Merge branch 'develop'

Illumina · Jun 13, 2017 · 82f37e9 · 82f37e9
2 parents 53edff6 + f0b4a05
commit 82f37e9
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diff --git a/.gitignore b/.gitignore
diff --git a/CacheUtils/CacheUtils.cs b/CacheUtils/CacheUtils.cs
@@ -1,49 +1,49 @@
-using System.Collections.Generic;
-using CacheUtils.CombineAndUpdateGenes;
-using CacheUtils.CombineCacheDirectories;
-using CacheUtils.CreateCache;
-using CacheUtils.ExtractRegulatoryElements;
-using CacheUtils.ExtractTranscripts;
-using CacheUtils.GFF;
-using CacheUtils.ParseVepCacheDirectory;
-using CacheUtils.RegulatoryGFF;
-using CacheUtils.UpdateMiniCacheFiles;
-using NDesk.Options;
-using VariantAnnotation.CommandLine;
-using VariantAnnotation.Utilities;
-
-namespace CacheUtils
-{
-    public class CacheUtils : TopLevelCommandLineHandler
-    {
-        /// <summary>
-        /// constructor
-        /// </summary>
-        private CacheUtils(string programDescription, Dictionary<string, TopLevelOption> ops, string authors,
-            IVersionProvider provider = null)
-            : base(programDescription, OutputHelper.GetExecutableName(), ops, authors, provider)
-        { }
-
-        public static int Main(string[] args)
-        {
-            var ops = new Dictionary<string, TopLevelOption>
-            {
-                ["combine"] = new TopLevelOption("combine cache directories", CombineCacheDirectoriesMain.Run),
-                ["create"]  = new TopLevelOption("create Nirvana cache files", CreateNirvanaDatabaseMain.Run),
-                ["extreg"]  = new TopLevelOption("extracts regulatory regions", ExtractRegulatoryElementsMain.Run),
-                ["exttran"] = new TopLevelOption("extracts transcripts", ExtractTranscriptsMain.Run),
-                ["gff"]     = new TopLevelOption("export transcripts to GFF", CreateGff.Run),
-                ["parse"]   = new TopLevelOption("parses the VEP cache files", ParseVepCacheDirectoryMain.Run),
-                ["rgff"]    = new TopLevelOption("export regulatory regions to GFF", CreateRegulatoryGff.Run),
-                ["gene"]    = new TopLevelOption("updates genes in intermediate files", CombineAndUpdateGenesMain.Run),
-                ["update"]  = new TopLevelOption("updates the mini-cache files", UpdateMiniCacheFilesMain.Run)
-            };
-
-            var utils = new CacheUtils("Utilities focused on querying the cache directory", ops, VariantAnnotation.DataStructures.Constants.Authors,
-                new CacheVersionProvider());
-
-            utils.ParseCommandLine(args);
-            return utils.ExitCode;
-        }
-    }
-}
+using System.Collections.Generic;
+using CacheUtils.CombineAndUpdateGenes;
+using CacheUtils.CombineCacheDirectories;
+using CacheUtils.CreateCache;
+using CacheUtils.ExtractRegulatoryElements;
+using CacheUtils.ExtractTranscripts;
+using CacheUtils.GFF;
+using CacheUtils.ParseVepCacheDirectory;
+using CacheUtils.RegulatoryGFF;
+using CacheUtils.UpdateMiniCacheFiles;
+using CommandLine.Handlers;
+using CommandLine.Utilities;
+using CommandLine.VersionProvider;
+
+namespace CacheUtils
+{
+    public class CacheUtils : TopLevelCommandLineHandler
+    {
+        /// <summary>
+        /// constructor
+        /// </summary>
+        private CacheUtils(string programDescription, Dictionary<string, TopLevelOption> ops, string authors,
+            IVersionProvider provider = null)
+            : base(programDescription, OutputHelper.GetExecutableName(), ops, authors, provider)
+        { }
+
+        public static int Main(string[] args)
+        {
+            var ops = new Dictionary<string, TopLevelOption>
+            {
+                ["combine"] = new TopLevelOption("combine cache directories", CombineCacheDirectoriesMain.Run),
+                ["create"]  = new TopLevelOption("create Nirvana cache files", CreateNirvanaDatabaseMain.Run),
+                ["extreg"]  = new TopLevelOption("extracts regulatory regions", ExtractRegulatoryElementsMain.Run),
+                ["exttran"] = new TopLevelOption("extracts transcripts", ExtractTranscriptsMain.Run),
+                ["gff"]     = new TopLevelOption("export transcripts to GFF", CreateGff.Run),
+                ["parse"]   = new TopLevelOption("parses the VEP cache files", ParseVepCacheDirectoryMain.Run),
+                ["rgff"]    = new TopLevelOption("export regulatory regions to GFF", CreateRegulatoryGff.Run),
+                ["gene"]    = new TopLevelOption("updates genes in intermediate files", CombineAndUpdateGenesMain.Run),
+                ["update"]  = new TopLevelOption("updates the mini-cache files", UpdateMiniCacheFilesMain.Run)
+            };
+
