From 74bc179807e80c1ee0f89cd98953263f68a05661 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 May 2021 19:40:46 +0000
Subject: Fixed generate_rqtl_cmd to make the kwarg hash from a combination of
 keywords and arguments + account for boolean kwargs without values (like
 --interval or --covar)

---
 gn3/computations/rqtl.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 0e8cd1f..855a819 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -2,24 +2,36 @@
 
 from typing import Dict
 from gn3.commands import compose_rqtl_cmd
+from gn3.computations.gemma import generate_hash_of_string
 from gn3.fs_helpers import get_hash_of_files
 
 def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
-                      rqtl_wrapper_kwargs: Dict) -> Dict:
+                      rqtl_wrapper_kwargs: Dict,
+                      rqtl_wrapper_bool_kwargs: list) -> Dict:
     """Given the base rqtl_wrapper command and
 dict of keyword arguments, return the full rqtl_wrapper command and an
 output filename generated from a hash of the genotype and phenotype files
 
     """
 
+    # Generate a hash from contents of the genotype and phenotype files
     _hash = get_hash_of_files(
         [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]])
 
+    # Append to hash a hash of keyword arguments
+    _hash += generate_hash_of_string(
+        ",".join([f"{k}:{v}" for k, v in rqtl_wrapper_kwargs.items() if k not in ["g", "p"]]))
+
+    # Append to hash a hash of boolean keyword arguments
+    _hash += generate_hash_of_string(
+        ",".join(rqtl_wrapper_bool_kwargs))
+
     _output_filename = f"{_hash}-output.json"
     return {
         "output_file":
         _output_filename,
         "rqtl_cmd":
         compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
-                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
+                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs,
+                         rqtl_wrapper_bool_kwargs=rqtl_wrapper_bool_kwargs)
     }
-- 
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