From 9b51f59bc4b598c1136525300af5f696bcf66fc0 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 15 Jan 2024 18:36:06 +0300
Subject: Process `na.strings` even for default cases

There was a bug where the `na.strings` were not processed correctly if
the user called the `r_qtl.r_qtl2.file_data(...)` function without
explicitly providing the `process_*` arguments.

This commit fixes that.
---
 tests/r_qtl/test_files/test_pheno.zip            | Bin 485 -> 503 bytes
 tests/r_qtl/test_files/test_pheno_transposed.zip | Bin 536 -> 557 bytes
 tests/r_qtl/test_r_qtl2_pheno.py                 |   8 ++++----
 3 files changed, 4 insertions(+), 4 deletions(-)

(limited to 'tests/r_qtl')

diff --git a/tests/r_qtl/test_files/test_pheno.zip b/tests/r_qtl/test_files/test_pheno.zip
index 5c709e7..ba9bbb0 100644
Binary files a/tests/r_qtl/test_files/test_pheno.zip and b/tests/r_qtl/test_files/test_pheno.zip differ
diff --git a/tests/r_qtl/test_files/test_pheno_transposed.zip b/tests/r_qtl/test_files/test_pheno_transposed.zip
index 9bff030..e6a87aa 100644
Binary files a/tests/r_qtl/test_files/test_pheno_transposed.zip and b/tests/r_qtl/test_files/test_pheno_transposed.zip differ
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index a7de675..c7c0c86 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -13,14 +13,14 @@ from r_qtl import r_qtl2 as rqtl2
       ({"id": "1", "liver": "61.92", "spleen": "153.16"},
        {"id": "2", "liver": "88.33", "spleen": "178.58"},
        {"id": "3", "liver": "58", "spleen": "131.91"},
-       {"id": "4", "liver": "78.06", "spleen": "126.13"},
-       {"id": "5", "liver": "65.31", "spleen": "181.05"})),
+       {"id": "4", "liver": "78.06", "spleen": None},
+       {"id": "5", "liver": None, "spleen": "181.05"})),
      ("tests/r_qtl/test_files/test_pheno_transposed.zip",
       ({"id": "1", "liver": "61.92", "spleen": "153.16"},
        {"id": "2", "liver": "88.33", "spleen": "178.58"},
        {"id": "3", "liver": "58", "spleen": "131.91"},
-       {"id": "4", "liver": "78.06", "spleen": "126.13"},
-       {"id": "5", "liver": "65.31", "spleen": "181.05"}))))
+       {"id": "4", "liver": "78.06", "spleen": None},
+       {"id": "5", "liver": None, "spleen": "181.05"}))))
 def test_parse_pheno_files(filepath, expected):
     """Test parsing of 'pheno' files from the R/qtl2 bundle.
 
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