+            var utils = new CacheUtils("Utilities focused on querying the cache directory", ops, VariantAnnotation.DataStructures.Constants.Authors,
+                new CacheVersionProvider());
+
+            utils.ParseCommandLine(args);
+            return utils.ExitCode;
+        }
+    }
+}
diff --git a/CacheUtils/CacheUtils.csproj b/CacheUtils/CacheUtils.csproj
@@ -1,14 +1,22 @@
-<Project Sdk="Microsoft.NET.Sdk">
-  <PropertyGroup>
-    <OutputType>Exe</OutputType>
-    <TargetFramework>netcoreapp1.1</TargetFramework>
-    <OutputPath>..\bin\$(Configuration)</OutputPath>
-  </PropertyGroup>
-  <ItemGroup>
-    <ProjectReference Include="..\ErrorHandling\ErrorHandling.csproj" />
-    <ProjectReference Include="..\NDesk.Options\NDesk.Options.csproj" />
-    <ProjectReference Include="..\VariantAnnotation.Interface\VariantAnnotation.Interface.csproj" />
-    <ProjectReference Include="..\VariantAnnotation\VariantAnnotation.csproj" />
-  </ItemGroup>
-  <Import Project="..\VariantAnnotation\CommonAssemblyInfo.props" />
+<Project Sdk="Microsoft.NET.Sdk">
+  <PropertyGroup Label="Configuration" Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">
+    <OutputType>exe</OutputType>
+  </PropertyGroup>
+  <PropertyGroup Label="Configuration" Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
+    <OutputType>exe</OutputType>
+  </PropertyGroup>
+  <PropertyGroup>
+    <TargetFramework>netcoreapp1.1</TargetFramework>
+    <OutputPath>..\bin\$(Configuration)</OutputPath>
+    <OutputTypeEx>exe</OutputTypeEx>
+    <ApplicationIcon />
+    <StartupObject />
+  </PropertyGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\ErrorHandling\ErrorHandling.csproj" />
+    <ProjectReference Include="..\CommandLine\CommandLine.csproj" />
+    <ProjectReference Include="..\VariantAnnotation.Interface\VariantAnnotation.Interface.csproj" />
+    <ProjectReference Include="..\VariantAnnotation\VariantAnnotation.csproj" />
+  </ItemGroup>
+  <Import Project="..\VariantAnnotation\CommonAssemblyInfo.props" />
 </Project>
diff --git a/CacheUtils/CacheVersionProvider.cs b/CacheUtils/CacheVersionProvider.cs
@@ -1,12 +1,13 @@
-using VariantAnnotation.FileHandling.TranscriptCache;
-using VariantAnnotation.Utilities;
-
-namespace CacheUtils
-{
-    public class CacheVersionProvider : IVersionProvider
-    {
-        public string GetProgramVersion() => $"Nirvana {CommandLineUtilities.InformationalVersion}";
-
-        public string GetDataVersion() => $"Cache version: {CacheConstants.DataVersion}";
-    }
-}
+using CommandLine.Utilities;
+using CommandLine.VersionProvider;
+using VariantAnnotation.FileHandling.TranscriptCache;
+
+namespace CacheUtils
+{
+    public class CacheVersionProvider : IVersionProvider
+    {
+        public string GetProgramVersion() => $"Nirvana {CommandLineUtilities.InformationalVersion}";
+
+        public string GetDataVersion() => $"Cache version: {CacheConstants.DataVersion}";
+    }
+}
diff --git a/CacheUtils/CombineAndUpdateGenes/Algorithms/GeneFlattener.cs b/CacheUtils/CombineAndUpdateGenes/Algorithms/GeneFlattener.cs
@@ -1,85 +1,85 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using CacheUtils.CombineAndUpdateGenes.DataStructures;
-using CacheUtils.CombineAndUpdateGenes.Utilities;
-using ErrorHandling.Exceptions;
-using VariantAnnotation.Algorithms;
-using VariantAnnotation.DataStructures;
-
-namespace CacheUtils.CombineAndUpdateGenes.Algorithms
-{
-    public class GeneFlattener
-    {
-        private readonly List<MutableGene> _genes;
-        private readonly string _description;
-        private readonly bool _isEnsembl;
-
-        private readonly bool _showOutput;
-
-        /// <summary>
-        /// constructor
-        /// </summary>
-        public GeneFlattener(List<MutableGene> genes, string description, bool showOutput = true)
-        {
-            _genes       = genes;
-            _description = description;
-            _isEnsembl   = genes.Count == 0 || genes.First().TranscriptDataSource == TranscriptDataSource.Ensembl;
-            _showOutput  = showOutput;
-        }
-
-        public List<MutableGene> Flatten(int overlapStart = -1, int overlapEnd = -1)
-        {
-            var combinedGenes = new List<MutableGene>();
-            var genesById     = GeneUtilities.GetGenesById(_genes, _isEnsembl);
-
-            foreach (var gene in _genes)
-            {
-                if (gene.Invalid) continue;
-
-                var geneId = _isEnsembl
-                    ? gene.EnsemblId.ToString()
-                    : gene.EntrezGeneId.ToString();
-
-                List<MutableGene> genesWithSameGeneId;
-                if (!genesById.TryGetValue(geneId, out genesWithSameGeneId))
-                {
-                    throw new UserErrorException($"Unable to find similar genes for {geneId}");
