diff --git a/.gitignore b/.gitignore
index bdc49a7..757fb4e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,5 @@ cyvcf.egg-info
 dist
 cyvcf/parser.c
 cyvcf/parser.so
+cyvcf/parser.*.so
+.history
diff --git a/cyvcf/parser.pyx b/cyvcf/parser.pyx
index 72b3c7a..5d0a163 100644
--- a/cyvcf/parser.pyx
+++ b/cyvcf/parser.pyx
@@ -4,6 +4,10 @@ import csv
 import gzip
 import sys
 import itertools
+import operator
+import codecs
+file=open
+PY3 = sys.version_info > (3,)
 
 from . import utils
 
@@ -34,9 +38,9 @@ HET = 1
 HOM_ALT = 3
 UNKNOWN = 2
 
-cdef _Call _parse_sample(char *sample, list samp_fmt,
+cdef _Call _parse_sample(str sample, list samp_fmt,
                                list samp_fmt_types, list samp_fmt_nums,
-                               char *name, Record rec):
+                               str name, Record rec):
 
     cdef dict sampdict = {x: None for x in samp_fmt}
     cdef list lvals
@@ -92,7 +96,7 @@ cdef _Call _parse_sample(char *sample, list samp_fmt,
             sampdict[fmt] = vals
     return _Call(rec, name, sampdict)
 
-cdef inline list _map(func, list iterable, char *bad='.'):
+cdef inline list _map(func, list iterable, str bad='.'):
     '''``map``, but make bad values None.'''
     return [func(x) if x != bad else None for x in iterable]
 
@@ -175,8 +179,9 @@ class _vcf_metadata_parser(object):
 cdef class _Call(object):
     """ A genotype call, a cell entry in a VCF file"""
 
-    cdef public bytes sample   #NA12878
-    cdef bytes gt_nums  #'0/1'
+    cdef public str sample   #NA12878
+    cdef str gt_nums  #'0/1'
+    # use str instead of bytes for python3 compatability
     # use bytes instead of char * because of C -> Python string complications
     # see: http://docs.cython.org/src/tutorial/strings.html
     cdef public Record site   #instance of Record
@@ -184,7 +189,7 @@ cdef class _Call(object):
     cdef public bint called, phased
     cdef list alleles
 
-    def __cinit__(self, Record site, char *sample, dict data):
+    def __cinit__(self, Record site, str sample, dict data):
         #: The ``Record`` for this ``_Call``
         self.site = site
         #: The sample name
@@ -426,7 +431,7 @@ cdef class Record(object):
               gt_phred_likelihoods
     # use bytes instead of char * because of C -> Python string complications
     # see: http://docs.cython.org/src/tutorial/strings.html
-    cdef readonly bytes CHROM, ID, FORMAT
+    cdef readonly str CHROM, ID, FORMAT
     cdef public REF
     cdef readonly object FILTER, QUAL
     cdef public int POS, start, end, num_hom_ref, num_het, num_hom_alt, \
@@ -435,8 +440,8 @@ cdef class Record(object):
     cdef public dict _sample_indexes
     cdef public bint has_genotypes
 
-    def __cinit__(self, char *CHROM, int POS, char *ID,
-                        char *REF, list ALT, object QUAL=None,
+    def __cinit__(self, str CHROM, int POS, str ID,
+                        str REF, list ALT, object QUAL=None,
                         object FILTER=None, dict INFO=None, object FORMAT=None,
                         dict sample_indexes=None, list samples=None,
                         list gt_bases=None, list gt_types=None,
@@ -493,6 +498,13 @@ cdef class Record(object):
                     self.POS == other.POS and
                     self.REF == other.REF and
                     self.ALT == other.ALT)
+        elif op == 3:
+            return not self.__richcmp__(other, 2)
+        else:
+            ops = { 0: operator.lt, 1: operator.le, 
+                    2: operator.eq, 3: operator.ne,
+                    4: operator.gt, 5: operator.ge }
+            return  ops[op]( (self.CHROM, self.POS), (other.CHROM, other.POS) )
 
     def __iter__(self):
         return iter(self.samples)
@@ -534,8 +546,8 @@ cdef class Record(object):
                           self._format_qual() or '.', self.FILTER or '.', self._format_info()])
 
