Linear Model Merging (#57)

* fixes the number of samples recorded in the association to be the number of samples used in the design matrix

* adds in predict function to linear model

* catch a convergence exception

* test and training partitions

* changes the predict function

* devin changes

* builds

* remove NaN

* implements math to more efficiently cache data necessary for a model merge

* build working

* merge models, but can't apply results yet

* break out results and model

* model merging working

* check point for api redesign

* api working for merging

* fixes POM issues

* add in tests, format code

* moves allelic assumption to genotype dataset

* LogisticSiteRegression returns LogisticRegressionResults object now

* fix up dataset holder

* Plink regression tests

* testing resources

* speed up the genotype loading

* LinearSiteRegression tests

* adds more tests

* remove unnecessary data formatting code

* adds in types for models, fixes avro/adam dependency issues

* adds in documentation for GnocchiSession

* adds in documentation

* adds in further documentation

* adds in documentation for variantModels and LogisticSiteRegression

* adds some docs and creates TransformVariants CLI

* fixes some stuff for cluster

* cli fix

* Fixes bugs found on cluster

bin/gnocchi-shell

@@ -55,17 +55,17 @@ GNOCCHI_CLI_JAR=
 if [ -d "$SCRIPT_DIR/repo" ]; then
   ASSEMBLY_DIR="$SCRIPT_DIR/repo"
 else
-  ASSEMBLY_DIR="$SCRIPT_DIR/gnocchi-cli/target"
+  ASSEMBLY_DIR="$SCRIPT_DIR/gnocchi-assembly/target"
 fi
 
-num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^gnocchi-cli_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | grep -v sources | wc -l)"
+num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^gnocchi-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | grep -v sources | wc -l)"
 if [ "$num_jars" -eq "0" ]; then
   echo "Failed to find GNOCCHI assembly in $ASSEMBLY_DIR." 1>&2
   echo "You need to build GNOCCHI before running this program." 1>&2
   exit 1
 fi
 
-ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^gnocchi-cli_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
+ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^gnocchi-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
 if [ "$num_jars" -gt "1" ]; then
   echo "Found multiple GNOCCHI cli assembly jars in $ASSEMBLY_DIR:" 1>&2
   echo "$ASSEMBLY_JARS" 1>&2

bin/gnocchi-submit

@@ -65,7 +65,7 @@ GNOCCHI_CLI_JAR=
 if [ -d "$INSTALL_DIR/repo" ]; then
   ASSEMBLY_DIR="$INSTALL_DIR/repo"
 else
-  ASSEMBLY_DIR="$INSTALL_DIR/gnocchi-cli/target"
+  ASSEMBLY_DIR="$INSTALL_DIR/gnocchi-assembly/target"
 fi
 
 num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^gnocchi[0-9A-Za-z\.\_\-]*\.jar$" | grep -v javadoc | grep -v sources | wc -l)"

bin/logo.txt

@@ -1,7 +1,9 @@
-   ___                                    _         _    
+                                               .-~~~-.
+                                              ( (     )
+                                               ( `   ) )
+   ___                                    _     \__ _ /
   / __|   _ _      ___     __      __    | |_      (_)   
  | (_ |  | ' \    / _ \   / _|    / _|   | ' \     | |   
   \___|  |_||_|   \___/   \__|_   \__|_  |_||_|   _|_|_  
 _|"""""|_|"""""|_|"""""|_|"""""|_|"""""|_|"""""|_|"""""| 
-"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-' 
-
+"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-'"`-0-0-'