Update pipe method calls due to latest ADAM 0.24.0 snapshot.

bigdatagenomics · Mar 22, 2018 · 32f8372 · 32f8372
1 parent 12f8800
commit 32f8372
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Showing 9 changed files with 25 additions and 9 deletions.
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bcftools.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bcftools.scala
@@ -20,13 +20,15 @@ package org.bdgenomics.cannoli.cli
 import htsjdk.samtools.ValidationStringency
 import org.apache.hadoop.fs.{ FileSystem, Path }
 import org.apache.spark.SparkContext
+import org.bdgenomics.adam.models.VariantContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.variant.{
   VariantContextRDD,
   VCFInFormatter,
   VCFOutFormatter
 }
+import org.bdgenomics.adam.sql.{ VariantContext => VariantContextProduct }
 import org.bdgenomics.cannoli.builder.CommandBuilders
 import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
@@ -96,7 +98,7 @@ class BcftoolsFn(
     implicit val tFormatter = VCFInFormatter
     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)
 
-    variantContexts.pipe(
+    variantContexts.pipe[VariantContext, VariantContextProduct, VariantContextRDD, VCFInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bedtools.scala
@@ -27,7 +27,9 @@ import org.bdgenomics.adam.rdd.feature.{
   BEDInFormatter,
   BEDOutFormatter
 }
+import org.bdgenomics.adam.sql.{ Feature => FeatureProduct }
 import org.bdgenomics.cannoli.builder.CommandBuilders
+import org.bdgenomics.formats.avro.Feature;
 import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
@@ -116,7 +118,7 @@ class BedtoolsFn(
     implicit val tFormatter = BEDInFormatter
     implicit val uFormatter = new BEDOutFormatter
 
-    features.pipe(
+    features.pipe[Feature, FeatureProduct, FeatureRDD, BEDInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala
@@ -24,7 +24,9 @@ import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.fragment.{ FragmentRDD, InterleavedFASTQInFormatter }
 import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, AnySAMOutFormatter }
+import org.bdgenomics.adam.sql.{ AlignmentRecord => AlignmentRecordProduct }
 import org.bdgenomics.cannoli.builder.CommandBuilders
+import org.bdgenomics.formats.avro.AlignmentRecord
 import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
@@ -96,7 +98,7 @@ class BowtieFn(
     implicit val tFormatter = InterleavedFASTQInFormatter
     implicit val uFormatter = new AnySAMOutFormatter
 
-    fragments.pipe(
+    fragments.pipe[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordRDD, InterleavedFASTQInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala
@@ -24,7 +24,9 @@ import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.fragment.{ FragmentRDD, InterleavedFASTQInFormatter }
 import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, AnySAMOutFormatter }
+import org.bdgenomics.adam.sql.{ AlignmentRecord => AlignmentRecordProduct }
 import org.bdgenomics.cannoli.builder.CommandBuilders
+import org.bdgenomics.formats.avro.AlignmentRecord
 import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
@@ -96,7 +98,7 @@ class Bowtie2Fn(
     implicit val tFormatter = InterleavedFASTQInFormatter
     implicit val uFormatter = new AnySAMOutFormatter
 
-    fragments.pipe(
+    fragments.pipe[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordRDD, InterleavedFASTQInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bwa.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Bwa.scala
@@ -25,8 +25,10 @@ import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.fragment.{ FragmentRDD, InterleavedFASTQInFormatter }
 import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, AnySAMOutFormatter }
+import org.bdgenomics.adam.sql.{ AlignmentRecord => AlignmentRecordProduct }
 import org.bdgenomics.cannoli.builder.CommandBuilders
 import org.bdgenomics.cannoli.util.QuerynameGrouper
+import org.bdgenomics.formats.avro.AlignmentRecord
 import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
@@ -141,7 +143,7 @@ class BwaFn(
     implicit val tFormatter = InterleavedFASTQInFormatter
     implicit val uFormatter = new AnySAMOutFormatter
 
-    fragments.pipe(
+    fragments.pipe[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordRDD, InterleavedFASTQInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
@@ -27,6 +27,7 @@ import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, BAMInFormatter }
 import org.bdgenomics.adam.rdd.variant.{ VariantContextRDD, VCFOutFormatter }
+import org.bdgenomics.adam.sql.{ VariantContext => VariantContextProduct }
 import org.bdgenomics.adam.util.FileExtensions._
 import org.bdgenomics.cannoli.builder.CommandBuilders
 import org.bdgenomics.utils.cli._
@@ -111,7 +112,7 @@ class FreebayesFn(
     implicit val tFormatter = BAMInFormatter
     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration, Some(accumulator))
 
-    val variantContexts = alignments.pipe[VariantContext, VariantContextRDD, BAMInFormatter](
+    val variantContexts = alignments.pipe[VariantContext, VariantContextProduct, VariantContextRDD, BAMInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Samtools.scala
@@ -25,6 +25,7 @@ import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, BAMInFormatter }
 import org.bdgenomics.adam.rdd.variant.{ VariantContextRDD, VCFOutFormatter }
+import org.bdgenomics.adam.sql.{ VariantContext => VariantContextProduct }
 import org.bdgenomics.adam.util.FileExtensions._
 import org.bdgenomics.cannoli.builder.CommandBuilders
 import org.bdgenomics.utils.cli._
@@ -98,7 +99,7 @@ class SamtoolsFn(
     implicit val tFormatter = BAMInFormatter
     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)
 
-    alignments.pipe[VariantContext, VariantContextRDD, BAMInFormatter](
+    alignments.pipe[VariantContext, VariantContextProduct, VariantContextRDD, BAMInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala
@@ -19,13 +19,15 @@ package org.bdgenomics.cannoli.cli
 
 import htsjdk.samtools.ValidationStringency
 import org.apache.spark.SparkContext
+import org.bdgenomics.adam.models.VariantContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.variant.{
   VariantContextRDD,
   VCFInFormatter,
   VCFOutFormatter
 }
+import org.bdgenomics.adam.sql.{ VariantContext => VariantContextProduct }
 import org.bdgenomics.cannoli.builder.CommandBuilders
 import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
@@ -85,7 +87,7 @@ class SnpEffFn(
     implicit val tFormatter = VCFInFormatter
     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)
 
-    variantContexts.pipe(
+    variantContexts.pipe[VariantContext, VariantContextProduct, VariantContextRDD, VCFInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )

diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Vt.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Vt.scala
@@ -20,13 +20,15 @@ package org.bdgenomics.cannoli.cli
 import htsjdk.samtools.ValidationStringency
 import org.apache.hadoop.fs.{ FileSystem, Path }
 import org.apache.spark.SparkContext
+import org.bdgenomics.adam.models.VariantContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.variant.{
   VariantContextRDD,
   VCFInFormatter,
   VCFOutFormatter
 }
+import org.bdgenomics.adam.sql.{ VariantContext => VariantContextProduct }
 import org.bdgenomics.cannoli.builder.CommandBuilders
 import org.bdgenomics.utils.cli._
 import org.bdgenomics.utils.misc.Logging
@@ -99,7 +101,7 @@ class VtFn(
     implicit val tFormatter = VCFInFormatter
     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)
 
-    variantContexts.pipe(
+    variantContexts.pipe[VariantContext, VariantContextProduct, VariantContextRDD, VCFInFormatter](
       cmd = builder.build(),
       files = builder.getFiles()
     )