[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/files/, sci-biology/NGSEPcore/

[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/files/, sci-biology/NGSEPcore/

[Andrew Ammerlaan]

commit:     1a264b0465fa3f8d9bcdf54f8df01d34c4d331e8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 12:20:39 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 12:20:39 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a264b04

sci-biology/NGSEPcore: cleanup old

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild       | 46 ------------
 .../files/NGSEPcore_drop_utf8_chars.patch          | 81 ----------------------
 2 files changed, 127 deletions(-)

diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
deleted file mode 100644
index 0addb08b8..000000000
--- a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="NGSEP (CNV and indel discovery)"
-HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
-	https://github.com/NGSEP/NGSEPcore"
-SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz
-	https://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V330.pdf -> ${P}_UserManual.pdf
-	https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt
-	https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	dev-java/htsjdk
-	dev-java/jsci-bin"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-PATCHES=( "${FILESDIR}"/NGSEPcore_drop_utf8_chars.patch )
-
-src_prepare(){
-	rm lib/htsjdk-1.129.jar || die
-	rm lib/jsci-core.jar || die
-	default
-}
-
-src_compile(){
-	emake -j1
-}
-
-src_install(){
-	java-pkg_dojar *.jar lib/*.jar
-	dodoc "${DISTDIR}"/${P}_UserManual.pdf \
-	"${DISTDIR}"/${P}_Tutorial.txt \
-	"${DISTDIR}"/${P}_QuickStart.txt \
-	README.txt
-}

diff --git a/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch b/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch
deleted file mode 100644
index eb61747be..000000000
--- a/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-From 5161e22e7730e2637376402718ed7048f838054a Mon Sep 17 00:00:00 2001
-From: jorge <jorge@jorge-0420006391>
-Date: Thu, 28 Mar 2019 16:24:24 -0500
-Subject: [PATCH] Fixed encoding and manual compilation issues
-
----
- makefile                                                 | 2 +-
- src/ngsep/discovery/TillingPoolsIndividualGenotyper.java | 5 ++---
- src/ngsep/simulation/TillingPopulationSimulator.java     | 2 +-
- src/ngsep/variants/CalledSNV.java                        | 2 +-
- 4 files changed, 5 insertions(+), 6 deletions(-)
-
-diff --git a/makefile b/makefile
-index 517895d..0532725 100755
---- a/makefile
-+++ b/makefile
-@@ -11,7 +11,7 @@ compile:
- copy: 
- 	cp -f src/ngsep/transcriptome/ProteinTranslatorDefaultBundle.properties bin/ngsep/transcriptome/
- 	cp -f src/ngsep/main/CommandsDescriptor.xml bin/ngsep/main/
--	cp -f src/ngsep/assembly/GenomesAlignerLinearVisualizer.js bin/ngsep/assembly/
-+	cp -f src/ngsep/genome/GenomesAlignerLinearVisualizer.js bin/ngsep/genome/
- 
- jar: 
- 	mkdir dist
-diff --git a/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java b/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java
-index c8c3d42..2e7a7bf 100644
---- a/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java
-+++ b/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java
-@@ -19,7 +19,6 @@
- import ngsep.main.CommandsDescriptor;
- import ngsep.main.ProgressNotifier;
- import ngsep.sequences.QualifiedSequenceList;
--import ngsep.simulation.TillingPopulationSimulator;
- import ngsep.variants.CalledGenomicVariant;
- import ngsep.variants.CalledGenomicVariantImpl;
- import ngsep.variants.GenomicVariant;
-@@ -31,7 +30,7 @@
- 
- public class TillingPoolsIndividualGenotyper {
- 
--	private Logger log = Logger.getLogger(TillingPopulationSimulator.class.getName());
-+	private Logger log = Logger.getLogger(TillingPoolsIndividualGenotyper.class.getName());
- 	private ProgressNotifier progressNotifier=null;
- 	
- 	private static HashMap<String,ArrayList<Integer>> poolConfiguration;
-@@ -111,7 +110,7 @@ public void loadPools(String poolsDescriptor, int num_columnPools, int num_rowPo
- 		while (line != null) {
- 
- 			String[] indInfo = line.split(";");
--			ArrayList<Integer> pools = new ArrayList();
-+			ArrayList<Integer> pools = new ArrayList<>();
- 			pools.add(Integer.parseInt(indInfo[1]));
- 			pools.add(Integer.parseInt(indInfo[2]));
- 			pools.add(Integer.parseInt(indInfo[3]));
-diff --git a/src/ngsep/simulation/TillingPopulationSimulator.java b/src/ngsep/simulation/TillingPopulationSimulator.java
-index ea44db2..37f9d3b 100644
---- a/src/ngsep/simulation/TillingPopulationSimulator.java
-+++ b/src/ngsep/simulation/TillingPopulationSimulator.java
-@@ -56,7 +56,7 @@
- /**
-  * 
-  * @author Juanita
-- * @author Juan Sebastián Andrade
-+ * @author Juan Sebastian Andrade
-  *
-  */
- public class TillingPopulationSimulator {
-diff --git a/src/ngsep/variants/CalledSNV.java b/src/ngsep/variants/CalledSNV.java
-index a40c8ac..773abe7 100755
---- a/src/ngsep/variants/CalledSNV.java
-+++ b/src/ngsep/variants/CalledSNV.java
-@@ -241,7 +241,7 @@ public void setGenotypeQuality(short genotypeQuality) {
- 	/**
- 	 * Changes the number of As, Cs, Gs and Ts observed in the sample
- 	 * @param allCounts Array of length 4 with the number of times that each allele appears. 
--	 * The order must be the cu¡ount for A, the count for C, the count for G, and the count for T 
-+	 * The order must be the count for A, the count for C, the count for G, and the count for T 
- 	 */
- 	public void setAllBaseCounts(int [] allCounts) {
- 		this.countA = allCounts[0];