re-org and bug fixes

fulcrumgenomics · Aug 24, 2020 · 242a786 · 242a786
1 parent e264f32
commit 242a786
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Showing 2 changed files with 11 additions and 7 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/vcf/ValidateVcf.scala b/src/main/scala/com/fulcrumgenomics/vcf/ValidateVcf.scala
@@ -29,7 +29,7 @@ import com.fulcrumgenomics.FgBioDef.{PathToVcf, SafelyClosable}
 import com.fulcrumgenomics.cmdline.{ClpGroups, FgBioTool}
 import com.fulcrumgenomics.commons.util.{LazyLogging, LogLevel, Logger, SimpleCounter}
 import com.fulcrumgenomics.sopt.{arg, clp}
-import com.fulcrumgenomics.util.Io
+import com.fulcrumgenomics.util.{Io, ProgressLogger}
 import com.fulcrumgenomics.vcf.api.VcfHeader._
 import com.fulcrumgenomics.vcf.api._
 import com.fulcrumgenomics.vcf.validation.GenotypeValidator.{PhaseSetGenotypeValidator, VariantFormatExtraFieldValidator, VariantFormatValidator}
@@ -93,6 +93,8 @@ class ValidateVcf
   override def execute(): Unit = {
     Logger.level = this.level
 
+    val progress = new ProgressLogger(logger=logger, noun="variants", verb="examined", unit=100000)
+
     // Validate the VCF header
     val reader                = VcfSource(path=input, allowKindMismatch=allowTypeMismatch, allowExtraFields=allowExtraFields)
     val headerValidators      = VcfHeaderValidator.Validators
@@ -111,8 +113,10 @@ class ValidateVcf
       case Some(n) => reader.take(n)
     }
     iter.foreach { variant: Variant =>
+      progress.record(variant=variant)
       variantValidators.foreach(_.validate(variant=variant).process())
     }
+    progress.logLast()
     reader.safelyClose
 
     // Summarize and log errors

diff --git a/src/main/scala/com/fulcrumgenomics/vcf/validation/ValidationResult.scala b/src/main/scala/com/fulcrumgenomics/vcf/validation/ValidationResult.scala
@@ -62,18 +62,18 @@ object ValidationResult {
   def info(message: String, variant: Option[Variant] = None, genotype: Option[Genotype] = None): ValidationResult = {
     ValidationResult(variant=variant, message=message, genotype=genotype, level=LogLevel.Info)
   }
-  def info(message: String, variant: Variant): ValidationResult = debug(message=message, variant=Some(variant))
-  def info(message: String, variant: Variant, genotype: Genotype): ValidationResult = debug(message=message, variant=Some(variant), genotype=Some(genotype))
+  def info(message: String, variant: Variant): ValidationResult = info(message=message, variant=Some(variant))
+  def info(message: String, variant: Variant, genotype: Genotype): ValidationResult = info(message=message, variant=Some(variant), genotype=Some(genotype))
 
   def warning(message: String, variant: Option[Variant] = None, genotype: Option[Genotype] = None): ValidationResult = {
     ValidationResult(variant=variant, message=message, genotype=genotype, level=LogLevel.Warning)
   }
-  def warning(message: String, variant: Variant): ValidationResult = debug(message=message, variant=Some(variant))
-  def warning(message: String, variant: Variant, genotype: Genotype): ValidationResult = debug(message=message, variant=Some(variant), genotype=Some(genotype))
+  def warning(message: String, variant: Variant): ValidationResult = warning(message=message, variant=Some(variant))
+  def warning(message: String, variant: Variant, genotype: Genotype): ValidationResult = warning(message=message, variant=Some(variant), genotype=Some(genotype))
 
   def error(message: String, variant: Option[Variant] = None, genotype: Option[Genotype] = None): ValidationResult = {
     ValidationResult(variant=variant, message=message, genotype=genotype, level=LogLevel.Error)
   }
-  def error(message: String, variant: Variant): ValidationResult = debug(message=message, variant=Some(variant))
-  def error(message: String, variant: Variant, genotype: Genotype): ValidationResult = debug(message=message, variant=Some(variant), genotype=Some(genotype))
+  def error(message: String, variant: Variant): ValidationResult = error(message=message, variant=Some(variant))
+  def error(message: String, variant: Variant, genotype: Genotype): ValidationResult = error(message=message, variant=Some(variant), genotype=Some(genotype))
 }