Bumped toolkit and dependency versions and resolved resulting issues. (…

…#30)

* Bumped toolkit and dependency versions and resolved resulting issues

.gitignore

@@ -7,3 +7,4 @@ target
 .bloop
 .metals
 .vscode
+.bsp

build.sc

@@ -1,12 +1,8 @@
-import java.text.SimpleDateFormat
-import java.util.Date
-
 import mill._
 import mill.scalalib._
-import mill.scalalib.publish.{Developer, License, PomSettings, SCM}
+import mill.scalalib.publish._
 import java.util.jar.Attributes.Name.{IMPLEMENTATION_VERSION => ImplementationVersion}
 
-import ammonite.ops._
 import coursier.maven.MavenRepository
 
 import scala.sys.process.Process
@@ -15,23 +11,23 @@ import scala.util.{Failure, Success, Try}
 /** Base trait for build modules. */
 trait CommonModule extends SbtModule {
   def deployLocal(assembly: PathRef, jarName:String) = {
-    mkdir(pwd / 'jars)
+    os.makeDir.all(os.pwd / Symbol("jars"))
     println(s"Copying artifact ${assembly.path} to jars / $jarName")
-    cp.over(assembly.path, pwd / 'jars / jarName)
+    os.copy(assembly.path, os.pwd / Symbol("jars") / jarName, replaceExisting = true)
   }
 
   override def repositories: Seq[coursier.Repository] = super.repositories ++ Seq(
     MavenRepository("https://oss.sonatype.org/content/repositories/public"),
     MavenRepository("https://oss.sonatype.org/content/repositories/snapshots"),
     MavenRepository("https://jcenter.bintray.com/"),
-    MavenRepository("https://artifactory.broadinstitute.org/artifactory/libs-snapshot/")
+    MavenRepository("https://broadinstitute.jfrog.io/artifactory/libs-snapshot/")
   )
 }
 
 /** A base trait for versioning modules. */
 trait ReleaseModule extends JavaModule {
   /** Execute Git arguments and return the standard output. */
-  private def git(args: String*): String = %%("git", args)(pwd).out.string.trim
+  private def git(args: String*): String = os.proc("git", args).call().out.text().trim
 
   /** Get the commit hash at the HEAD of this branch. */
   private def gitHead: String = git("rev-parse", "HEAD")
@@ -73,21 +69,18 @@ trait ReleaseModule extends JavaModule {
 
 
 object tools extends CommonModule with PublishModule with ReleaseModule {
-  def scalaVersion = "2.13.3"
-  def millSourcePath = super.millSourcePath / ammonite.ops.up
-  def mainClass = Some("com.fulcrumgenomics.sv.cmdline.SvMain")
-  def artifactName = "fgsv"
+  def scalaVersion = "2.13.8"
+  override def millSourcePath = super.millSourcePath / os.up
+  override def mainClass = Some("com.fulcrumgenomics.sv.cmdline.SvMain")
+  override def artifactName = "fgsv"
   def gitHash = Process("git rev-parse --short HEAD").lineStream.head
-  def publishVersion = s"0.0.4-${gitHash}-SNAPSHOT"
+  def publishVersion = s"0.1.0-${gitHash}-SNAPSHOT"
   def pomSettings = PomSettings(
     description = artifactName(),
     organization = "com.fulcrumgenomics",
     url = "https://github.com/fulcrumgenomics/fgsv",
-    licenses = Seq(License("MIT License", "http://www.fulcrumgenomics.com")),
-    scm = SCM(
-      "git://github.com:fulcrumgenomics/fgsv.git",
-      "scm:git://github.com:fulcrumgenomics/fgsv.git"
-    ),
+    licenses = Seq(License.MIT),
+    versionControl = VersionControl.github("fulcrumgenomics","fgsv"),
     developers = Seq(
       Developer("tfenne", "Tim Fennell", "https://github.com/tfenne"),
       Developer("nh13", "Nils Homer", "https://github.com/nh13"),
@@ -101,23 +94,22 @@ object tools extends CommonModule with PublishModule with ReleaseModule {
     "com.google.cloud.genomics"
   )
 
-  def ivyDeps = Agg(
+  override def ivyDeps = Agg(
     ivy"org.scala-lang:scala-compiler:${scalaVersion()}",
-    ivy"com.fulcrumgenomics:fgbio_2.13:1.5.0".excludeOrg(orgsToExclude:_*),
-    ivy"org.xerial.snappy:snappy-java:1.1.8.4"
+    ivy"com.fulcrumgenomics:fgbio_2.13:2.1.0".excludeOrg(orgsToExclude:_*)
   )
 
   object test extends Tests {
-    def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.1.0")
-    def testFramework = "org.scalatest.tools.Framework"
+    override def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.1.0")
+    override def testFramework = "org.scalatest.tools.Framework"
 
     // run mill tools.test.singleTest com.fulcrumgenomics.sv.x.y.x.TestClassName
     def singleTest(args: String*) = T.command {
       super.runMain("org.scalatest.run", args: _*)
     }
   }
 
-  def javacOptions = Seq("-source", "1.8", "-target", "1.8")
+  override def javacOptions = Seq("-source", "1.8", "-target", "1.8")
 
   def deployLocal = T { super.deployLocal(assembly(), "fgsv.jar")  }
 }

docs/tools/AggregateSvPileup.md

@@ -40,8 +40,8 @@ pileups in the cluster.
 
