Merge branch 'dev' into dev

Author: VJalili

GeUtilities.Tests/GeUtilities.Tests.csproj

@@ -18,6 +18,11 @@
     <RepositoryUrl>https://github.com/Genometric/GeUtilities</RepositoryUrl>
     <Version>4.0.0</Version>
     <Description>Implements unit test functions for the GeUtilities.</Description>
+    <PackageTags>genomics; genome analysis; building-blocks; parser; BED; VCF; GTF; RefSeq;</PackageTags>
+    <PackageReleaseNotes>A major overhaul on the interfaces, functions signatures, and namespace naming. Namely:
+- Parsers constructors take least possible information, and all the other configuration could be set on an instace of the parser class. 
+- By moving source file name from constructor to Parse function, now single instance of Parser can be used to parse multiple files.
+- A major overhaul of classes inheritance with the objective of making them more coherent.</PackageReleaseNotes>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">

GeUtilities/GeUtilities.csproj

@@ -14,8 +14,12 @@
     <PackageRequireLicenseAcceptance>true</PackageRequireLicenseAcceptance>
     <GeneratePackageOnBuild>true</GeneratePackageOnBuild>
     <PackageId>Genometric.GeUtilities</PackageId>
-    <Description>This package implements a set of tools required to develop any genome data analysis program.</Description>
-    <PackageReleaseNotes>A major overhaul on the interfaces, and function and name space naming.</PackageReleaseNotes>
+    <Description>Genome Utilities (GeUtilities) provides open-source building-blocks for genomic data analysis tools.</Description>
+    <PackageReleaseNotes>A major overhaul on the interfaces, functions signatures, and namespace naming. Namely:
+- Parsers constructors take least possible information, and all the other configuration could be set on an instace of the parser class. 
+- By moving source file name from constructor to Parse function, now single instance of Parser can be used to parse multiple files.
+- A major overhaul of classes inheritance with the objective of making them more coherent.</PackageReleaseNotes>
+    <PackageTags>genomics; genome analysis; building-blocks; parser; BED; VCF; GTF; RefSeq;</PackageTags>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">

GeUtilities/IntervalParsers/Parser.cs

@@ -214,70 +214,70 @@ private void Parse()
 
                 while ((line = fileReader.ReadLine()) != null)
                 {
-                    lineCounter++;
+                    if (++lineCounter > MaxLinesToRead) break;
+
                     lineSize += fileReader.CurrentEncoding.GetByteCount(line);
                     Status = (Math.Round((lineSize * 100.0) / fileSize, 0)).ToString();
 
-                    if (line.Trim().Length > 0 && lineCounter <= MaxLinesToRead)
+                    if (line.Trim().Length <= 0) continue;
+
+                    DropReadingPeak = false;
+                    string[] splittedLine = line.Split(Delimiter);
+
+                    if (!(_leftColumn < splittedLine.Length && int.TryParse(splittedLine[_leftColumn], out left)))
+                    {
+                        DropLine("\tLine " + lineCounter.ToString() + "\t:\tInvalid start/position column number");
+                        continue;
+                    }
+
+                    if (_rightColumn >= 0 && !(_rightColumn < splittedLine.Length && int.TryParse(splittedLine[_rightColumn], out right)))
+                    {
+                        DropLine("\tLine " + lineCounter.ToString() + "\t:\tInvalid stop column number");
+                        continue;
+                    }
+
+                    I readingInterval = BuildInterval(left, right, splittedLine, lineCounter);
+                    if (DropReadingPeak)
+                        continue;
+
+                    chrName = null;
+                    if (_chrColumn < splittedLine.Length)
                     {
-                        DropReadingPeak = false;
-                        string[] splittedLine = line.Split(Delimiter);
-
-                        if (!(_leftColumn < splittedLine.Length && int.TryParse(splittedLine[_leftColumn], out left)))
-                        {
-                            DropLine("\tLine " + lineCounter.ToString() + "\t:\tInvalid start/position column number");
-                            continue;
-                        }
-
-                        if (_rightColumn >= 0 && !(_rightColumn < splittedLine.Length && int.TryParse(splittedLine[_rightColumn], out right)))
-                        {
-                            DropLine("\tLine " + lineCounter.ToString() + "\t:\tInvalid stop column number");
-                            continue;
-                        }
-
-                        I readingInterval = BuildInterval(left, right, splittedLine, lineCounter);
-                        if (DropReadingPeak)
-                            continue;
-
-                        chrName = null;
-                        if (_chrColumn < splittedLine.Length)
-                        {
-                            if (Regex.IsMatch(splittedLine[_chrColumn].ToLower(), "chr"))
-                                chrName = splittedLine[_chrColumn];
-                            else if (int.TryParse(splittedLine[_chrColumn], out int chrNumber))
-                                chrName = "chr" + chrNumber;
-                            else if (_assemblyData.ContainsKey("chr" + splittedLine[_chrColumn]))
-                                chrName = "chr" + splittedLine[_chrColumn];
-                            else
-                                chrName = splittedLine[_chrColumn];
-                            if (ReadOnlyAssemblyChrs && !_assemblyData.ContainsKey(chrName))
-                                chrName = null;
-                        }
-                        if (chrName == null)
-                        {
-                            DropLine("\tLine " + lineCounter.ToString() + "\t:\tInvalid chromosome number ( " + splittedLine[_chrColumn].ToString() + " )");
-                            continue;
-                        }
+                        if (Regex.IsMatch(splittedLine[_chrColumn].ToLower(), "chr"))
+                            chrName = splittedLine[_chrColumn];
+                        else if (int.TryParse(splittedLine[_chrColumn], out int chrNumber))
+                            chrName = "chr" + chrNumber;
+                        else if (_assemblyData.ContainsKey("chr" + splittedLine[_chrColumn]))
+                            chrName = "chr" + splittedLine[_chrColumn];
+                        else
+                            chrName = splittedLine[_chrColumn];
+                        if (ReadOnlyAssemblyChrs && !_assemblyData.ContainsKey(chrName))
+                            chrName = null;
+                    }
+                    if (chrName == null)
+                    {
+                        DropLine("\tLine " + lineCounter.ToString() + "\t:\tInvalid chromosome number ( " + splittedLine[_chrColumn].ToString() + " )");
+                        continue;
+                    }
 
