 class SnpEffArgs extends SnpEffFnArgs with ADAMSaveAnyArgs with ParquetArgs {
-  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in VCF format.", index = 0)
+  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe variant contexts from (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe to, in VCF format.", index = 1)
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe variant contexts to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
@@ -69,8 +70,19 @@ class SnpEff(protected val args: SnpEffArgs) extends BDGSparkCommand[SnpEffArgs]
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
-    val variantContexts = sc.loadVcf(args.inputPath, stringency = stringency)
+    val variantContexts = sc.loadVariantContexts(args.inputPath)
     val pipedVariantContexts = new SnpEffFn(args, stringency, sc).apply(variantContexts)
-    pipedVariantContexts.saveAsVcf(args, stringency)
+
+    if (isVcfExt(args.outputPath)) {
+      pipedVariantContexts.saveAsVcf(
+        args.outputPath,
+        asSingleFile = args.asSingleFile,
+        deferMerging = args.deferMerging,
+        disableFastConcat = args.disableFastConcat,
+        stringency
+      )
+    } else {
+      pipedVariantContexts.saveAsParquet(args)
+    }
   }
 }

cli/src/main/scala/org/bdgenomics/cannoli/cli/Vep.scala

@@ -22,6 +22,7 @@ import htsjdk.samtools.ValidationStringency
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.util.FileExtensions._
 import org.bdgenomics.cannoli.{ Vep => VepFn, VepArgs => VepFnArgs }
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
@@ -39,10 +40,10 @@ object Vep extends BDGCommandCompanion {
  * Vep command line arguments.
  */
 class VepArgs extends VepFnArgs with ADAMSaveAnyArgs with ParquetArgs {
-  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in VCF format.", index = 0)
+  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe variant contexts from (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe to, in VCF format.", index = 1)
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe variant contexts to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
@@ -69,8 +70,19 @@ class Vep(protected val args: VepArgs) extends BDGSparkCommand[VepArgs] with Log
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
-    val variantContexts = sc.loadVcf(args.inputPath, stringency = stringency)
+    val variantContexts = sc.loadVariantContexts(args.inputPath)
     val pipedVariantContexts = new VepFn(args, stringency, sc).apply(variantContexts)
-    pipedVariantContexts.saveAsVcf(args, stringency)
+
+    if (isVcfExt(args.outputPath)) {
+      pipedVariantContexts.saveAsVcf(
+        args.outputPath,
+        asSingleFile = args.asSingleFile,
+        deferMerging = args.deferMerging,
+        disableFastConcat = args.disableFastConcat,
+        stringency
+      )
+    } else {
+      pipedVariantContexts.saveAsParquet(args)
+    }
   }
 }

cli/src/main/scala/org/bdgenomics/cannoli/cli/VtNormalize.scala

@@ -22,6 +22,7 @@ import htsjdk.samtools.ValidationStringency
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
+import org.bdgenomics.adam.util.FileExtensions._
 import org.bdgenomics.cannoli.{
   VtNormalize => VtNormalizeFn,
   VtNormalizeArgs => VtNormalizeFnArgs
@@ -42,10 +43,10 @@ object VtNormalize extends BDGCommandCompanion {
  * Vt normalize command line arguments.
  */
 class VtNormalizeArgs extends VtNormalizeFnArgs with ADAMSaveAnyArgs with ParquetArgs {
-  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe from, in VCF format.", index = 0)
+  @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe variant contexts from (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
-  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe to, in VCF format.", index = 1)
+  @Argument(required = true, metaVar = "OUTPUT", usage = "Location to pipe variant contexts to (e.g. .vcf, .vcf.gz, .vcf.bgz). If extension is not detected, Parquet is assumed.", index = 1)
   var outputPath: String = null
 
   @Args4jOption(required = false, name = "-single", usage = "Saves OUTPUT as single file.")
@@ -72,8 +73,19 @@ class VtNormalize(protected val args: VtNormalizeArgs) extends BDGSparkCommand[V
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
-    val variantContexts = sc.loadVcf(args.inputPath, stringency = stringency)
+    val variantContexts = sc.loadVariantContexts(args.inputPath)
     val pipedVariantContexts = new VtNormalizeFn(args, stringency, sc).apply(variantContexts)
-    pipedVariantContexts.saveAsVcf(args, stringency)
+
+    if (isVcfExt(args.outputPath)) {
+      pipedVariantContexts.saveAsVcf(
+        args.outputPath,
+        asSingleFile = args.asSingleFile,
+        deferMerging = args.deferMerging,
+        disableFastConcat = args.disableFastConcat,
+        stringency
+      )
+    } else {
+      pipedVariantContexts.saveAsParquet(args)
+    }
   }
 }