From 3ee5a931b740922b13c402acc4180be6b73bb175 Mon Sep 17 00:00:00 2001
From: Justin Koestinger <jkoestinger@gmail.com>
Date: Tue, 2 Oct 2018 14:43:44 +0200
Subject: [PATCH 1/3] Added support for bytes read files (ie. for remote files)

---
 vcf/parser.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/vcf/parser.py b/vcf/parser.py
index c3c3d08..766a105 100644
--- a/vcf/parser.py
+++ b/vcf/parser.py
@@ -297,9 +297,9 @@ def __init__(self, fsock=None, filename=None, compressed=None, prepend_chr=False
         self._column_headers = []
         self._tabix = None
         self._prepend_chr = prepend_chr
+        self.encoding = encoding
         self._parse_metainfo()
         self._format_cache = {}
-        self.encoding = encoding
 
     def __iter__(self):
         return self
@@ -314,6 +314,11 @@ def _parse_metainfo(self):
 
         parser = _vcf_metadata_parser()
 
+        try:
+            line = line.decode(self.encoding)
+        except AttributeError:
+            pass
+
         line = next(self.reader)
         while line.startswith('##'):
             self._header_lines.append(line)
@@ -347,7 +352,10 @@ def _parse_metainfo(self):
                         self.metadata[key] = []
                     self.metadata[key].append(val)
 
-            line = next(self.reader)
+            try:
+                line = line.decode(self.encoding)
+            except AttributeError:
+                pass
 
         fields = self._row_pattern.split(line[1:])
         self._column_headers = fields[:9]
@@ -551,6 +559,12 @@ def _parse_alt(self, str):
     def next(self):
         '''Return the next record in the file.'''
         line = next(self.reader)
+
+        try:
+            line = line.decode(self.encoding)
+        except AttributeError:
+            pass
+
         row = self._row_pattern.split(line.rstrip())
         chrom = row[0]
         if self._prepend_chr:

From 8df5301037288dcb9b97859e95f0b5c51e243e14 Mon Sep 17 00:00:00 2001
From: Justin Koestinger <jkoestinger@gmail.com>
Date: Tue, 2 Oct 2018 14:52:37 +0200
Subject: [PATCH 2/3] Rectified error in implementation

---
 vcf/parser.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/vcf/parser.py b/vcf/parser.py
index 766a105..14266c4 100644
--- a/vcf/parser.py
+++ b/vcf/parser.py
@@ -313,13 +313,14 @@ def _parse_metainfo(self):
             setattr(self, attr, OrderedDict())
 
         parser = _vcf_metadata_parser()
+        
+        line = next(self.reader)
 
         try:
             line = line.decode(self.encoding)
         except AttributeError:
             pass
 
-        line = next(self.reader)
         while line.startswith('##'):
             self._header_lines.append(line)
 

From 46c1c8a45ab8aa3a658233959f110490d3016cb2 Mon Sep 17 00:00:00 2001
From: Justin Koestinger <jkoestinger@gmail.com>
Date: Tue, 2 Oct 2018 14:58:51 +0200
Subject: [PATCH 3/3] Fixed typo

---
 vcf/parser.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/vcf/parser.py b/vcf/parser.py
index 14266c4..08daa08 100644
--- a/vcf/parser.py
+++ b/vcf/parser.py
@@ -313,7 +313,7 @@ def _parse_metainfo(self):
             setattr(self, attr, OrderedDict())
 
         parser = _vcf_metadata_parser()
-        
+
         line = next(self.reader)
 
         try:
@@ -353,6 +353,7 @@ def _parse_metainfo(self):
                         self.metadata[key] = []
                     self.metadata[key].append(val)
 
+            line = next(self.reader)
             try:
                 line = line.decode(self.encoding)
             except AttributeError: