Refactor Bwa class names to BwaMem.

README.md

@@ -53,7 +53,7 @@ alignments, features, fragments, genotypes, reads, sequences, slices, variant co
 or variants, such as `sc.loadPairedFastqAsFragments` below.
 
 Wildcard import from `Cannoli` to add implicit methods for calling external commands to the
-genomic datasets loaded by ADAM, such as `reads.alignWithBwa` below.
+genomic datasets loaded by ADAM, such as `reads.alignWithBwaMem` below.
 
 ```
 $ ./bin/cannoli-shell \
@@ -68,8 +68,8 @@ import org.bdgenomics.cannoli.Cannoli._
 scala> import org.bdgenomics.cannoli.BwaArgs
 import org.bdgenomics.cannoli.BwaArgs
 
-scala> val args = new BwaArgs()
-args: org.bdgenomics.cannoli.BwaArgs = org.bdgenomics.cannoli.BwaArgs@54234569
+scala> val args = new BwaMemArgs()
+args: org.bdgenomics.cannoli.BwaMemArgs = org.bdgenomics.cannoli.BwaMemArgs@54234569
 
 scala> args.indexPath = "hg38.fa"
 args.indexPath: String = hg38.fa
@@ -81,7 +81,7 @@ scala> val reads = sc.loadPairedFastqAsFragments("sample1.fq", "sample2.fq")
 reads: org.bdgenomics.adam.rdd.fragment.FragmentRDD = RDDBoundFragmentRDD with 0 reference
 sequences, 0 read groups, and 0 processing steps
 
-scala> val alignments = reads.alignWithBwa(args)
+scala> val alignments = reads.alignWithBwaMem(args)
 alignments: org.bdgenomics.adam.rdd.read.AlignmentRecordRDD = RDDBoundAlignmentRecordRDD with
 0 reference sequences, 0 read groups, and 0 processing steps
 
@@ -118,7 +118,7 @@ CANNOLI
               bowtie : Align paired-end reads in a fragment dataset with Bowtie.
              bowtie2 : Align paired-end reads in a fragment dataset with Bowtie 2.
     singleEndBowtie2 : Align unaligned single-end reads in an alignment dataset with Bowtie 2.
-                 bwa : Align paired-end reads in a fragment dataset with BWA.
+              bwaMem : Align paired-end reads in a fragment dataset with bwa mem.
              bwaMem2 : Align paired-end reads in a fragment dataset with Bwa-mem2.
            freebayes : Call variants from an alignment dataset with Freebayes.
                  gem : Align paired-end reads in a fragment dataset with GEM-Mapper.
@@ -144,7 +144,7 @@ External commands wrapped by Cannoli should be installed to each executor node i
 $ ./bin/cannoli-submit \
     <spark-args>
     -- \
-    bwa \
+    bwaMem \
     sample.unaligned.fragments.adam \
     sample.bwa.hg38.alignments.adam \
     sample \
@@ -160,7 +160,7 @@ or can be run using Docker
 $ ./bin/cannoli-submit \
     <spark-args>
     -- \
-    bwa \
+    bwaMem \
     sample.unaligned.fragments.adam \
     sample.bwa.hg38.alignments.adam \
     sample \
@@ -178,7 +178,7 @@ or can be run using Singularity
 $ ./bin/cannoli-submit \
     <spark-args>
     -- \
-    bwa \
+    bwaMem \
     sample.unaligned.fragments.adam \
     sample.bwa.hg38.alignments.adam \
     sample \

cli/src/main/scala/org/bdgenomics/cannoli/cli/Bwa.scala → cli/src/main/scala/org/bdgenomics/cannoli/cli/BwaMem.scala

@@ -24,24 +24,24 @@ import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.fragment.FragmentDataset
 import org.bdgenomics.adam.rdd.read.AlignmentDataset
-import org.bdgenomics.cannoli.{ Bwa => BwaFn, BwaArgs => BwaFnArgs }
+import org.bdgenomics.cannoli.{ BwaMem => BwaMemFn, BwaMemArgs => BwaMemFnArgs }
 import org.bdgenomics.cannoli.util.QuerynameGrouper
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
-object Bwa extends BDGCommandCompanion {
-  val commandName = "bwa"
-  val commandDescription = "Align paired-end reads in a fragment dataset with BWA."
+object BwaMem extends BDGCommandCompanion {
+  val commandName = "bwaMem"
+  val commandDescription = "Align paired-end reads in a fragment dataset with bwa mem."
 
   def apply(cmdLine: Array[String]) = {
-    new Bwa(Args4j[BwaArgs](cmdLine))
+    new BwaMem(Args4j[BwaMemArgs](cmdLine))
   }
 }
 
 /**
- * Bwa command line arguments.
+ * Bwa mem command line arguments.
  */
-class BwaArgs extends BwaFnArgs with ADAMSaveAnyArgs with ParquetArgs {
