K-mer.scala code

[Pavan637]

K-mer.scala code given at https://github.com/bigdatagenomics/adam is giving me errors.
I ran that code in two ways "

adam-shell -i kmer.scala

scalac kmer.scala

I am getting following errors
$scalac kmer.scala
kmer.scala:5: error: expected class or object definition
val ac = new ADAMContext(sc)
^
kmer.scala:7: error: expected class or object definition
val reads = ac.loadAlignments(
^
kmer.scala:19: error: expected class or object definition
val kmers =
^
kmer.scala:26: error: expected class or object definition
kmers.take(10).foreach(println)
^
four errors found

And when i run on spark "adam-shell -i kmer.scala". I am getting following errors
:19: error: object rdd is not a member of package org.bdgenomics.adam
import org.bdgenomics.adam.rdd.ADAMContext
^
:19: error: object rdd is not a member of package org.bdgenomics.adam
import org.bdgenomics.adam.rdd.ADAMContext._
^
:19: error: object projections is not a member of package org.bdgenomics.adam
import org.bdgenomics.adam.projections.{ AlignmentRecordField, Projection }
^
:21: error: not found: type ADAMContext
val ac = new ADAMContext(sc)
^
:19: error: not found: value ac
val reads = ac.loadAlignments(
^
:20: error: not found: value reads
reads
^
:1: error: illegal start of definition
.flatMap(.getSequence.sliding(21).map(k => (k, 1L)))
^
:1: error: illegal start of definition
.reduceByKey( + )
^
:1: error: illegal start of definition
.map(.swap)
^
:1: error: illegal start of definition
.sortByKey(ascending = false)
^
:20: error: not found: value kmers
kmers.take(10).foreach(println)
^
Kindly help me to solve the issues.

Regards
Pavan

[fnothaft]

Hi @Pavan637! What is the content of kmers.scala? Can you post it as a gist?

[Pavan637]

Thanks for replying...
Here is the code from the link (https://github.com/bigdatagenomics/adam)

`import org.bdgenomics.adam.rdd.ADAMContext
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.projections.{AlignmentRecordField, Projection}

val ac = new ADAMContext(sc)
// Load alignments from disk
val reads = ac.loadAlignments(
"/data/NA21144.chrom11.ILLUMINA.adam",
projection = Some(
Projection(
AlignmentRecordField.sequence,
AlignmentRecordField.readMapped,
AlignmentRecordField.mapq
)
)
)

// Generate, count and sort 21-mers
val kmers =
reads
.flatMap(.getSequence.sliding(21).map(k => (k, 1L)))
.reduceByKey( + )
.map(.swap)
.sortByKey(ascending = false)

// Print the top 10 most common 21-mers
kmers.take(10).foreach(println)`

[fnothaft]

Hi @Pavan637! We changed our build recently, and accidentally broke ./bin/adam-shell. I've just opened #1111 with a fix for this. Can you try this on your side?

[heuermh]

Thank you for reporting this, @Pavan637.

This issue was closed when I merged the pull request. If the change does not work for you, please reopen this issue.