From 8a0505c9de3d819baf9e3a76a512fd7a5c131f5e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Tue, 6 Jun 2017 10:14:58 +0100
Subject: [PATCH] app: implement variant association test CLI, #126

---
 .../app/cli/local/LocalCliOptionsParser.java  |  1 +
 .../local/options/VariantCommandOptions.java  | 35 ++++++++++++++++---
 2 files changed, 31 insertions(+), 5 deletions(-)

diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java
index fe207e79..c679c362 100644
--- a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java
+++ b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/LocalCliOptionsParser.java
@@ -86,6 +86,7 @@ public LocalCliOptionsParser() {
         variantSubCommands.addCommand("query", variantCommandOptions.queryVariantCommandOptions);
         variantSubCommands.addCommand("metadata", variantCommandOptions.metadataVariantCommandOptions);
         variantSubCommands.addCommand("rvtests", variantCommandOptions.rvtestsVariantCommandOptions);
+        variantSubCommands.addCommand("association", variantCommandOptions.associationVariantCommandOptions);
 
         toolCommandOptions = new ToolCommandOptions(commonCommandOptions, jcommander);
         jcommander.addCommand("tool", toolCommandOptions);
diff --git a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java
index 1e779038..bb5a613d 100644
--- a/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java
+++ b/hpg-bigdata-app/src/main/java/org/opencb/hpg/bigdata/app/cli/local/options/VariantCommandOptions.java
@@ -21,6 +21,7 @@ public class VariantCommandOptions {
     public QueryVariantCommandOptions queryVariantCommandOptions;
     public MetadataVariantCommandOptions metadataVariantCommandOptions;
     public RvTestsVariantCommandOptions rvtestsVariantCommandOptions;
+    public AssociationVariantCommandOptions associationVariantCommandOptions;
 
     public LocalCliOptionsParser.CommonCommandOptions commonCommandOptions;
     public JCommander jCommander;
@@ -36,6 +37,7 @@ public VariantCommandOptions(LocalCliOptionsParser.CommonCommandOptions commonCo
         this.queryVariantCommandOptions = new QueryVariantCommandOptions();
         this.metadataVariantCommandOptions = new MetadataVariantCommandOptions();
         this.rvtestsVariantCommandOptions = new RvTestsVariantCommandOptions();
+        this.associationVariantCommandOptions = new AssociationVariantCommandOptions();
     }
 
     @Parameters(commandNames = {"convert"}, commandDescription = "Convert gVCF/VCF files to different big data"
@@ -128,14 +130,12 @@ public class AnnotateVariantCommandOptions {
         @ParametersDelegate
         public LocalCliOptionsParser.CommonCommandOptions commonOptions = commonCommandOptions;
 
-        @Parameter(names = {"-i", "--input"}, description = "0000 Input file name, usually a gVCF/VCF but it can be"
+        @Parameter(names = {"-i", "--input"}, description = "Input file name, usually a gVCF/VCF but it can be"
                 + " an Avro file when converting to Parquet.",
                 required = true, arity = 1)
         public String input;
 
-        @Parameter(names = {"-o", "--output"}, description = "Input file name, usually a gVCF/VCF but it can be an"
-                + " Avro file when converting to Parquet.",
-                required = true, arity = 1)
+        @Parameter(names = {"-o", "--output"}, description = "Output file name.", required = true, arity = 1)
         public String ouput;
     }
 
@@ -327,7 +327,7 @@ public class MetadataVariantCommandOptions {
         public boolean summary = false;
     }
 
-    @Parameters(commandNames = {"rvtests"}, commandDescription = "Execute the 'rvtests' program.")
+    @Parameters(commandNames = {"rvtests"}, commandDescription = "Execute the 'rvtests' program")
     public class RvTestsVariantCommandOptions {
 
         @ParametersDelegate
@@ -353,4 +353,29 @@ public class RvTestsVariantCommandOptions {
                 required = true, arity = 1)
         public String confFilename;
     }
+
+    @Parameters(commandNames = {"association"}, commandDescription = "Execute association tests such as chi-square,"
+            + " linear and logistic regressions for additive, dominant or recessive genetic models")
+    public class AssociationVariantCommandOptions {
+
+        @ParametersDelegate
+        public LocalCliOptionsParser.CommonCommandOptions commonOptions = commonCommandOptions;
+
+        @Parameter(names = {"-i", "--input"}, description = "Input file name in Avro file format", required = true,
+                arity = 1)
+        public String input;
+
+        @Parameter(names = {"-o", "--output"}, description = "Output file name to save results", required = true,
+                arity = 1)
+        public String output;
+
+        @Parameter(names = {"--pheno"}, description = "Name of the phenotype trait to test", arity = 1)
+        public String pheno = "affection";
+
+        @Parameter(names = {"--logistic"}, description = "Logistic regression (for qualitative traits)")
+        public boolean logistic = false;
+
+        @Parameter(names = {"--linear"}, description = "Linear regression (for quantitative traits)")
+        public boolean linear = false;
+    }
 }