+class BwaMemArgs extends BwaMemFnArgs with ADAMSaveAnyArgs with ParquetArgs {
   @Argument(required = true, metaVar = "INPUT", usage = "Location to pipe fragments from (e.g. interleaved FASTQ format, .ifq) If extension is not detected, Parquet is assumed.", index = 0)
   var inputPath: String = null
 
@@ -77,10 +77,10 @@ class BwaArgs extends BwaFnArgs with ADAMSaveAnyArgs with ParquetArgs {
 }
 
 /**
- * Bwa command line wrapper.
+ * Bwa mem command line wrapper.
  */
-class Bwa(protected val args: BwaArgs) extends BDGSparkCommand[BwaArgs] with Logging {
-  val companion = Bwa
+class BwaMem(protected val args: BwaMemArgs) extends BDGSparkCommand[BwaMemArgs] with Logging {
+  val companion = BwaMem
   val stringency: ValidationStringency = ValidationStringency.valueOf(args.stringency)
 
   def run(sc: SparkContext) {
@@ -96,7 +96,7 @@ class Bwa(protected val args: BwaArgs) extends BDGSparkCommand[BwaArgs] with Log
       sc.loadFragments(args.inputPath, stringency = stringency)
     }
 
-    val output: AlignmentDataset = new BwaFn(args, sc).apply(input)
+    val output: AlignmentDataset = new BwaMemFn(args, sc).apply(input)
 
     val outputMaybeWithSequences = Option(args.sequenceDictionary).fold(output)(sdPath => {
       val sequences = sc.loadSequenceDictionary(sdPath)

cli/src/main/scala/org/bdgenomics/cannoli/cli/Cannoli.scala

@@ -36,7 +36,7 @@ object Cannoli {
     Bowtie,
     Bowtie2,
     SingleEndBowtie2,
-    Bwa,
+    BwaMem,
     BwaMem2,
     Freebayes,
     Gem,

core/src/main/scala/org/bdgenomics/cannoli/Bwa.scala → core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala

@@ -30,9 +30,9 @@ import org.kohsuke.args4j.{ Option => Args4jOption }
 import scala.collection.JavaConversions._
 
 /**
- * Bwa function arguments.
+ * Bwa mem function arguments.
  */
-class BwaArgs extends ReadGroupArgs {
+class BwaMemArgs extends ReadGroupArgs {
   @Args4jOption(required = true, name = "-index", usage = "Path to the BWA index to be searched, e.g. <idxbase> in bwa [options]* <idxbase>. Required.")
   var indexPath: String = null
 
@@ -48,22 +48,22 @@ class BwaArgs extends ReadGroupArgs {
   @Args4jOption(required = false, name = "-add_files", usage = "If true, use the SparkFiles mechanism to distribute files to executors.")
   var addFiles: Boolean = false
 
-  @Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch BWA.")
+  @Args4jOption(required = false, name = "-use_docker", usage = "If true, uses Docker to launch bwa mem.")
   var useDocker: Boolean = false
 
-  @Args4jOption(required = false, name = "-use_singularity", usage = "If true, uses Singularity to launch BWA.")
+  @Args4jOption(required = false, name = "-use_singularity", usage = "If true, uses Singularity to launch bwa mem.")
   var useSingularity: Boolean = false
 }
 
 /**
- * Bwa wrapper as a function FragmentDataset &rarr; AlignmentDataset,
+ * Bwa mem wrapper as a function FragmentDataset &rarr; AlignmentDataset,
  * for use in cannoli-shell or notebooks.
  *
- * @param args Bwa function arguments.
+ * @param args Bwa mem function arguments.
  * @param sc Spark context.
  */
-class Bwa(
-    val args: BwaArgs,
+class BwaMem(
+    val args: BwaMemArgs,
     sc: SparkContext) extends CannoliFn[FragmentDataset, AlignmentDataset](sc) {
 
   override def apply(fragments: FragmentDataset): AlignmentDataset = {

core/src/main/scala/org/bdgenomics/cannoli/Cannoli.scala

@@ -128,13 +128,13 @@ object Cannoli {
     }
 
     /**
-     * Align the paired-end reads in this FragmentDataset with BWA via Cannoli.
+     * Align the paired-end reads in this FragmentDataset with bwa mem via Cannoli.
      *
-     * @param args Bwa function arguments.
+     * @param args Bwa mem function arguments.
      * @return AlignmentDataset.
      */
-    def alignWithBwa(args: BwaArgs): AlignmentDataset = {
-      new Bwa(args, fragments.rdd.context).apply(fragments)
+    def alignWithBwaMem(args: BwaMemArgs): AlignmentDataset = {
+      new BwaMem(args, fragments.rdd.context).apply(fragments)
     }
 
     /**