 
-    def __cmp__(self, other):
-        return cmp( (self.CHROM, self.POS), (other.CHROM, other.POS))
+    # def __cmp__(self, other):
+    #     return cmp( (self.CHROM, self.POS), (other.CHROM, other.POS))
 
     def add_format(self, fmt):
         tmp = self.FORMAT + ':' + fmt
@@ -660,10 +672,10 @@ cdef class Record(object):
         if self.is_snp:
             # just one alt allele
             alt_allele = self.ALT[0]
-            if ((self.REF == b'A' and alt_allele == b'G') or
-                (self.REF == b'G' and alt_allele == b'A') or
-                (self.REF == b'C' and alt_allele == b'T') or
-                (self.REF == b'T' and alt_allele == b'C')):
+            if ((self.REF == 'A' and alt_allele == 'G') or
+                (self.REF == 'G' and alt_allele == 'A') or
+                (self.REF == 'C' and alt_allele == 'T') or
+                (self.REF == 'T' and alt_allele == 'C')):
                 return True
             else: return False
         else: return False
@@ -775,20 +787,20 @@ cdef class Record(object):
 cdef class Reader(object):
 
     """ Reader for a VCF v 4.1 file, an iterator returning ``Record objects`` """
-    cdef bytes _col_defn_line
-    cdef char _prepend_chr
+    cdef str _col_defn_line
     cdef public object reader
-    cdef bint compressed, prepend_chr
+    cdef bint compressed, _prepend_chr
     cdef public dict metadata, infos, filters, formats,
     cdef readonly dict _sample_indexes
     cdef list _header_lines, samp_data
     cdef public list samples
     cdef object _tabix
-    cdef public object filename
+    cdef public str filename
     cdef int num_samples
+    cdef str encoding
 
-    def __init__(self, fsock=None, filename=None,
-                        bint compressed=False, bint prepend_chr=False):
+    def __init__(self, fsock=None, str filename=None,
+                        bint compressed=False, bint prepend_chr=False, encoding='ascii'):
         """ Create a new Reader for a VCF file.
 
             You must specify a filename.  Gzipped streams
@@ -797,13 +809,14 @@ cdef class Reader(object):
         """
         super(VCFReader, self).__init__()
 
+        self.encoding = encoding
         if not (fsock or filename):
             raise Exception('You must provide at least fsock or filename')
 
         if filename:
             self.filename = filename
             if fsock is None:
-                self.reader = file(filename)
+                self.reader = file(filename, 'rb')
 
         if fsock:
             self.reader = fsock
@@ -814,6 +827,8 @@ cdef class Reader(object):
 
         if compressed or (filename and filename.endswith('.gz')):
             self.reader = gzip.GzipFile(fileobj=self.reader)
+            if PY3:
+                self.reader = codecs.getreader(self.encoding)(self.reader)
 
         #: metadata fields from header
         self.metadata = {}
@@ -857,7 +872,10 @@ cdef class Reader(object):
 
         parser = _vcf_metadata_parser()
 
-        line = self.reader.next()
+        line = next(self.reader)
+        if PY3 and type(line) is bytes:
+            self.reader = codecs.getreader(self.encoding)(self.reader)
+            line = line.decode(self.encoding)
         while line.startswith('##'):
             self._header_lines.append(line)
             line = line.rstrip('\n')
@@ -878,7 +896,7 @@ cdef class Reader(object):
                 key, val = parser.read_meta(line.strip())
                 self.metadata[key] = val
 
-            line = self.reader.next()
+            line = next(self.reader)
 
         if line.startswith('#'):  # the column def'n line - REQ'D
             self._col_defn_line = line
@@ -888,10 +906,10 @@ cdef class Reader(object):
             self.num_samples = len(self.samples)
             self._sample_indexes = dict([(x,i) for (i,x) in enumerate(self.samples)])
         else:
-             sys.exit("Expected column definition line beginning with #.  Not found - exiting.")
+            sys.exit("Expected column definition line beginning with #.  Not found - exiting.")
 
 
-    cdef list _map(Reader self, func, iterable, char *bad='.'):
+    cdef list _map(Reader self, func, iterable, str bad='.'):
         '''``map``, but make bad values None.'''
         return [func(x) if x != bad else None for x in iterable]
 
@@ -909,7 +927,7 @@ cdef class Reader(object):
 
         cdef int i = 0
         cdef int n = len(entries)
-        cdef char *entry_type
+        cdef str entry_type
         cdef list entry
         # for entry in entries:
         for i in xrange(n):
@@ -926,18 +944,18 @@ cdef class Reader(object):
                 else:
                     entry_type = 'String'
 
