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Merged
merged 6 commits into from
May 26, 2015
Merged

upgrade to bdg utils 0.2.1 #678

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95f4749
[ADAM-657, 581] Move to org.bdgenomics.utils:0.2.0 and from utils-par…
fnothaft Apr 30, 2015
0e1ef10
[ADAM-536] Add infrastructure for cross building to Scala 2.10 and Sc…
fnothaft Apr 30, 2015
6aa2198
[ADAM-603] Migrate CLI classes to BDG.
fnothaft Apr 30, 2015
0059c85
kill Job arg to ADAMSparkCommand
ryan-williams Apr 30, 2015
1508031
Merge remote-tracking branch 'origin/master' into utils
ryan-williams May 26, 2015
2b885c4
remove a couple of unused imports
ryan-williams May 26, 2015
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18 changes: 9 additions & 9 deletions adam-apis/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-parent</artifactId>
<artifactId>adam-parent_2.10</artifactId>
<version>0.16.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

<artifactId>adam-apis</artifactId>
<artifactId>adam-apis_2.10</artifactId>
<packaging>jar</packaging>
<name>ADAM: APIs for Java</name>
<name>ADAM_2.10: APIs for Java</name>
<build>
<plugins>
<!-- disable surefire -->
Expand Down Expand Up @@ -95,11 +95,11 @@
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.artifact.suffix}</artifactId>
<artifactId>spark-core_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-misc</artifactId>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-misc_2.10</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
Expand All @@ -109,11 +109,11 @@
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core</artifactId>
<artifactId>adam-core_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core</artifactId>
<artifactId>adam-core_2.10</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
Expand All @@ -131,7 +131,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.artifact.suffix}</artifactId>
<artifactId>scalatest_2.10</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
Expand Down
48 changes: 20 additions & 28 deletions adam-cli/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-parent</artifactId>
<artifactId>adam-parent_2.10</artifactId>
<version>0.16.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

<artifactId>adam-cli</artifactId>
<artifactId>adam-cli_2.10</artifactId>
<packaging>jar</packaging>
<name>ADAM: CLI</name>
<name>ADAM_2.10: CLI</name>
<build>
<plugins>
<plugin>
Expand Down Expand Up @@ -104,47 +104,51 @@
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.artifact.suffix}</artifactId>
<artifactId>spark-core_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-misc</artifactId>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-misc_2.10</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-parquet</artifactId>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-io_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-metrics</artifactId>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-cli_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-metrics_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.scoverage</groupId>
<artifactId>scalac-scoverage-plugin_${scala.artifact.suffix}</artifactId>
<artifactId>scalac-scoverage-plugin_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-formats</groupId>
<artifactId>bdg-formats</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core</artifactId>
<artifactId>adam-core_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core</artifactId>
<artifactId>adam-core_2.10</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-apis</artifactId>
<artifactId>adam-apis_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-apis</artifactId>
<artifactId>adam-apis_2.10</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
Expand All @@ -160,21 +164,9 @@
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
</dependency>
<dependency>
<groupId>org.fusesource.scalate</groupId>
<artifactId>scalate-core_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.scalatra</groupId>
<artifactId>scalatra-json_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.scalatra</groupId>
<artifactId>scalatra_2.10</artifactId>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.artifact.suffix}</artifactId>
<artifactId>scalatest_2.10</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
Expand Down
15 changes: 8 additions & 7 deletions adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Vcf.scala
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Expand Up @@ -17,17 +17,18 @@
*/
package org.bdgenomics.adam.cli

import org.bdgenomics.formats.avro.Genotype
import org.bdgenomics.adam.rdd.ADAMContext._
import org.kohsuke.args4j.{ Option => Args4jOption, Argument }
import java.io.File
import org.apache.spark.rdd.RDD
import org.apache.spark.{ Logging, SparkContext }
import org.apache.hadoop.mapreduce.Job
import java.io.File
import org.bdgenomics.adam.models.SequenceDictionary
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.formats.avro.Genotype
import org.bdgenomics.utils.cli._
import org.kohsuke.args4j.{ Option => Args4jOption, Argument }
import scala.Option

object ADAM2Vcf extends ADAMCommandCompanion {
object ADAM2Vcf extends BDGCommandCompanion {