+                    strand = '*';
+                    if (_strandColumn != -1 && _strandColumn < line.Length &&
+                       (char.TryParse(splittedLine[_strandColumn], out strand) && strand != '+' && strand != '-' && strand != '*'))
                         strand = '*';
-                        if (_strandColumn != -1 && _strandColumn < line.Length &&
-                           (char.TryParse(splittedLine[_strandColumn], out strand) && strand != '+' && strand != '-' && strand != '*'))
-                            strand = '*';
-
-                        switch (HashFunction)
-                        {
-                            case HashFunctions.FNV:
-                                readingInterval.HashKey = FNVHashFunction(readingInterval, lineCounter);
-                                break;
-
-                            default:
-                                readingInterval.HashKey = OneAtATimeHashFunction(readingInterval, lineCounter);
-                                break;
-                        }
-
-                        _data.Add(readingInterval, chrName, strand);
-                        _data.IntervalsCount++;
+
+                    switch (HashFunction)
+                    {
+                        case HashFunctions.FNV:
+                            readingInterval.HashKey = FNVHashFunction(readingInterval, lineCounter);
+                            break;
+
+                        default:
+                            readingInterval.HashKey = OneAtATimeHashFunction(readingInterval, lineCounter);
+                            break;
                     }
+
+                    _data.Add(readingInterval, chrName, strand);
+                    _data.IntervalsCount++;
                 }
             }
         }

README.md

@@ -1,4 +1,5 @@
-# GeUtilities
+# GeUtilities 
+[![Latest version](https://img.shields.io/nuget/v/Genometric.GeUtilities.svg?style=for-the-badge)](https://www.nuget.org/packages/Genometric.GeUtilities/)
 
 Genome Utilities (GeUtilities) provides open-source building-blocks for genomic data analysis tools. The following components are currently implemented: 
 -	**IGenomics**: interfaces to build portable objects. For instance, ChIP-seq peaks, variations, or general features. 

appveyor.yml

@@ -61,6 +61,12 @@ for:
         $env:PATH = 'C:\msys64\usr\bin;' + $env:PATH
         Invoke-WebRequest -Uri 'https://codecov.io/bash' -OutFile codecov.sh
         bash codecov.sh -f "GeUtilities.Tests/GeUtilities_coverage.xml" -t $env:codecovtoken
+    - MSBuild.SonarQube.Runner.exe begin /k:"geutilities" /o:"genometric" /d:"sonar.host.url=https://sonarcloud.io" /d:"sonar.login=%sonartoken%" /d:sonar.cs.opencover.reportsPaths="\GeUtilities.Tests\GeUtilities_coverage.xml"
+    - MSBuild.exe /t:Rebuild
+    - ps: cd GeUtilities.Tests
+    - OpenCover.Console.exe -register:"user" -target:"C:/Program Files/dotnet/dotnet.exe" -targetargs:"xunit -noshadow" -filter:"+[*]*" -oldStyle -output:"GeUtilities_coverage.xml"
+    - ps: cd ..
+    - MSBuild.SonarQube.Runner.exe end /d:"sonar.login=%sonartoken%"
 
   artifacts: 
     - path: GeUtilities/bin/Release/Genometric.GeUtilities*.nupkg