move haplogrep folder to top

seppinho · Jun 21, 2018 · 22563ed · 22563ed
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commit 22563ed
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Showing 35 changed files with 60,973 additions and 71 deletions.
diff --git a/haplogrep/annotation/aminoacidchange.txt → annotation/aminoacidchange.txt b/haplogrep/annotation/aminoacidchange.txt → annotation/aminoacidchange.txt
diff --git a/haplogrep/.classpath b/haplogrep/.classpath
diff --git a/haplogrep/.gitignore b/haplogrep/.gitignore
diff --git a/haplogrep/.project b/haplogrep/.project
diff --git a/haplogrep/.settings/org.eclipse.core.resources.prefs b/haplogrep/.settings/org.eclipse.core.resources.prefs
diff --git a/haplogrep/.settings/org.eclipse.jdt.core.prefs b/haplogrep/.settings/org.eclipse.jdt.core.prefs
diff --git a/haplogrep/.settings/org.eclipse.m2e.core.prefs b/haplogrep/.settings/org.eclipse.m2e.core.prefs
diff --git a/...bs/genepi/haplogrep/2.0/haplogrep-2.0.jar → libs/genepi/haplogrep/2.0/haplogrep-2.0.jar b/...bs/genepi/haplogrep/2.0/haplogrep-2.0.jar → libs/genepi/haplogrep/2.0/haplogrep-2.0.jar
diff --git a/haplogrep/phylotree/phylotree10.xml → phylotree/phylotree10.xml b/haplogrep/phylotree/phylotree10.xml → phylotree/phylotree10.xml
diff --git a/haplogrep/phylotree/phylotree11.xml → phylotree/phylotree11.xml b/haplogrep/phylotree/phylotree11.xml → phylotree/phylotree11.xml
diff --git a/haplogrep/phylotree/phylotree12.xml → phylotree/phylotree12.xml b/haplogrep/phylotree/phylotree12.xml → phylotree/phylotree12.xml
diff --git a/haplogrep/phylotree/phylotree13.xml → phylotree/phylotree13.xml b/haplogrep/phylotree/phylotree13.xml → phylotree/phylotree13.xml
diff --git a/haplogrep/phylotree/phylotree14.xml → phylotree/phylotree14.xml b/haplogrep/phylotree/phylotree14.xml → phylotree/phylotree14.xml
diff --git a/haplogrep/phylotree/phylotree15.xml → phylotree/phylotree15.xml b/haplogrep/phylotree/phylotree15.xml → phylotree/phylotree15.xml
diff --git a/haplogrep/phylotree/phylotree16.xml → phylotree/phylotree16.xml b/haplogrep/phylotree/phylotree16.xml → phylotree/phylotree16.xml
diff --git a/haplogrep/phylotree/phylotree17.xml → phylotree/phylotree17.xml b/haplogrep/phylotree/phylotree17.xml → phylotree/phylotree17.xml
diff --git a/haplogrep/pom.xml → pom.xml b/haplogrep/pom.xml → pom.xml
diff --git a/...main/java/genepi/haplogrep/Haplogrep.java → ...main/java/genepi/haplogrep/Haplogrep.java b/...main/java/genepi/haplogrep/Haplogrep.java → ...main/java/genepi/haplogrep/Haplogrep.java
@@ -626,8 +626,8 @@ public static void main(String[] args) throws IOException {
 
 		Haplogrep haplogrep = new Haplogrep(args);
 
-		//haplogrep = new Haplogrep(new String[] { "--in", "test-data/ALL.chrMT.phase1.vcf", "--out",
-		//		"test-data/h100-haplogrep.txt", "--format", "vcf", "--lineage" });
+		haplogrep = new Haplogrep(new String[] { "--in", "test-data/ALL.chrMT.phase1.vcf", "--out",
+				"test-data/h100-haplogrep.txt", "--format", "vcf"});
 
 		haplogrep.start();
 

diff --git a/...c/main/java/genepi/haplogrep/Session.java → src/main/java/genepi/haplogrep/Session.java b/...c/main/java/genepi/haplogrep/Session.java → src/main/java/genepi/haplogrep/Session.java
diff --git a/.../test/java/genepi/haplogrep/AllTests.java → src/test/java/genepi/haplogrep/AllTests.java b/.../test/java/genepi/haplogrep/AllTests.java → src/test/java/genepi/haplogrep/AllTests.java
diff --git a/...java/genepi/haplogrep/HaplogroupTest.java → ...java/genepi/haplogrep/HaplogroupTest.java b/...java/genepi/haplogrep/HaplogroupTest.java → ...java/genepi/haplogrep/HaplogroupTest.java
diff --git a/haplogrep/test-data/ALL.chrMT.phase1.vcf → test-data/ALL.chrMT.phase1.vcf b/haplogrep/test-data/ALL.chrMT.phase1.vcf → test-data/ALL.chrMT.phase1.vcf