From fa9d7099165a943536a8701bc0fadd0ffe56610b Mon Sep 17 00:00:00 2001
From: rnmitchell <57150382+rnmitchell@users.noreply.github.com>
Date: Thu, 27 Jul 2023 12:58:55 -0400
Subject: [PATCH] updated manifest, setup.py and fixed bug in snp config (#55)

---
 MANIFEST.in          | 1 +
 lusSTR/cli/config.py | 4 ++++
 setup.py             | 1 +
 3 files changed, 6 insertions(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 2f197b20..6dbeb7e5 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -13,3 +13,4 @@ include lusSTR/tests/data/snps/*
 include lusSTR/tests/data/RU_stutter_test/*
 include lusSTR/tests/data/NGS_stutter_test/*
 include lusSTR/tests/data/kinsnps/*
+include lusSTR/tests/data/lusstr_output/*
diff --git a/lusSTR/cli/config.py b/lusSTR/cli/config.py
index ae0dd49e..f8592584 100644
--- a/lusSTR/cli/config.py
+++ b/lusSTR/cli/config.py
@@ -55,6 +55,10 @@ def edit_snp_config(config, args):
             data["references"] = None
         if args.strand:
             data["strand"] = args.strand
+        if args.input:
+            data["samp_input"] = args.input
+        else:
+            data["samp_input"] = os.getcwd()
         return data
 
 
diff --git a/setup.py b/setup.py
index 9780bd8d..9deac591 100755
--- a/setup.py
+++ b/setup.py
@@ -31,6 +31,7 @@
             "lusSTR/tests/data/RU_stutter_test/*",
             "lusSTR/tests/data/NGS_stutter_test/*",
             "lusSTR/tests/data/kinsnps/*",
+            "lusSTR/tests/data/lusstr_output/*",
             "lusSTR/workflows/*",
             "lusSTR/wrappers/*",
         ]