-            if entry_type == b'Integer':
+            if entry_type == 'Integer':
                 vals = entry[1].split(',')
                 try:
                     val = _map(int, vals)
                 except ValueError:
                     val = _map(float, vals)
-            elif entry_type == b'Float':
+            elif entry_type == 'Float':
                 vals = entry[1].split(',')
                 val = _map(float, vals)
-            elif entry_type == b'Flag':
+            elif entry_type == 'Flag':
                 val = True
-            elif entry_type == b'String':
+            elif entry_type == 'String':
                 if len(entry) > 1:
                     val = entry[1]
                 else:
@@ -959,7 +977,7 @@ cdef class Reader(object):
         return retdict
 
 
-    def _parse_samples(self, Record rec, list samples, char *samp_fmt_s):
+    def _parse_samples(self, Record rec, list samples, str samp_fmt_s):
         '''Parse a sample entry according to the format specified in the FORMAT
         column.'''
         cdef list samp_fmt = samp_fmt_s.split(':')
@@ -968,7 +986,7 @@ cdef class Reader(object):
         cdef list samp_fmt_nums = [None] * n
 
         cdef int i = 0
-        cdef char *fmt
+        cdef str fmt
         # for fmt in samp_fmt:
         for i in xrange(n):
             fmt = samp_fmt[i]
@@ -1045,7 +1063,7 @@ cdef class Reader(object):
 
     def __next__(self):
         '''Return the next record in the file.'''
-        line = self.reader.next().rstrip()
+        line = next(self.reader).rstrip()
         return self.parse(line)
 
     def parse(self, line):
@@ -1053,20 +1071,21 @@ cdef class Reader(object):
         cdef list row = line.split('\t')
 
         #CHROM
-        cdef bytes chrom = row[0]
+        cdef str chrom = row[0]
         if self._prepend_chr:
-            chrom = 'chr' + str(chrom)
+            tmp = 'chr' + str(chrom)
+            chrom = tmp
         # POS
         cdef int pos = int(row[1])
         # ID
-        cdef bytes id = row[2]
+        cdef str id = row[2]
         #REF
-        cdef bytes ref = row[3]
+        cdef str ref = row[3]
         #ALT
         cdef list alt = self._map(str, row[4].split(','))
         #QUAL
         cdef object qual
-        if row[5] == b'.':
+        if row[5] == '.':
             qual = None
         else:
             qual = float(row[5])
@@ -1077,7 +1096,7 @@ cdef class Reader(object):
         #INFO
         cdef dict info = self._parse_info(row[7])
         #FORMAT
-        cdef bytes fmt
+        cdef str fmt
         try:
             fmt = row[8]
         except IndexError:
@@ -1113,13 +1132,19 @@ cdef class Reader(object):
         if end is None:
             self.reader = self._tabix.fetch(chrom, start, start+1)
             try:
-                return self.next()
+                return next(self)
             except StopIteration:
                 return None
 
         self.reader = self._tabix.fetch(chrom, start, end)
         return self
 
+    def close(self):
+        try:
+            self.reader.close()
+        finally:
+            return
+
 
 class Writer(object):
     """ VCF Writer """
diff --git a/ez_setup.py b/ez_setup.py
index b74adc0..01e57ad 100644
--- a/ez_setup.py
+++ b/ez_setup.py
@@ -13,6 +13,7 @@
 
 This file can also be run as a script to install or upgrade setuptools.
 """
+from __future__ import print_function
 import sys
 DEFAULT_VERSION = "0.6c11"
 DEFAULT_URL     = "http://pypi.python.org/packages/%s/s/setuptools/" % sys.version[:3]
@@ -70,10 +71,10 @@ def _validate_md5(egg_name, data):
     if egg_name in md5_data:
         digest = md5(data).hexdigest()
         if digest != md5_data[egg_name]:
-            print >>sys.stderr, (
+            print((
                 "md5 validation of %s failed!  (Possible download problem?)"
                 % egg_name
-            )
+            ), file=sys.stderr)
             sys.exit(2)
     return data
 
