diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..9546fc661ae673f31198c8a535f3a71d2db64662
Binary files /dev/null and b/.DS_Store differ
diff --git a/.idea/.gitignore b/.idea/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..13566b81b018ad684f3a35fee301741b2734c8f4
--- /dev/null
+++ b/.idea/.gitignore
@@ -0,0 +1,8 @@
+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml
diff --git a/.idea/cdna-generator.iml b/.idea/cdna-generator.iml
new file mode 100644
index 0000000000000000000000000000000000000000..d0876a78d06ac03b5d78c8dcdb95570281c6f1d6
--- /dev/null
+++ b/.idea/cdna-generator.iml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 0000000000000000000000000000000000000000..25bde2c3afaab1a315ae039135cb178c10118d3f
--- /dev/null
+++ b/.idea/inspectionProfiles/Project_Default.xml
@@ -0,0 +1,14 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredPackages">
+        <value>
+          <list size="1">
+            <item index="0" class="java.lang.String" itemvalue="numpy" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+  </profile>
+</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 0000000000000000000000000000000000000000..105ce2da2d6447d11dfe32bfb846c3d5b199fc99
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d1e22ecb89619a9c2dcf51a28d891a196d2462a0
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.8" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000000000000000000000000000000000000..77e11905a5f9573959d9d8e478c7fe18853d732f
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/cdna-generator.iml" filepath="$PROJECT_DIR$/.idea/cdna-generator.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/.idea/sonarlint/issuestore/index.pb b/.idea/sonarlint/issuestore/index.pb
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..94a25f7f4cb416c083d265558da75d457237d671
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/test_files/copy_number_file.csv b/test_files/copy_number_file.csv
new file mode 100644
index 0000000000000000000000000000000000000000..690325102432fce639e42cb900e67a6adac9280c
--- /dev/null
+++ b/test_files/copy_number_file.csv
@@ -0,0 +1,6 @@
+ID of transcript, ID of parent transcript, Transcript copy number
+1,1,12
+2,1,11
+3,2,33
+4,3,11
+5,4,55