Add examples

Illumina · Nov 2, 2020 · 86a1b63 · 86a1b63
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diff --git a/Ilmn.Das.App.Wittyer.sln b/Ilmn.Das.App.Wittyer.sln
@@ -26,8 +26,44 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ReleaseNotes", "ReleaseNote
 		docs\release-notes\v0.3.1.md = docs\release-notes\v0.3.1.md
 		docs\release-notes\v0.3.2.md = docs\release-notes\v0.3.2.md
 		docs\release-notes\v0.3.3.md = docs\release-notes\v0.3.3.md
+		docs\release-notes\v0.3.4.md = docs\release-notes\v0.3.4.md
 	EndProjectSection
 EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "examples", "examples", "{3CCBABA0-BF50-4691-86B3-B2AC662A4F30}"
+ProjectSection(SolutionItems) = preProject
+	docs\examples\README.md = docs\examples\README.md
+EndProjectSection
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "SV", "SV", "{204A99D9-C74C-4D7B-B4A2-148A819B4EAE}"
+ProjectSection(SolutionItems) = preProject
+	docs\examples\SV\config.json = docs\examples\SV\config.json
+	docs\examples\SV\HG002.sv.vcf.gz = docs\examples\SV\HG002.sv.vcf.gz
+	docs\examples\SV\README.md = docs\examples\SV\README.md
+EndProjectSection
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "CNV", "CNV", "{0405A3B5-8043-4058-A541-DF0E3CB6F63B}"
+ProjectSection(SolutionItems) = preProject
+	docs\examples\CNV\config.json = docs\examples\CNV\config.json
+	docs\examples\CNV\HG002.cnv.vcf.gz = docs\examples\CNV\HG002.cnv.vcf.gz
+	docs\examples\CNV\README.md = docs\examples\CNV\README.md
+EndProjectSection
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "output", "output", "{8F931635-2D47-4C50-A44F-44561B11612D}"
+ProjectSection(SolutionItems) = preProject
+	docs\examples\SV\output\Wittyer.ConfigFileUsed.json = docs\examples\SV\output\Wittyer.ConfigFileUsed.json
+	docs\examples\SV\output\Wittyer.HG002.Vs.HG2.vcf.gz = docs\examples\SV\output\Wittyer.HG002.Vs.HG2.vcf.gz
+	docs\examples\SV\output\Wittyer.HG002.Vs.HG2.vcf.gz.tbi = docs\examples\SV\output\Wittyer.HG002.Vs.HG2.vcf.gz.tbi
+	docs\examples\SV\output\Wittyer.Stats.json = docs\examples\SV\output\Wittyer.Stats.json
+EndProjectSection
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "output", "output", "{CA36CA82-F8E1-445B-9B1F-D08DE432C923}"
+ProjectSection(SolutionItems) = preProject
+	docs\examples\CNV\output\Wittyer.ConfigFileUsed.json = docs\examples\CNV\output\Wittyer.ConfigFileUsed.json
+	docs\examples\CNV\output\Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz = docs\examples\CNV\output\Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz
+	docs\examples\CNV\output\Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz.tbi = docs\examples\CNV\output\Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz.tbi
+	docs\examples\CNV\output\Wittyer.Stats.json = docs\examples\CNV\output\Wittyer.Stats.json
+EndProjectSection
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -52,6 +88,11 @@ Global
 	EndGlobalSection
 	GlobalSection(NestedProjects) = preSolution
 		{F1D00B2C-E9A7-4AAA-ACDE-72572A9A0FA6} = {C30AA211-D9AE-474B-9340-66E7636F307D}
+		{3CCBABA0-BF50-4691-86B3-B2AC662A4F30} = {C30AA211-D9AE-474B-9340-66E7636F307D}
+		{204A99D9-C74C-4D7B-B4A2-148A819B4EAE} = {3CCBABA0-BF50-4691-86B3-B2AC662A4F30}
+		{0405A3B5-8043-4058-A541-DF0E3CB6F63B} = {3CCBABA0-BF50-4691-86B3-B2AC662A4F30}
+		{8F931635-2D47-4C50-A44F-44561B11612D} = {204A99D9-C74C-4D7B-B4A2-148A819B4EAE}
+		{CA36CA82-F8E1-445B-9B1F-D08DE432C923} = {0405A3B5-8043-4058-A541-DF0E3CB6F63B}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {F8B9CA36-CEC4-4D1B-84CC-F8BDC6ED3947}

diff --git a/docs/examples/CNV/HG002.cnv.vcf.gz b/docs/examples/CNV/HG002.cnv.vcf.gz
diff --git a/docs/examples/CNV/README.md b/docs/examples/CNV/README.md
@@ -0,0 +1,20 @@
+# CNV witty.er Examples
+
+In this folder, you will find a dragen CNV output file ([HG002.cnv.vcf.gz](HG002.cnv.vcf.gz)) and a [config.json](config.json), which will be used as input.  Example output can be found in the [output folder](output).