@@ -103,14 +104,14 @@ def do_download():
         return do_download()       
     try:
         pkg_resources.require("setuptools>="+version); return
-    except pkg_resources.VersionConflict, e:
+    except pkg_resources.VersionConflict as e:
         if was_imported:
-            print >>sys.stderr, (
+            print((
             "The required version of setuptools (>=%s) is not available, and\n"
             "can't be installed while this script is running. Please install\n"
             " a more recent version first, using 'easy_install -U setuptools'."
             "\n\n(Currently using %r)"
-            ) % (version, e.args[0])
+            ) % (version, e.args[0]), file=sys.stderr)
             sys.exit(2)
     except pkg_resources.DistributionNotFound:
         pass
@@ -129,7 +130,13 @@ def download_setuptools(
     with a '/'). `to_dir` is the directory where the egg will be downloaded.
     `delay` is the number of seconds to pause before an actual download attempt.
     """
-    import urllib2, shutil
+    #import urllib.request, urllib.error, urllib.parse, shutil
+    from future.standard_library import hooks
+    with hooks():
+        from urllib.parse import urlparse, urlencode
+        from urllib.request import urlopen, Request
+        from urllib.error import HTTPError
+    import shutil
     egg_name = "setuptools-%s-py%s.egg" % (version,sys.version[:3])
     url = download_base + egg_name
     saveto = os.path.join(to_dir, egg_name)
@@ -155,7 +162,7 @@ def download_setuptools(
                     version, download_base, delay, url
                 ); from time import sleep; sleep(delay)
             log.warn("Downloading %s", url)
-            src = urllib2.urlopen(url)
+            src = urlopen(url)
             # Read/write all in one block, so we don't create a corrupt file
             # if the download is interrupted.
             data = _validate_md5(egg_name, src.read())
@@ -216,10 +223,10 @@ def main(argv, version=DEFAULT_VERSION):
                 os.unlink(egg)
     else:
         if setuptools.__version__ == '0.0.1':
-            print >>sys.stderr, (
+            print((
             "You have an obsolete version of setuptools installed.  Please\n"
             "remove it from your system entirely before rerunning this script."
-            )
+            ), file=sys.stderr)
             sys.exit(2)
 
     req = "setuptools>="+version
@@ -238,8 +245,8 @@ def main(argv, version=DEFAULT_VERSION):
             from setuptools.command.easy_install import main
             main(argv)
         else:
-            print "Setuptools version",version,"or greater has been installed."
-            print '(Run "ez_setup.py -U setuptools" to reinstall or upgrade.)'
+            print("Setuptools version",version,"or greater has been installed.")
+            print('(Run "ez_setup.py -U setuptools" to reinstall or upgrade.)')
 
 def update_md5(filenames):
     """Update our built-in md5 registry"""
@@ -252,7 +259,7 @@ def update_md5(filenames):
         md5_data[base] = md5(f.read()).hexdigest()
         f.close()
 
-    data = ["    %r: %r,\n" % it for it in md5_data.items()]
+    data = ["    %r: %r,\n" % it for it in list(md5_data.items())]
     data.sort()
     repl = "".join(data)
 
@@ -262,7 +269,7 @@ def update_md5(filenames):
 
     match = re.search("\nmd5_data = {\n([^}]+)}", src)
     if not match:
-        print >>sys.stderr, "Internal error!"
+        print("Internal error!", file=sys.stderr)
         sys.exit(2)
 
     src = src[:match.start(1)] + repl + src[match.end(1):]
diff --git a/setup.py b/setup.py
index 997c56f..baf1877 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,13 @@ def build_extensions(self):
 
 if 'setuptools.extension' in sys.modules:
     m = sys.modules['setuptools.extension']
-    m.Extension.__dict__ = m._Extension.__dict__
+    for attr, val in m._Extension.__dict__.items():
+        try:
+            setattr(m.Extension, attr, val)
+        except BaseException as  e:
+            # print(e)
+            pass
+    # m.Extension.__dict__ = m._Extension.__dict__
 
 version_py = os.path.join(os.path.dirname(__file__), 'cyvcf', 'version.py')
 version = open(version_py).read().strip().split('=')[-1].replace('"','')
@@ -63,4 +69,4 @@ def build_extensions(self):
             'License :: OSI Approved :: GNU General Public License (GPL)',
             'Topic :: Scientific/Engineering :: Bio-Informatics']
 
-    )
\ No newline at end of file
+    )
diff --git a/test/test_vcf.py b/test/test_vcf.py
index bcfb098..f7f3630 100644
--- a/test/test_vcf.py
+++ b/test/test_vcf.py
@@ -1,17 +1,29 @@
 import unittest
 import doctest
 import os
-import commands
-from StringIO import StringIO
+import subprocess
+try:
+    from StringIO import StringIO
+except ImportError: # py3
+    from io import StringIO
 
 import cyvcf
 from cyvcf import utils
+import gzip
+
+import sys
+PY3 = sys.version_info > (3,)
+
+file=open
 
 suite = doctest.DocTestSuite(cyvcf.parser)
 
 
 def fh(fname):
-    return file(os.path.join(os.path.dirname(__file__), fname))
+    path = os.path.join(os.path.dirname(__file__), fname)
+    if PY3 and fname.endswith(".gz"):
+        return file(path, 'rb')
+    return file(path)
 
 
 class TestVcfSpecs(unittest.TestCase):
@@ -68,9 +80,9 @@ def test_vcf_4_1_sv(self):
 