val commandName = "adam2vcf"
val commandDescription = "Convert an ADAM variant to the VCF ADAM format"
Expand All @@ -54,10 +55,10 @@ class ADAM2VcfArgs extends Args4jBase with ParquetArgs {
var sort: Boolean = false
}

class ADAM2Vcf(val args: ADAM2VcfArgs) extends ADAMSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging {
class ADAM2Vcf(val args: ADAM2VcfArgs) extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging {
val companion = ADAM2Vcf

def run(sc: SparkContext, job: Job) {
def run(sc: SparkContext) {
var dictionary: Option[SequenceDictionary] = loadSequenceDictionary(args.dictionaryFile)
if (dictionary.isDefined)
log.info("Using contig translation")
Expand Down
91 changes: 0 additions & 91 deletions adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMCommand.scala
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7 changes: 3 additions & 4 deletions adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala
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Expand Up @@ -17,15 +17,14 @@
*/
package org.bdgenomics.adam.cli

import java.util.logging.Level._
import org.apache.spark.Logging
import scala.Some
import scala.collection.mutable.ListBuffer
import org.bdgenomics.adam.util.ParquetLogger
import java.util.logging.Level._
import org.bdgenomics.utils.cli._

object ADAMMain extends Logging {

case class CommandGroup(name: String, commands: List[ADAMCommandCompanion])
case class CommandGroup(name: String, commands: List[BDGCommandCompanion])

private val commandGroups =
List(
Expand Down
7 changes: 4 additions & 3 deletions adam-cli/src/main/scala/org/bdgenomics/adam/cli/Adam2Fastq.scala
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Expand Up @@ -25,6 +25,7 @@ import org.apache.spark.storage.StorageLevel
import org.bdgenomics.adam.projections.{ AlignmentRecordField, Projection }
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.formats.avro.AlignmentRecord
import org.bdgenomics.utils.cli._
import org.kohsuke.args4j.{ Option => Args4JOption, Argument }

class Adam2FastqArgs extends ParquetLoadSaveArgs {
Expand All @@ -40,18 +41,18 @@ class Adam2FastqArgs extends ParquetLoadSaveArgs {
var disableProjection: Boolean = false
}

object Adam2Fastq extends ADAMCommandCompanion {
object Adam2Fastq extends BDGCommandCompanion {
override val commandName = "adam2fastq"
override val commandDescription = "Convert BAM to FASTQ files"

override def apply(cmdLine: Array[String]): Adam2Fastq =
new Adam2Fastq(Args4j[Adam2FastqArgs](cmdLine))
}

class Adam2Fastq(val args: Adam2FastqArgs) extends ADAMSparkCommand[Adam2FastqArgs] {
class Adam2Fastq(val args: Adam2FastqArgs) extends BDGSparkCommand[Adam2FastqArgs] {
override val companion = Adam2Fastq

override def run(sc: SparkContext, job: Job): Unit = {
override def run(sc: SparkContext): Unit = {

val projectionOpt =
if (!args.disableProjection)
Expand Down
7 changes: 4 additions & 3 deletions adam-cli/src/main/scala/org/bdgenomics/adam/cli/AlleleCount.scala
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Expand Up @@ -23,9 +23,10 @@ import org.apache.spark.{ Logging, SparkContext }
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.formats.avro.{ Genotype, GenotypeAllele }
import org.bdgenomics.utils.cli._
import org.kohsuke.args4j.Argument

object AlleleCount extends ADAMCommandCompanion {
object AlleleCount extends BDGCommandCompanion {
val commandName = "allelecount"
val commandDescription = "Calculate Allele frequencies"

Expand Down Expand Up @@ -65,10 +66,10 @@ object AlleleCountHelper extends Serializable {
}
}

class AlleleCount(val args: AlleleCountArgs) extends ADAMSparkCommand[AlleleCountArgs] with Logging {
class AlleleCount(val args: AlleleCountArgs) extends BDGSparkCommand[AlleleCountArgs] with Logging {
val companion = AlleleCount

def run(sc: SparkContext, job: Job) {
def run(sc: SparkContext) {

val adamVariants: RDD[Genotype] = sc.loadGenotypes(args.adamFile)
AlleleCountHelper.countAlleles(adamVariants, args)
Expand Down
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