+
+1. Download the NIST truth set [VCF file](ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz) and [BED file](ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.bed)
+2. Install dotnet if you don't already have it installed on your system (you can google directions on how to install based on your system).
+3. Build witty.er with the `dotnet publish` command under the Wittyer project folder
+4. Run the following command line:
+
+```bash
+# DOTNET is your path to your dotnet executable
+# WITTYER_DLL is the path to the wittyer dll.
+$DOTNET $WITTYER_DLL \
+         -t NIST_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz \
+         -i HG002.cnv.vcf.gz \
+         -em CrossTypeAndSimpleCounting \
+         --configFile config.json \
+         --includeBed NIST_v0.6/HG002_SVs_Tier1_v0.6.bed \
+         -o output/
+```
diff --git a/docs/examples/CNV/config.json b/docs/examples/CNV/config.json
@@ -0,0 +1,26 @@
+[
+  {
+    "variantType": "Duplication",
+    "binSizes": "1000,5000,10000,20000,50000",
+    "bpDistance": 10000,
+    "percentDistance": 0.25,
+    "includedFilters": "PASS",
+    "excludedFilters": ""
+  },
+  {
+    "variantType": "Deletion",
+    "binSizes": "1000,5000,10000,20000,50000",
+    "bpDistance": 10000,
+    "percentDistance": 0.25,
+    "includedFilters": "PASS",
+    "excludedFilters": ""
+  },
+  {
+    "variantType": "CopyNumberReference",
+    "binSizes": "1000,5000,10000,20000,50000",
+    "bpDistance": 10000,
+    "percentDistance": 0.25,
+    "includedFilters": "PASS",
+    "excludedFilters": ""
+  }
+]
diff --git a/docs/examples/CNV/output/Wittyer.ConfigFileUsed.json b/docs/examples/CNV/output/Wittyer.ConfigFileUsed.json
@@ -0,0 +1,29 @@
+[
+  {
+    "variantType": "Duplication",
+    "binSizes": "1000,5000,10000,20000,50000",
+    "bpDistance": 10000,
+    "percentDistance": 0.25,
+    "includedFilters": "PASS",
+    "excludedFilters": "",
+    "includeBed": "NIST_v0.6/HG002_SVs_Tier1_v0.6.bed"
+  },
+  {
+    "variantType": "Deletion",
+    "binSizes": "1000,5000,10000,20000,50000",
+    "bpDistance": 10000,
+    "percentDistance": 0.25,
+    "includedFilters": "PASS",
+    "excludedFilters": "",
+    "includeBed": "NIST_v0.6/HG002_SVs_Tier1_v0.6.bed"
+  },
+  {
+    "variantType": "CopyNumberReference",
+    "binSizes": "1000,5000,10000,20000,50000",
+    "bpDistance": 10000,
+    "percentDistance": 0.25,
+    "includedFilters": "PASS",
+    "excludedFilters": "",
+    "includeBed": "NIST_v0.6/HG002_SVs_Tier1_v0.6.bed"
+  }
+]
diff --git a/docs/examples/CNV/output/Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz b/docs/examples/CNV/output/Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz
diff --git a/docs/examples/CNV/output/Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz.tbi b/docs/examples/CNV/output/Wittyer.HG002.Vs.PrecisionFDA_HG002.vcf.gz.tbi