-                }
-
-                combinedGenes.Add(GetFlattenedGene(gene, genesWithSameGeneId, overlapStart, overlapEnd));
-            }
-
-            if(_showOutput) Console.WriteLine($"  - {_description}: {combinedGenes.Count} genes.");
-
-            return combinedGenes;
-        }
-
-        private static MutableGene GetFlattenedGene(MutableGene seedGene, List<MutableGene> genesWithSameGeneId,
-            int overlapStart, int overlapEnd)
-        {
-            var flattenedGene = MutableGene.Clone(seedGene);
-            bool useOverlap   = overlapStart != -1 && overlapEnd != -1;
-
-            foreach (var gene in genesWithSameGeneId)
-            {
-                if (gene.Invalid || flattenedGene.OnReverseStrand != gene.OnReverseStrand ||
-                    flattenedGene.ReferenceIndex != gene.ReferenceIndex) continue;
-
-                if (useOverlap  && !Overlap.Partial(overlapStart, overlapEnd, gene.Start, gene.End)) continue;
-                if (!useOverlap && !Overlap.Partial(flattenedGene.Start, flattenedGene.End, gene.Start, gene.End)) continue;
-
-                UpdateCoordinates(gene, flattenedGene);
-                gene.Invalid = true;
-            }
-
-            return flattenedGene;
-        }
-
-        private static void UpdateCoordinates(MutableGene source, MutableGene dest)
-        {
-            if (source.Start < dest.Start) dest.Start = source.Start;
-            if (source.End > dest.End) dest.End = source.End;
-        }
-    }
-}
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using CacheUtils.CombineAndUpdateGenes.DataStructures;
+using CacheUtils.CombineAndUpdateGenes.Utilities;
+using ErrorHandling.Exceptions;
+using VariantAnnotation.Algorithms;
+using VariantAnnotation.DataStructures.Transcript;
+
+namespace CacheUtils.CombineAndUpdateGenes.Algorithms
+{
+    public class GeneFlattener
+    {
+        private readonly List<MutableGene> _genes;
+        private readonly string _description;
+        private readonly bool _isEnsembl;
+
+        private readonly bool _showOutput;
+
+        /// <summary>
+        /// constructor
+        /// </summary>
+        public GeneFlattener(List<MutableGene> genes, string description, bool showOutput = true)
+        {
+            _genes       = genes;
+            _description = description;
+            _isEnsembl   = genes.Count == 0 || genes.First().TranscriptDataSource == TranscriptDataSource.Ensembl;
+            _showOutput  = showOutput;
+        }
+
+        public List<MutableGene> Flatten(int overlapStart = -1, int overlapEnd = -1)
+        {
+            var combinedGenes = new List<MutableGene>();
+            var genesById     = GeneUtilities.GetGenesById(_genes, _isEnsembl);
+
+            foreach (var gene in _genes)
+            {
+                if (gene.Invalid) continue;
+
+                var geneId = _isEnsembl
+                    ? gene.EnsemblId.ToString()
+                    : gene.EntrezGeneId.ToString();
+
+                List<MutableGene> genesWithSameGeneId;
+                if (!genesById.TryGetValue(geneId, out genesWithSameGeneId))
+                {
+                    throw new UserErrorException($"Unable to find similar genes for {geneId}");
+                }
+
+                combinedGenes.Add(GetFlattenedGene(gene, genesWithSameGeneId, overlapStart, overlapEnd));
+            }
+
+            if(_showOutput) Console.WriteLine($"  - {_description}: {combinedGenes.Count} genes.");
+
+            return combinedGenes;
+        }
+
+        private static MutableGene GetFlattenedGene(MutableGene seedGene, List<MutableGene> genesWithSameGeneId,
+            int overlapStart, int overlapEnd)
+        {
+            var flattenedGene = MutableGene.Clone(seedGene);
+            bool useOverlap   = overlapStart != -1 && overlapEnd != -1;
+
+            foreach (var gene in genesWithSameGeneId)
+            {
+                if (gene.Invalid || flattenedGene.OnReverseStrand != gene.OnReverseStrand ||
+                    flattenedGene.ReferenceIndex != gene.ReferenceIndex) continue;
+
+                if (useOverlap  && !Overlap.Partial(overlapStart, overlapEnd, gene.Start, gene.End)) continue;
+                if (!useOverlap && !Overlap.Partial(flattenedGene.Start, flattenedGene.End, gene.Start, gene.End)) continue;
+
+                UpdateCoordinates(gene, flattenedGene);
+                gene.Invalid = true;
+            }
+
+            return flattenedGene;
+        }
+
+        private static void UpdateCoordinates(MutableGene source, MutableGene dest)
+        {
+            if (source.Start < dest.Start) dest.Start = source.Start;
+            if (source.End > dest.End) dest.End = source.End;
+        }
+    }
+}