From de8fc3bc68bc7180cd74dc061dbd773c5f536c55 Mon Sep 17 00:00:00 2001
From: E Croot <20226124+ecroot@users.noreply.github.com>
Date: Wed, 9 Apr 2025 12:47:53 +0100
Subject: [PATCH 1/2] prevent negative start coordinate

patch for bug 313 (https://github.com/sims-lab/CapCruncher/issues/313)
---
 capcruncher/api/pileup.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/capcruncher/api/pileup.py b/capcruncher/api/pileup.py
index 557dd16e..ed85075a 100644
--- a/capcruncher/api/pileup.py
+++ b/capcruncher/api/pileup.py
@@ -428,7 +428,14 @@ def cooler_to_bedgraph(
     if viewpoint_distance:
         viewpoint_coords = cooler.Cooler(clr).info["metadata"]["viewpoint_coords"][0]
         viewpoint_coords = re.split("[:-]", viewpoint_coords)
-        region_to_limit = f"{viewpoint_coords[0]}:{int(viewpoint_coords[1]) - viewpoint_distance}-{int(viewpoint_coords[1]) + viewpoint_distance}"
+        vpstart = (int(viewpoint_coords[1]) - viewpoint_distance)
+        vpend = (int(viewpoint_coords[1]) + viewpoint_distance)
+        # set start to 1 if (start - viewpoint distance) would be negative, because a negative coordinate causes
+        # 'ValueError: Unexpected token "-"'
+        if vpstart <=0:
+            vpstart = 1
+        # TODO: IF VPEND > CHR SIZE, SET TO CHR SIZE (not sure if this is needed as well?)
+            region_to_limit = f"{viewpoint_coords[0]}:{vpstart}-{vpend}"
     else:
         region_to_limit = None
 

From 11d578cc4692f02c77b543ed9d9a598625fd212a Mon Sep 17 00:00:00 2001
From: E Croot <20226124+ecroot@users.noreply.github.com>
Date: Fri, 11 Apr 2025 10:15:19 +0100
Subject: [PATCH 2/2] fix spacing error

---
 capcruncher/api/pileup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/capcruncher/api/pileup.py b/capcruncher/api/pileup.py
index ed85075a..551bcefa 100644
--- a/capcruncher/api/pileup.py
+++ b/capcruncher/api/pileup.py
@@ -435,7 +435,7 @@ def cooler_to_bedgraph(
         if vpstart <=0:
             vpstart = 1
         # TODO: IF VPEND > CHR SIZE, SET TO CHR SIZE (not sure if this is needed as well?)
-            region_to_limit = f"{viewpoint_coords[0]}:{vpstart}-{vpend}"
+        region_to_limit = f"{viewpoint_coords[0]}:{vpstart}-{vpend}"
     else:
         region_to_limit = None