New upstream version 4.3t+dfsg (47019c09) · Commits · Debian Med / snpeff

.classpath

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		@@ -22,10 +22,6 @@
		<attribute name="maven.pomderived" value="true"/>
		</attributes>
		</classpathentry>
		<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
		<attributes>
		<attribute name="maven.pomderived" value="true"/>
		</attributes>
		</classpathentry>
		<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
		<classpathentry kind="output" path="target/classes"/>
		</classpath>

.gitignore

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		@@ -3,3 +3,4 @@
		/target
		snpEff_genes.txt
		snpEff_summary.html
		*/.swp

.settings/org.eclipse.jdt.core.prefs

+3 −3

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		eclipse.preferences.version=1
		org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
		org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
		org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
		org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
		org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
		org.eclipse.jdt.core.compiler.compliance=1.7
		org.eclipse.jdt.core.compiler.compliance=1.8
		org.eclipse.jdt.core.compiler.debug.lineNumber=generate
		org.eclipse.jdt.core.compiler.debug.localVariable=generate
		org.eclipse.jdt.core.compiler.debug.sourceFile=generate
		org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
		org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
		org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
		org.eclipse.jdt.core.compiler.source=1.7
		org.eclipse.jdt.core.compiler.source=1.8

SnpEf - Featured by SourceForge.pdf

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+428 KiB

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config/snpEff.ENSEMBL_86.config

