From eecfa5653020b80e31eed1ae5d2b13068e17a2df Mon Sep 17 00:00:00 2001
From: r3fang <r3fang@ucsd.edu>
Date: Wed, 4 Sep 2019 16:30:18 -0700
Subject: [PATCH] fix barcode.txt

---
 setup.py                    |  2 +-
 snaptools.egg-info/PKG-INFO |  2 +-
 snaptools/__init__.py       |  2 +-
 snaptools/snap.py           |  4 +++-
 snaptools/snap_pre.py       | 15 ++++++++++-----
 5 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/setup.py b/setup.py
index 2b1fdc2..0e6f44e 100755
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup
 
-snaptools_version = '1.4.7'
+snaptools_version = '1.4.8'
 
 setup(
       name='snaptools',
diff --git a/snaptools.egg-info/PKG-INFO b/snaptools.egg-info/PKG-INFO
index 00d2b2f..cc346be 100644
--- a/snaptools.egg-info/PKG-INFO
+++ b/snaptools.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 1.2
 Name: snaptools
-Version: 1.4.7
+Version: 1.4.8
 Summary: A module for working with snap files in Python
 Home-page: https://github.com/r3fang/SnapTools.git
 Author: Rongxin Fang
diff --git a/snaptools/__init__.py b/snaptools/__init__.py
index 1be3a88..fedbd84 100755
--- a/snaptools/__init__.py
+++ b/snaptools/__init__.py
@@ -1 +1 @@
-__version__ = '1.4.7'
+__version__ = '1.4.8'
diff --git a/snaptools/snap.py b/snaptools/snap.py
index b1640bb..f244f4f 100755
--- a/snaptools/snap.py
+++ b/snaptools/snap.py
@@ -192,7 +192,9 @@ def getBarcodesFromTxt(fname):
     with open(fname) as fin:
         for line in fin:
             if line.startswith("#"): continue;
-            barcode = line.split()[0].upper()
+            if type(line) is bytes:
+                line = line.decode();
+            barcode = line.split()[0].upper();
             barcode_list.append(barcode);            
     barocde_num = len(set(barcode_list));
     if barocde_num < len(barcode_list):
diff --git a/snaptools/snap_pre.py b/snaptools/snap_pre.py
index 1d12ff6..f6b32d1 100755
--- a/snaptools/snap_pre.py
+++ b/snaptools/snap_pre.py
@@ -222,15 +222,20 @@ def snap_pre(input_file,
         barcode_dict = snaptools.snap.getBarcodesFromTxt(barcode_file);
     else:
         barcode_dict = snaptools.snap.getBarcodesFromInput(input_file, file_format);
-    
-    if min_cov == 0 and max_num == 10000000:
-        barcode_dict = barcode_dict;
-    else:       
         barcode_cov = snaptools.snap.getBarcodeCov(list(barcode_dict.keys()), input_file, file_format);
         barcode_cov = sorted(list(barcode_cov.items()), key=operator.itemgetter(1), reverse=True);
         barcode_cov = barcode_cov[0:min(len(barcode_cov), max_num)];
         barcodes = [key for [key, value] in barcode_cov if value > min_cov];
-        barcode_dict = collections.OrderedDict(list(zip(sorted(barcodes), list(range(1,(len(barcodes)+1))))));       
+        barcode_dict = collections.OrderedDict(list(zip(sorted(barcodes), list(range(1,(len(barcodes)+1))))));   
+    
+    #if min_cov == 0 and max_num == 10000000:
+    #    barcode_dict = barcode_dict;
+    #else:       
+    #    barcode_cov = snaptools.snap.getBarcodeCov(list(barcode_dict.keys()), input_file, file_format);
+    #    barcode_cov = sorted(list(barcode_cov.items()), key=operator.itemgetter(1), reverse=True);
+    #    barcode_cov = barcode_cov[0:min(len(barcode_cov), max_num)];
+    #    barcodes = [key for [key, value] in barcode_cov if value > min_cov];
+    #    barcode_dict = collections.OrderedDict(list(zip(sorted(barcodes), list(range(1,(len(barcodes)+1))))));       
     
     f = h5py.File(output_snap, "w", libver='earliest');
     f.create_group("HD");