Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Closed
heuermh opened this issue Jul 23, 2017 · 0 comments
Closed

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

heuermh opened this issue Jul 23, 2017 · 0 comments
Milestone

Comments

@heuermh
Copy link
Member

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 Seq<VCFCompoundHeaderLine> vs. Seq<VCFHeaderLine> in javac Seq<VCFCompoundHeaderLine> vs. Seq<VCFHeaderLine> with javac Jul 23, 2017
@heuermh heuermh modified the milestone: 0.23.0 Jul 23, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant