From d6be631af735a9286d50a46988b883e08ce22f1b Mon Sep 17 00:00:00 2001
From: Haibao Tang <tanghaibao@gmail.com>
Date: Sun, 4 Aug 2024 16:43:49 -0700
Subject: [PATCH] Allow bed format to contain browser/track headers (#698)

---
 jcvi/formats/bed.py           |  7 ++++---
 tests/formats/data/custom.bed | 10 ++++++++++
 tests/formats/test_bed.py     | 10 ++++++++++
 3 files changed, 24 insertions(+), 3 deletions(-)
 create mode 100644 tests/formats/data/custom.bed
 create mode 100644 tests/formats/test_bed.py

diff --git a/jcvi/formats/bed.py b/jcvi/formats/bed.py
index eb6886f5..05ca8ddb 100755
--- a/jcvi/formats/bed.py
+++ b/jcvi/formats/bed.py
@@ -155,9 +155,10 @@ def __init__(self, filename=None, key=None, sorted=True, juncs=False, include=No
 
         for line in must_open(filename):
             if (
-                line[0] == "#"
-                or (juncs and line.startswith("track name"))
-                or line.strip() == ""
+                line.strip() == ""
+                or line[0] == "#"
+                or line.startswith("browser ")
+                or line.startswith("track name")
             ):
                 continue
             b = BedLine(line)
diff --git a/tests/formats/data/custom.bed b/tests/formats/data/custom.bed
new file mode 100644
index 00000000..6ae23420
--- /dev/null
+++ b/tests/formats/data/custom.bed
@@ -0,0 +1,10 @@
+browser position chr7:4499924-4500043
+track name="Covered" description="Agilent SureSelect DNA - Custom Exome_1 - Genomic regions expected to be sequenced" color=0,128,0 visibility=dense db=hg38
+chr7	4499923	4500043	7P22.1
+chr7	4500475	4501075	7P22.1
+chr7	4501706	4501844	7P22.1
+chr7	4503679	4503919	7P22.1
+chr7	4504362	4505023	7P22.1
+chr7	4505688	4505990	7P22.1
+chr7	4506376	4506496	7P22.1
+chr7	4506928	4507768	7P22.1
diff --git a/tests/formats/test_bed.py b/tests/formats/test_bed.py
new file mode 100644
index 00000000..dc742f62
--- /dev/null
+++ b/tests/formats/test_bed.py
@@ -0,0 +1,10 @@
+import os
+import os.path as op
+
+from jcvi.formats.bed import summary
+
+def test_summary():
+    cwd = os.getcwd()
+    os.chdir(op.join(op.dirname(__file__), "data"))
+    summary(["custom.bed"])
+    os.chdir(cwd)