         # test we can walk the file at least
         for r in reader:
-            print r
+            print(r)
             for c in r:
-                print c
+                print(c)
                 assert c
 
         # asserting False while I work out what to check
@@ -135,7 +147,7 @@ class TestFreebayesOutput(TestGatkOutput):
 
     def testParse(self):
         reader = cyvcf.Reader(fh('freebayes.vcf'))
-        print reader.samples
+        print(reader.samples)
         self.assertEqual(len(reader.samples), 7)
         n = 0
         for r in reader:
@@ -173,18 +185,18 @@ def testWrite(self):
 
         records = list(reader)
 
-        map(writer.write_record, records)
+        list(map(writer.write_record, records))
         out.seek(0)
         reader2 = cyvcf.Reader(out)
 
-        self.assertEquals(reader.samples, reader2.samples)
-        self.assertEquals(reader.formats, reader2.formats)
+        self.assertEqual(reader.samples, reader2.samples)
+        self.assertEqual(reader.formats, reader2.formats)
 
         for k in reader.infos:
-            self.assertEquals(reader.infos[k], reader2.infos[k], (reader.infos[k], reader2.infos[k]))
+            self.assertEqual(reader.infos[k], reader2.infos[k], (reader.infos[k], reader2.infos[k]))
 
         for l, r in zip(records, reader2):
-            self.assertEquals(l.samples, r.samples)
+            self.assertEqual(l.samples, r.samples)
 
 class TestRecord(unittest.TestCase):
 
@@ -194,6 +206,7 @@ def test_num_calls(self):
             num_calls = (var.num_hom_ref + var.num_hom_alt + \
                          var.num_het + var.num_unknown)
             self.assertEqual(len(var.samples), num_calls)
+        reader.close()
 
     def test_call_rate(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -209,6 +222,7 @@ def test_call_rate(self):
                 self.assertEqual(3.0/3.0, call_rate)
             elif var.POS == 1234567:
                 self.assertEqual(2.0/3.0, call_rate)
+        reader.close()
 
     def test_aaf(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -224,6 +238,7 @@ def test_aaf(self):
                 self.assertEqual(0.0/6.0, aaf)
             elif var.POS == 1234567:
                 self.assertEqual(None, aaf)
+        reader.close()
 
     def test_pi(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -239,6 +254,7 @@ def test_pi(self):
                 self.assertEqual(0.0/6.0, pi)
             elif var.POS == 1234567:
                 self.assertEqual(None, pi)
+        reader.close()
 
     def test_is_snp(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -254,6 +270,7 @@ def test_is_snp(self):
                 self.assertEqual(False, is_snp)
             elif var.POS == 1234567:
                 self.assertEqual(False, is_snp)
+        reader.close()
 
     def test_is_indel(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -269,6 +286,7 @@ def test_is_indel(self):
                 self.assertEqual(True, is_indel)
             elif var.POS == 1234567:
                 self.assertEqual(True, is_indel)
+        reader.close()
 
     def test_is_transition(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -284,6 +302,7 @@ def test_is_transition(self):
                 self.assertEqual(False, is_trans)
             elif var.POS == 1234567:
                 self.assertEqual(False, is_trans)
+        reader.close()
 
     def test_is_deletion(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -299,6 +318,7 @@ def test_is_deletion(self):
                 self.assertEqual(True, is_del)
             elif var.POS == 1234567:
                 self.assertEqual(False, is_del)
+        reader.close()
 
     def test_var_type(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
@@ -314,6 +334,7 @@ def test_var_type(self):
                 self.assertEqual("indel", type)
             elif var.POS == 1234567:
                 self.assertEqual("indel", type)
+        reader.close()
         # SV tests
         reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
         for var in reader:
@@ -330,6 +351,7 @@ def test_var_type(self):
                 self.assertEqual("sv", type)
             elif var.POS == 18665128:
                 self.assertEqual("sv", type)
+        reader.close()
 
 
     def test_var_subtype(self):
@@ -346,6 +368,7 @@ def test_var_subtype(self):
                 self.assertEqual("del", subtype)
             elif var.POS == 1234567:
                 self.assertEqual("unknown", subtype)
+        reader.close()
         # SV tests
         reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
         for var in reader:
@@ -362,6 +385,7 @@ def test_var_subtype(self):
                 self.assertEqual("DUP", subtype)
             elif var.POS == 18665128:
                 self.assertEqual("DUP:TANDEM", subtype)
+        reader.close()
 
     def test_is_sv(self):
         reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
@@ -379,6 +403,7 @@ def test_is_sv(self):
                 self.assertEqual(True, is_sv)
             elif var.POS == 18665128:
                 self.assertEqual(True, is_sv)
+        reader.close()
 
