New upstream version 1.23+dfsg (debb98f9) · Commits · Debian Med / pilon

COPYRIGHT

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		Copyright 2012-2014 Broad Institute, Inc.
		Copyright (c) 2012-2018 Broad Institute, Inc.

		Pilon is free software: you can redistribute it and/or modify
		it under the terms of the GNU General Public License version 2

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		name := "pilon"

		version := "1.22"
		version := "1.23"

		scalaVersion := "2.11.8"
		scalaVersion := "2.12.7"

		scalacOptions += "-deprecation"

		scalacOptions += "-feature"

		Seq(com.github.retronym.SbtOneJar.oneJarSettings: _*)

		libraryDependencies += "commons-lang" % "commons-lang" % "2.6"

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		@@ -11,6 +11,6 @@ sed -e "s/$date.=$./\\1 \"$commitdate\"/" \
		-e "s/$sbt.=$./\\1 \"$version\"/" \
		<$tmp >$f
		#sbt $* package
		sbt $* one-jar
		ln -sf `pwd`/target/scala-2.11/pilon_2.11-$version-one-jar.jar ~/lib/pilon/pilon-dev.jar
		sbt $* assembly
		ln -sf `pwd`/target/scala-2.12/pilon-assembly-$version.jar ~/lib/pilon/pilon-dev.jar
		mv $tmp $f

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		addSbtPlugin("com.github.retronym" % "sbt-onejar" % "0.8")
		addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.14.6")

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		/*
		* Copyright 2012-2015 Broad Institute, Inc.
		* Copyright (c) 2012-2018 Broad Institute, Inc.
		*
		* This file is part of Pilon.
		*
		@@ -14,12 +14,11 @@
		*
		* You should have received a copy of the GNU General Public License
		* along with Pilon. If not, see <http://www.gnu.org/licenses/>.
		*
		*/

		package org.broadinstitute.pilon
		import scala.annotation.tailrec
		import collection.JavaConversions._
		import collection.mutable.{ Map, HashMap, Set, HashSet }
		import collection.mutable.{ HashMap, HashSet }
		import htsjdk.samtools._

		object Assembler {