sci-biology/NGSEPcore: cleanup old

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

3 files changed, 0 insertions, 131 deletions

diff --git a/sci-biology/NGSEPcore/Manifest b/sci-biology/NGSEPcore/Manifest
index 382f0b245..ef9c10376 100644
--- a/sci-biology/NGSEPcore/Manifest
+++ b/sci-biology/NGSEPcore/Manifest
@@ -1,8 +1,4 @@
-DIST NGSEPcore-3.3.1_QuickStart.txt 23701 BLAKE2B 0b3433a771e0121d4f38362f331e87c2597b7cbca4b63f26504807b2a84de2a3636e711c6bdee86c575810d6aff44996cb75663739ff5e184542f7f598f546be SHA512 d1eff40ca54a1e9bbdbda59511eb9e63ace2b001024df4119f0751b2e00dcf9219eb2eaa6407b2ccd1df71cf93d9b8e39088a59b7a6200fd966502c1b680eedd
-DIST NGSEPcore-3.3.1_Tutorial.txt 17070 BLAKE2B 9af46173da8cb1b1746118d186da0794c0b9ad11d22109bdf96ed9df6d21df2495e8be3e5e75ef013a11922aa697ceb85ee280199eebbb2afadc180d3d86c0a6 SHA512 844138e0be2038d3f4656a55a8129819f08361cb6447a7fdb261b48c1f50e7aad1234079cbb01746bc7084d59c79589538883ecc0b0bb4bd8e07f61861ef80c1
-DIST NGSEPcore-3.3.1_UserManual.pdf 29071950 BLAKE2B fd16b44e3668f61013772965378bf4fa604b2467839810392d26a27e1a6e52f961cecc5097728bb67d10b68556bd406ec044b439c5ad1b3e614bfc7866afed43 SHA512 6d697f6945bdecb4f30712d3ae94615c85180a53750ba92357f81bf060b3f5bec3f6d1a03115c1a3791f5bf050b115cd09fd8729d885d4ec34b10024082ebb3c
 DIST NGSEPcore-4.0.3_QuickStart.txt 21313 BLAKE2B b897e25945d337f85f0c525ce93221440f6f1577ad1bde6fa3884a74e4366c2e17d7ef1d8603acba02ab21bdaa63fdfcc4d4251273f5e77b938e2318b13bdc19 SHA512 f5d528555c6115cdbddddbfc1c24939d1ca4776b16a5b848b4b9321cb882903d70eeef00c08e032dce4b6fe5551cea881570fc6f5975837e4f9eaf646de0c363
 DIST NGSEPcore-4.0.3_Tutorial.txt 16946 BLAKE2B 0f397c6cd6d0f57f219d3f7963df32263347345a2e6231c7ccbc1a433d8de6350c6653e1a260182aa3ea5fa6a0bf88f47b659df236c78c8289914823b92f5778 SHA512 b110a0058962e1dc899183d3ca73cdfdd5f9b729561d35fe8d25e2fbeaa9b4647cbb768b047fa6df80b7926b1a34e4dc87c13979b66e6e6fe83f6f0c991fe6a8
 DIST NGSEPcore-4.0.3_UserManual.pdf 10516580 BLAKE2B abe69a790413851181cbd210c8389fd302d917a1f6b4d425fbda2389808234290d38f31532933c0fc8505ca8b530f1b778bb58ce041783d184a85c2d5a716cd9 SHA512 cff9176f0a791b5b3e24fdba681bd71a3c39cb4593c01631e722e60e238140c80f292286454b7337a741a2f54fa6d5db30146c5bfdb02d5d5dd8d65322e3dc6e
-DIST NGSEPcore_3.3.1.tar.gz 19818149 BLAKE2B 4233730649263cbca5a870b4eb9e041359b7b368b52465203d7b713ff924d3fbdfbe0fbbce0a11dd2d0fc5e190edeb3e89e176fd3f3ed2ecef7adf3853799f85 SHA512 f81b2e626d7b5c6367b58613e1cbf72dbdc782396bca8284501f5fbab2173290a91e4a89a2cbda1b316638254aea26a281e3a586773709577b14a889a07eca20
 DIST NGSEPcore_4.0.3.tar.gz 11668258 BLAKE2B de8bdeee18c8647e93dcf8adf0751660618bb54208160a15de184680459122ef6fb62ea6c1ae8d3e81b6ada11ab4a1b2f18ee575b4fdc4543f3c30b9077ffc1d SHA512 12c73243cc026fc37424fc8b5112179288bf569c3e06208bfc768420874dc676a23f10a8fd067eb0120fa8f188556e2a91e22fc4e54a8cd3e7851a0b2e32e036
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];