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
         for var in reader:
@@ -393,6 +418,7 @@ def test_is_sv(self):
                 self.assertEqual(False, is_sv)
             elif var.POS == 1234567:
                 self.assertEqual(False, is_sv)
+        reader.close()
 
     def test_is_sv_precise(self):
         reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
@@ -410,6 +436,7 @@ def test_is_sv_precise(self):
                 self.assertEqual(False, is_precise)
             elif var.POS == 18665128:
                 self.assertEqual(False, is_precise)
+        reader.close()
 
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
         for var in reader:
@@ -424,6 +451,7 @@ def test_is_sv_precise(self):
                 self.assertEqual(False, is_precise)
             elif var.POS == 1234567:
                 self.assertEqual(False, is_precise)
+        reader.close()
 
     def test_sv_end(self):
         reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
@@ -441,6 +469,7 @@ def test_sv_end(self):
                 self.assertEqual(12686200, sv_end)
             elif var.POS == 18665128:
                 self.assertEqual(18665204, sv_end)
+        reader.close()
 
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
         for var in reader:
@@ -455,6 +484,7 @@ def test_sv_end(self):
                 self.assertEqual(None, sv_end)
             elif var.POS == 1234567:
                 self.assertEqual(None, sv_end)
+        reader.close()
 
 
 class TestCall(unittest.TestCase):
@@ -463,7 +493,7 @@ def test_phased(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
         for var in reader:
             phases = var.gt_phases
-            print var
+            print(var)
             if var.POS == 14370:
                 self.assertEqual([True, True, False], phases)
             if var.POS == 17330:
@@ -494,7 +524,7 @@ def test_gt_types(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
         for var in reader:
             for s in var:
-                print s.data
+                print(s.data)
             gt_types = [s.gt_type for s in var.samples]
             if var.POS == 14370:
                 self.assertEqual([0,1,3], gt_types)
@@ -511,7 +541,7 @@ def test_gt_depths(self):
         reader = cyvcf.Reader(fh('example-4.0.vcf'))
         for var in reader:
             for s in var:
-                print s.data
+                print(s.data)
             gt_depths = [s.gt_depth for s in var.samples]
             if var.POS == 14370:
                 self.assertEqual([1,8,5], gt_depths)
@@ -573,17 +603,17 @@ def testFetchRange(self):
         if not self.run:
             return
         lines = list(self.reader.fetch('20', 14370, 14370))
-        self.assertEquals(len(lines), 1)
+        self.assertEqual(len(lines), 1)
         self.assertEqual(lines[0].POS, 14370)
 
         lines = list(self.reader.fetch('20', 14370, 17330))
-        self.assertEquals(len(lines), 2)
+        self.assertEqual(len(lines), 2)
         self.assertEqual(lines[0].POS, 14370)
         self.assertEqual(lines[1].POS, 17330)
 
 
         lines = list(self.reader.fetch('20', 1110695, 1234567))
-        self.assertEquals(len(lines), 3)
+        self.assertEqual(len(lines), 3)
 
     def testFetchSite(self):
         if not self.run:
@@ -623,21 +653,21 @@ class TestFilter(unittest.TestCase):
 
 
     def testApplyFilter(self):
-        s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq')
+        s, out = subprocess.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq')
         #print out
         assert s == 0
         buf = StringIO()
         buf.write(out)
         buf.seek(0)
 
-        print buf.getvalue()
+        print(buf.getvalue())
         reader = cyvcf.Reader(buf)
 
 
         # check filter got into output file
         assert 'sq30' in reader.filters
 
-        print reader.filters
+        print(reader.filters)
 
         # check sites were filtered
         n = 0
@@ -651,7 +681,7 @@ def testApplyFilter(self):
 
 
     def testApplyMultipleFilters(self):
-        s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 '
+        s, out = subprocess.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 '
         '--genotype-quality 50 test/example-4.0.vcf sq mgq')
         assert s == 0
         #print out
@@ -660,7 +690,7 @@ def testApplyMultipleFilters(self):
         buf.seek(0)
         reader = cyvcf.Reader(buf)
 