 ## Arguments
 
-|Name|Flag|Type|Description|Required?|Max Values|Default Value(s)|
-|----|----|----|-----------|---------|----------|----------------|
+|Name|Flag|Type|Description|Required?|Max # of Values|Default Value(s)|
+|----|----|----|-----------|---------|---------------|----------------|
 |input|i|FilePath|Input text file of pileups generated by SvPileup|Required|1||
 |bam|b|PathToBam|Bam file for allele frequency analysis. Must be coordinate sorted version of the file that was input to SvPileup.|Optional|1||
 |flank|f|Int|If BAM file is provided: distance upstream and downstream of aggregated breakpoint regions to search for mapped templates that overlap breakends. These are the templates that will be partitioned into those supporting the breakpoint vs. reading through it for the allele frequency calculation. Recommended to use at least the max read pair inner distance used by SvPileup.|Optional|1|1000|

docs/tools/FilterAndMerge.md

@@ -11,8 +11,8 @@ Filters and merges SVPileup output.
 
 ## Arguments
 
-|Name|Flag|Type|Description|Required?|Max Values|Default Value(s)|
-|----|----|----|-----------|---------|----------|----------------|
+|Name|Flag|Type|Description|Required?|Max # of Values|Default Value(s)|
+|----|----|----|-----------|---------|---------------|----------------|
 |input|i|FilePath|The input pileup file from SvPileup|Required|1||
 |output|o|FilePath|The output filtered and merged SvPileup file|Required|1||
 |dict|d|PathToSequenceDictionary|The path to the reference sequence dictionary.|Required|1||

docs/tools/SvPileup.md

@@ -23,7 +23,7 @@ The `be` SAM tag contains a comma-delimited list of breakpoints to which a given
 semi-colon delimited, with four fields:
 
 1. The unique breakpoint identifier (same identifier found in the tab-delimited output).
-2. Either "left" or "right, corresponding to whether the read shows evidence of the genomic left or right side of 
+2. Either "left" or "right, corresponding to whether the read shows evidence of the genomic left or right side of
    the breakpoint as found in the breakpoint file (i.e. `left_pos` or `right_pos`).
 3. Either "from" or "into", such that when traversing the breakpoint would read through "from" and then into
    "into" in the sequencing order of the read pair.  For a split-read alignment, the "from" contains the aligned
@@ -36,7 +36,7 @@ As described in the Algorithm Overview below, split-read evidence is favored ove
 Therefore, if the template (alignments for a read pair) contain both types of evidence, then the `be` tag
 will only be added to the split-read alignments (i.e. the primary and supplementary alignments of the read
 in the pair that has split-read evidence), and will not be found in the mate's alignment.
- 
+
 ## Example output
 
 The following shows two breakpoints:
@@ -79,8 +79,8 @@ Split read evidence will be returned in favor of across-read-pair evidence when
 
 ## Arguments
 
-|Name|Flag|Type|Description|Required?|Max Values|Default Value(s)|
-|----|----|----|-----------|---------|----------|----------------|
+|Name|Flag|Type|Description|Required?|Max # of Values|Default Value(s)|
+|----|----|----|-----------|---------|---------------|----------------|
 |input|i|PathToBam|The input query sorted or grouped BAM|Required|1||
 |output|o|PathPrefix|The output path prefix|Required|1||
 |max-read-pair-inner-distance|d|Int|The maximum _inner_ distance for normal read pair|Optional|1|1000|

docs/tools/index.md

@@ -4,8 +4,7 @@ title: fgsv tools
 
 # fgsv tools
 
-The following tools are available in fgsv version 0.0.3-3f469cb.
-
+The following tools are available in fgsv version 0.1.0-fd73568.
 ## All tools
 
 All tools.

mill

@@ -3,7 +3,7 @@
 # This is a wrapper script, that automatically download mill from GitHub release pages
 # You can give the required mill version with MILL_VERSION env variable
 # If no version is given, it falls back to the value of DEFAULT_MILL_VERSION
-DEFAULT_MILL_VERSION=0.9.12
+DEFAULT_MILL_VERSION=0.10.4
 
 set -e
 

src/main/scala/com/fulcrumgenomics/sv/internal/FgSvMetricsDoclet.scala

@@ -56,7 +56,7 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
   }
 
   /** Locates the metrics documentation templates and turns them into simple case classes with comments as markdown. */
-  private lazy val metrics: Seq[MetricDescription] = {
+  override protected lazy val metrics: Seq[MetricDescription] = {
     def simplify(name: String) = if (name.indexOf('.') > 0) name.substring(name.lastIndexOf('.') + 1) else name
 
     findMetricsClasses.map{ template =>
@@ -89,7 +89,7 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
   }
 
   /** Take the body of a scaladoc comment and renders it into MarkDown. */
-  private def renderBody(body: Body): String = {
+  override protected def renderBody(body: Body): String = {
     val buffer = new StringBuilder
 
     // Takes a block element and renders it into MarkDown and writes it into the buffer
@@ -125,6 +125,6 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
   }
 
   /** Turns the text from a heading into the text to use as a link target. */
-  private def toLinkTarget(heading: String): String = heading.toLowerCase.replace(' ', '-')
+  override protected def toLinkTarget(heading: String): String = heading.toLowerCase.replace(' ', '-')
 }