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Seq<VCFCompoundHeaderLine> vs. Seq<VCFHeaderLine> with javac #1625

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heuermh opened this Issue Jul 23, 2017 · 0 comments

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heuermh commented Jul 23, 2017

Attempting to call

return VariantRDD.apply(
  variants.rdd(),
  SequenceDictionary.empty(),
  DefaultHeaderLines.allHeaderLines()
);

results in a compile error in javac, as Seq<VCFCompoundHeaderLine> and Seq<VCFHeaderLine> do not match

$ mvn compile
...
[ERROR] dishevelled-bio/adam/src/main/java/org/dishevelled/bio/adam/DishevelledAdamContext.java:[181,30] no suitable method found for apply(org.apache.spark.rdd.RDD<org.bdgenomics.formats.avro.Variant>,org.bdgenomics.adam.models.SequenceDictionary,scala.collection.Seq<htsjdk.variant.vcf.VCFCompoundHeaderLine>)
[ERROR]     method org.bdgenomics.adam.rdd.variant.VariantRDD.apply(org.apache.spark.sql.Dataset<org.bdgenomics.adam.sql.Variant>,org.bdgenomics.adam.models.SequenceDictionary,scala.collection.Seq<htsjdk.variant.vcf.VCFHeaderLine>) is not applicable
[ERROR]       (argument mismatch; org.apache.spark.rdd.RDD<org.bdgenomics.formats.avro.Variant> cannot be converted to org.apache.spark.sql.Dataset<org.bdgenomics.adam.sql.Variant>)
[ERROR]     method org.bdgenomics.adam.rdd.variant.VariantRDD.apply(org.apache.spark.rdd.RDD<org.bdgenomics.formats.avro.Variant>,org.bdgenomics.adam.models.SequenceDictionary,scala.collection.Seq<htsjdk.variant.vcf.VCFHeaderLine>) is not applicable
[ERROR]       (argument mismatch; scala.collection.Seq<htsjdk.variant.vcf.VCFCompoundHeaderLine> cannot be converted to scala.collection.Seq<htsjdk.variant.vcf.VCFHeaderLine>)
[ERROR] dishevelled-bio/adam/src/main/java/org/dishevelled/bio/adam/DishevelledAdamContext.java:[197,31] no suitable method found for apply(org.apache.spark.rdd.RDD<org.bdgenomics.formats.avro.Genotype>,org.bdgenomics.adam.models.SequenceDictionary,scala.collection.Seq<htsjdk.variant.vcf.VCFCompoundHeaderLine>)
[ERROR]     method org.bdgenomics.adam.rdd.variant.GenotypeRDD.apply(org.apache.spark.sql.Dataset<org.bdgenomics.adam.sql.Genotype>,org.bdgenomics.adam.models.SequenceDictionary,scala.collection.Iterable<org.bdgenomics.formats.avro.Sample>,scala.collection.Seq<htsjdk.variant.vcf.VCFHeaderLine>) is not applicable
[ERROR]       (actual and formal argument lists differ in length)
[ERROR]     method org.bdgenomics.adam.rdd.variant.GenotypeRDD.apply(org.apache.spark.rdd.RDD<org.bdgenomics.formats.avro.Genotype>,org.bdgenomics.adam.models.SequenceDictionary,scala.collection.Iterable<org.bdgenomics.formats.avro.Sample>,scala.collection.Seq<htsjdk.variant.vcf.VCFHeaderLine>) is not applicable
[ERROR]       (actual and formal argument lists differ in length)
[ERROR] -> [Help 1]

@heuermh heuermh changed the title from Seq<VCFCompoundHeaderLine> vs. Seq<VCFHeaderLine> in javac to Seq<VCFCompoundHeaderLine> vs. Seq<VCFHeaderLine> with javac Jul 23, 2017

@heuermh heuermh modified the milestone: 0.23.0 Jul 23, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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