-        print reader.filters
+        print(reader.filters)
 
         assert 'mgq50' in reader.filters
         assert 'sq30' in reader.filters
@@ -670,20 +700,20 @@ class TestRegression(unittest.TestCase):
 
     def test_issue_16(self):
         reader = cyvcf.Reader(fh('issue-16.vcf'))
-        assert reader.next().QUAL == None
+        assert next(reader).QUAL == None
 
     def test_null_mono(self):
         # null qualities were written as blank, causing subsequent parse to fail
-        print os.path.abspath(os.path.join(os.path.dirname(__file__),  'null_genotype_mono.vcf'))
+        print(os.path.abspath(os.path.join(os.path.dirname(__file__),  'null_genotype_mono.vcf')))
         p = cyvcf.Reader(fh('null_genotype_mono.vcf'))
         assert p.samples
         out = StringIO()
         writer = cyvcf.Writer(out, p)
-        map(writer.write_record, p)
+        list(map(writer.write_record, p))
         out.seek(0)
-        print out.getvalue()
+        print(out.getvalue())
         p2 = cyvcf.Reader(out)
-        rec = p2.next()
+        rec = next(p2)
         assert rec.samples
 
 
@@ -726,7 +756,7 @@ def setUp(self):
         self.reader = cyvcf.Reader(fh('test.vcf'))
 
     def testRefDepth(self):
-        v = self.reader.next()
+        v = next(self.reader)
         self.assertEqual(v.samples[0].gt_ref_depth, -1)
 
