From f45d1c4acedce020c0857d21752cbdb535d693c8 Mon Sep 17 00:00:00 2001
From: Asa Thibodeau <asa.thibodeau@jax.org>
Date: Fri, 10 Sep 2021 14:09:20 -0400
Subject: [PATCH] Added code to skip commented lines so that AMULET can run on
 Cell Ranger ATAC 2.0 fragment file outputs.

---
 FragmentFileOverlapCounter.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/FragmentFileOverlapCounter.py b/FragmentFileOverlapCounter.py
index 7d2248f..d8e43ae 100644
--- a/FragmentFileOverlapCounter.py
+++ b/FragmentFileOverlapCounter.py
@@ -261,7 +261,12 @@ def findOverlaps(fragmentfile, singlecellfile, expectedoverlap, chrlist, path, m
         stats_readcount += 1
         
         decodedline = linedecoder(curline)
+
+        if decodedline.strip().startswith("#"):
+            continue
+
         split = decodedline.split("\t")
+
         curchr = split[0]
         curstart = int(split[1])+startbases
         curend = int(split[2])+endbases