From 25996f351364a5728686f4af18f79225002602f2 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Tue, 16 Feb 2016 11:15:12 +0100
Subject: [PATCH 1/2] Handle labels and comment lines in BED files better

---
 deeptools/heatmapper.py | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/deeptools/heatmapper.py b/deeptools/heatmapper.py
index 159f4b33d..5410ece28 100644
--- a/deeptools/heatmapper.py
+++ b/deeptools/heatmapper.py
@@ -786,16 +786,23 @@ def get_regions_and_groups(regions_file, onlyMultiplesOf=1,
         previnterval = None
         duplicates = 0
         totalintervals = 0
+        groupintervals = 0
         includedintervals = 0
         group_labels = []
         group_idx = 0
         bed_file = deeptools.readBed.ReadBed(regions_file)
         for ginterval in bed_file:
-            totalintervals += 1
             if ginterval.line.startswith("track") or ginterval.line.startswith("browser"):
                 continue
+            if ginterval.line.startswith('#') and totalintervals == 0:
+                continue
 
             if ginterval.line.startswith('#'):
+                # check for labels with no associated entries
+                if groupintervals == 0:
+                    continue
+                else:
+                    groupintervals = 0
                 group_idx += 1
                 label = ginterval.line[1:].strip()
                 if label in group_labels:
@@ -815,6 +822,7 @@ def get_regions_and_groups(regions_file, onlyMultiplesOf=1,
             #    continue
             # check for regions that have the same position as the previous.
             # This assumes that the regions file given is sorted
+            totalintervals += 1
             if previnterval is not None:
                 if previnterval.chrom == ginterval.chrom and \
                    previnterval.start == ginterval.start and \
@@ -832,6 +840,7 @@ def get_regions_and_groups(regions_file, onlyMultiplesOf=1,
                                                                  ginterval.end))
                     duplicates += 1
 
+            groupintervals += 1
             previnterval = ginterval
             ginterval.group_idx = group_idx
             regions.append(ginterval)
@@ -844,8 +853,10 @@ def get_regions_and_groups(regions_file, onlyMultiplesOf=1,
         if not group_labels:
             group_labels.append(default_group_name)
             using_default_group_name = True
+            groupintervals = 0
 
-        if len(group_labels) < group_idx - 1:
+        # If there are any remaining intervals with no group label then add a fake one
+        if groupintervals > 0:
             # There was a missing "#" at the end
             label = default_group_name
             if label in group_labels:

From 1c0e6d1dbbb97f811f9220ed420c38bb2ca47af3 Mon Sep 17 00:00:00 2001
From: dpryan79 <dpryan79@gmail.com>
Date: Tue, 16 Feb 2016 11:54:18 +0100
Subject: [PATCH 2/2] Remove unneeded test

---
 deeptools/heatmapper.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/deeptools/heatmapper.py b/deeptools/heatmapper.py
index 5410ece28..fb9b9139c 100644
--- a/deeptools/heatmapper.py
+++ b/deeptools/heatmapper.py
@@ -794,8 +794,6 @@ def get_regions_and_groups(regions_file, onlyMultiplesOf=1,
         for ginterval in bed_file:
             if ginterval.line.startswith("track") or ginterval.line.startswith("browser"):
                 continue
-            if ginterval.line.startswith('#') and totalintervals == 0:
-                continue
 
             if ginterval.line.startswith('#'):
                 # check for labels with no associated entries