From 18cb113450b8ef17d1d1ca81062e05ce27657c00 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 12 Aug 2022 14:18:22 +0000
Subject: Change homology logic to include lines that start/end outside of the
 given mb range

This is to avoid a situation where a user zooms in and a bar should
encompass the whole area but isn't displayed (because its start/end
don't both fall within the given Mb range)

This commit also renames mm10/hg38 to ref/query to be more generic
---
 wqflask/wqflask/interval_analyst/GeneUtil.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 5b28f458..a3fe1269 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -9,16 +9,21 @@ def load_homology(chr_name, start_mb, end_mb, source_file):
         for line in h_file:
             line_items = line.split()
             this_dict = {
-                "mm10_chr": line_items[2][3:],
-                "mm10_start": float(line_items[5])/1000000,
-                "mm10_end": float(line_items[6])/1000000,
-                "hg38_chr": line_items[7][3:],
-                "hg38_strand": line_items[9],
-                "hg38_start": float(line_items[10])/1000000,
-                "hg38_end": float(line_items[11])/1000000
+                "ref_chr": line_items[2][3:],
+                "ref_strand": line_items[4],
+                "ref_start": float(line_items[5])/1000000,
+                "ref_end": float(line_items[6])/1000000,
+                "query_chr": line_items[7][3:],
+                "query_strand": line_items[9],
+                "query_start": float(line_items[10])/1000000,
+                "query_end": float(line_items[11])/1000000
             }
 
-            if str(this_dict["mm10_chr"]) == str(chr_name) and this_dict["mm10_start"]>= start_mb and this_dict["mm10_end"] <= end_mb:
+            if str(this_dict["ref_chr"]) == str(chr_name) and
+                ((this_dict["ref_start"]>= start_mb and this_dict["ref_end"] <= end_mb) or
+                    (this_dict["ref_start"] < start_mb and this_dict["ref_end"] <= end_mb) or
+                    (this_dict["ref_start"] >= start_mb and this_dict["ref_end"] > end_mb) or
+                    (this_dict["ref_start"] < start_mb and this_dict["ref_end"] > end_mb)):
                 homology_list.append(this_dict)
 
     return homology_list
-- 
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