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Original line number	Diff line number	Diff line
		ailMel1.86.genome : Ailuropoda_melanoleuca
		ailMel1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		BGI_duck_1.0.86.genome : Anas_platyrhynchos
		BGI_duck_1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		AnoCar2.0.86.genome : Anolis_carolinensis
		AnoCar2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		AstMex102.86.genome : Astyanax_mexicanus
		AstMex102.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		UMD3.1.86.genome : Bos_taurus
		UMD3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		WBcel235.86.genome : Caenorhabditis_elegans
		WBcel235.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		C_jacchus3.2.1.86.genome : Callithrix_jacchus
		C_jacchus3.2.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		CanFam3.1.86.genome : Canis_familiaris
		CanFam3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		cavPor3.86.genome : Cavia_porcellus
		cavPor3.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		ChlSab1.1.86.genome : Chlorocebus_sabaeus
		ChlSab1.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		choHof1.86.genome : Choloepus_hoffmanni
		choHof1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		KH.86.genome : Ciona_intestinalis
		KH.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		CSAV2.0.86.genome : Ciona_savignyi
		CSAV2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		GRCz10.86.genome : Danio_rerio
		GRCz10.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Dasnov3.0.86.genome : Dasypus_novemcinctus
		Dasnov3.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		dipOrd1.86.genome : Dipodomys_ordii
		dipOrd1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		BDGP6.86.genome : Drosophila_melanogaster
		BDGP6.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		TENREC.86.genome : Echinops_telfairi
		TENREC.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		EquCab2.86.genome : Equus_caballus
		EquCab2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		HEDGEHOG.86.genome : Erinaceus_europaeus
		HEDGEHOG.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Felis_catus_6.2.86.genome : Felis_catus
		Felis_catus_6.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		FicAlb_1.4.86.genome : Ficedula_albicollis
		FicAlb_1.4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		gadMor1.86.genome : Gadus_morhua
		gadMor1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Gallus_gallus-5.0.86.genome : Gallus_gallus
		Gallus_gallus-5.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		BROADS1.86.genome : Gasterosteus_aculeatus
		BROADS1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		gorGor3.1.86.genome : Gorilla_gorilla
		gorGor3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		GRCh38.86.genome : Homo_sapiens
		GRCh38.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		spetri2.86.genome : Ictidomys_tridecemlineatus
		spetri2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		LatCha1.86.genome : Latimeria_chalumnae
		LatCha1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		LepOcu1.86.genome : Lepisosteus_oculatus
		LepOcu1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		loxAfr3.86.genome : Loxodonta_africana
		loxAfr3.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Mmul_8.0.1.86.genome : Macaca_mulatta
		Mmul_8.0.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Meug_1.0.86.genome : Macropus_eugenii
		Meug_1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		UMD2.86.genome : Meleagris_gallopavo
		UMD2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Mmur_2.0.86.genome : Microcebus_murinus
		Mmur_2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		BROADO5.86.genome : Monodelphis_domestica
		BROADO5.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		GRCm38.86.genome : Mus_musculus
		GRCm38.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		129S1_SvImJ_v1.86.genome : Mus_musculus_129s1svimj
		129S1_SvImJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		A_J_v1.86.genome : Mus_musculus_aj
		A_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		AKR_J_v1.86.genome : Mus_musculus_akrj
		AKR_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		BALB_cJ_v1.86.genome : Mus_musculus_balbcj
		BALB_cJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		C3H_HeJ_v1.86.genome : Mus_musculus_c3hhej
		C3H_HeJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		C57BL_6NJ_v1.86.genome : Mus_musculus_c57bl6nj
		C57BL_6NJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		CAST_EiJ_v1.86.genome : Mus_musculus_casteij
		CAST_EiJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		CBA_J_v1.86.genome : Mus_musculus_cbaj
		CBA_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		DBA_2J_v1.86.genome : Mus_musculus_dba2j
		DBA_2J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		FVB_NJ_v1.86.genome : Mus_musculus_fvbnj
		FVB_NJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		LP_J_v1.86.genome : Mus_musculus_lpj
		LP_J_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		NOD_ShiLtJ_v1.86.genome : Mus_musculus_nodshiltj
		NOD_ShiLtJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		NZO_HlLtJ_v1.86.genome : Mus_musculus_nzohlltj
		NZO_HlLtJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		PWK_PhJ_v1.86.genome : Mus_musculus_pwkphj
		PWK_PhJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		WSB_EiJ_v1.86.genome : Mus_musculus_wsbeij
		WSB_EiJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		SPRET_EiJ_v1.86.genome : Mus_spretus_spreteij
		SPRET_EiJ_v1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		MusPutFur1.0.86.genome : Mustela_putorius_furo
		MusPutFur1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Myoluc2.0.86.genome : Myotis_lucifugus
		Myoluc2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Nleu1.0.86.genome : Nomascus_leucogenys
		Nleu1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		pika.86.genome : Ochotona_princeps
		pika.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Orenil1.0.86.genome : Oreochromis_niloticus
		Orenil1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		OANA5.86.genome : Ornithorhynchus_anatinus
		OANA5.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		OryCun2.0.86.genome : Oryctolagus_cuniculus
		OryCun2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		MEDAKA1.86.genome : Oryzias_latipes
		MEDAKA1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		OtoGar3.86.genome : Otolemur_garnettii
		OtoGar3.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Oar_v3.1.86.genome : Ovis_aries
		Oar_v3.1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		CHIMP2.1.4.86.genome : Pan_troglodytes
		CHIMP2.1.4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		PapAnu2.0.86.genome : Papio_anubis
		PapAnu2.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		PelSin_1.0.86.genome : Pelodiscus_sinensis
		PelSin_1.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Pmarinus_7.0.86.genome : Petromyzon_marinus
		Pmarinus_7.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		PoeFor_5.1.2.86.genome : Poecilia_formosa
		PoeFor_5.1.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		PPYG2.86.genome : Pongo_abelii
		PPYG2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		proCap1.86.genome : Procavia_capensis
		proCap1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		pteVam1.86.genome : Pteropus_vampyrus
		pteVam1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Rnor_6.0.86.genome : Rattus_norvegicus
		Rnor_6.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		R64-1-1.86.genome : Saccharomyces_cerevisiae
		R64-1-1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		DEVIL7.0.86.genome : Sarcophilus_harrisii
		DEVIL7.0.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		COMMON_SHREW1.86.genome : Sorex_araneus
		COMMON_SHREW1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Sscrofa10.2.86.genome : Sus_scrofa
		Sscrofa10.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		taeGut3.2.4.86.genome : Taeniopygia_guttata
		taeGut3.2.4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		FUGU4.86.genome : Takifugu_rubripes
		FUGU4.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		tarSyr1.86.genome : Tarsius_syrichta
		tarSyr1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		TETRAODON8.86.genome : Tetraodon_nigroviridis
		TETRAODON8.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		TREESHREW.86.genome : Tupaia_belangeri
		TREESHREW.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		turTru1.86.genome : Tursiops_truncatus
		turTru1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		vicPac1.86.genome : Vicugna_pacos
		vicPac1.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		JGI_4.2.86.genome : Xenopus_tropicalis
		JGI_4.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
		Xipmac4.4.2.86.genome : Xiphophorus_maculatus
		Xipmac4.4.2.86.reference : ftp://ftp.ensembl.org/pub/release-86/gtf/
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