 class TestGLInt(unittest.TestCase):
diff --git a/test/test_vcf.py.bak b/test/test_vcf.py.bak
new file mode 100644
index 0000000..bcfb098
--- /dev/null
+++ b/test/test_vcf.py.bak
@@ -0,0 +1,753 @@
+import unittest
+import doctest
+import os
+import commands
+from StringIO import StringIO
+
+import cyvcf
+from cyvcf import utils
+
+suite = doctest.DocTestSuite(cyvcf.parser)
+
+
+def fh(fname):
+    return file(os.path.join(os.path.dirname(__file__), fname))
+
+
+class TestVcfSpecs(unittest.TestCase):
+
+    def test_vcf_4_0(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        assert reader.metadata['fileformat'] == 'VCFv4.0'
+
+        # test we can walk the file at least
+        for r in reader:
+
+            if r.POS == 1230237:
+                assert r.is_monomorphic
+            else:
+                assert not r.is_monomorphic
+
+            if 'AF' in r.INFO:
+                self.assertEqual(type(r.INFO['AF']),  type([]))
+
+            for c in r:
+                assert c
+
+                # issue 19, in the example ref the GQ is length 1
+                if c.called:
+                    self.assertEqual(type(c.data['GQ']),  type(1))
+                    if 'HQ' in c.data and c.data['HQ'] is not None:
+                        self.assertEqual(type(c.data['HQ']),  type([]))
+
+
+
+    def test_vcf_4_1(self):
+        return
+        reader = cyvcf.Reader(fh('example-4.1.vcf'))
+        self.assertEqual(reader.metadata['fileformat'],  'VCFv4.1')
+
+        # contigs were added in vcf4.1
+        # probably need to add a reader.contigs attribute
+        assert 'contig' in reader.metadata
+
+        # test we can walk the file at least
+        for r in reader:
+            for c in r:
+                assert c
+
+        # asserting False while I work out what to check
+        assert False
+
+    def test_vcf_4_1_sv(self):
+        return
+
+        reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
+
+        assert 'SVLEN' in reader.infos
+
+        # test we can walk the file at least
+        for r in reader:
+            print r
+            for c in r:
+                print c
+                assert c
+
+        # asserting False while I work out what to check
+        assert False
+
+
+class TestGatkOutput(unittest.TestCase):
+
+    filename = 'gatk.vcf'
+
+    samples = ['BLANK', 'NA12878', 'NA12891', 'NA12892',
+            'NA19238', 'NA19239', 'NA19240']
+    formats = ['AD', 'DP', 'GQ', 'GT', 'PL']
+    infos = ['AC', 'AF', 'AN', 'BaseQRankSum', 'DB', 'DP', 'DS',
+            'Dels', 'FS', 'HRun', 'HaplotypeScore', 'InbreedingCoeff',
+            'MQ', 'MQ0', 'MQRankSum', 'QD', 'ReadPosRankSum']
+
+    n_calls = 37
+
+    def setUp(self):
+        self.reader = cyvcf.Reader(fh(self.filename))
+
+    def testSamples(self):
+        self.assertEqual(self.reader.samples, self.samples)
+
+    def testFormats(self):
+        self.assertEqual(set(self.reader.formats), set(self.formats))
+
+    def testInfos(self):
+        self.assertEqual(set(self.reader.infos), set(self.infos))
+
+
+    def testCalls(self):
+        n = 0
+
+        for site in self.reader:
+            n += 1
+            self.assertEqual(len(site.samples), len(self.samples))
+
+
+            # check sample name lookup
+            for s in self.samples:
+                assert site.genotype(s)
+
+            # check ordered access
+            self.assertEqual([x.sample for x in site.samples], self.samples)
+        self.assertEqual(len(site.gt_phred_likelihoods), len(self.samples))
+        self.assertEqual(n,  self.n_calls)
+
+
+class TestFreebayesOutput(TestGatkOutput):
+
+    filename = 'freebayes.vcf'
+    formats = ['AO', 'DP', 'GL', 'GLE', 'GQ', 'GT', 'QA', 'QR', 'RO']
+    infos = ['AB', 'ABP', 'AC', 'AF', 'AN', 'AO', 'BVAR', 'CIGAR',
+            'DB', 'DP', 'DPRA', 'EPP', 'EPPR', 'HWE', 'LEN', 'MEANALT',
+            'NUMALT', 'RPP', 'MQMR', 'ODDS', 'MQM', 'PAIREDR', 'PAIRED',
+            'SAP', 'XRM', 'RO', 'REPEAT', 'XRI', 'XAS', 'XAI', 'SRP',
+            'XAM', 'XRS', 'RPPR', 'NS', 'RUN', 'CpG', 'TYPE']
+    n_calls = 104
+
+
+    def testParse(self):
+        reader = cyvcf.Reader(fh('freebayes.vcf'))
+        print reader.samples
+        self.assertEqual(len(reader.samples), 7)
+        n = 0
+        for r in reader:
+            n+=1
+            for x in r:
+                assert x
+        assert n == self.n_calls
+
+class TestSamtoolsOutput(unittest.TestCase):
+
+    def testParse(self):
+        reader = cyvcf.Reader(fh('samtools.vcf'))
+
+        self.assertEqual(len(reader.samples), 1)
+        self.assertEqual(sum(1 for _ in reader), 11)
+
+
+class Test1kg(unittest.TestCase):
+
+    def testParse(self):
+        reader = cyvcf.Reader(fh('1kg.vcf.gz'))
+
+        self.assertEqual(len(reader.samples), 629)
+        for _ in reader:
+            pass
+
+
+class TestWriter(unittest.TestCase):
+
+    def testWrite(self):
+
+        reader = cyvcf.Reader(fh('gatk.vcf'))
+        out = StringIO()
+        writer = cyvcf.Writer(out, reader)
+
+        records = list(reader)
+
+        map(writer.write_record, records)
+        out.seek(0)
+        reader2 = cyvcf.Reader(out)
+
+        self.assertEquals(reader.samples, reader2.samples)
+        self.assertEquals(reader.formats, reader2.formats)
+
+        for k in reader.infos:
+            self.assertEquals(reader.infos[k], reader2.infos[k], (reader.infos[k], reader2.infos[k]))
+
+        for l, r in zip(records, reader2):
+            self.assertEquals(l.samples, r.samples)
+
+class TestRecord(unittest.TestCase):
+
+    def test_num_calls(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            num_calls = (var.num_hom_ref + var.num_hom_alt + \
+                         var.num_het + var.num_unknown)
+            self.assertEqual(len(var.samples), num_calls)
+
+    def test_call_rate(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            call_rate = var.call_rate
+            if var.POS == 14370:
+                self.assertEqual(3.0/3.0, call_rate)
+            if var.POS == 17330:
+                self.assertEqual(3.0/3.0, call_rate)
+            if var.POS == 1110696:
+                self.assertEqual(3.0/3.0, call_rate)
+            if var.POS == 1230237:
+                self.assertEqual(3.0/3.0, call_rate)
+            elif var.POS == 1234567:
+                self.assertEqual(2.0/3.0, call_rate)
+
+    def test_aaf(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            aaf = var.aaf
+            if var.POS == 14370:
+                self.assertEqual(3.0/6.0, aaf)
+            if var.POS == 17330:
+                self.assertEqual(1.0/6.0, aaf)
+            if var.POS == 1110696:
+                self.assertEqual(None, aaf)
+            if var.POS == 1230237:
+                self.assertEqual(0.0/6.0, aaf)
+            elif var.POS == 1234567:
+                self.assertEqual(None, aaf)
+
+    def test_pi(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            pi = var.nucl_diversity
+            if var.POS == 14370:
+                self.assertEqual(6.0/10.0, pi)
+            if var.POS == 17330:
+                self.assertEqual(1.0/3.0, pi)
+            if var.POS == 1110696:
+                self.assertEqual(None, pi)
+            if var.POS == 1230237:
+                self.assertEqual(0.0/6.0, pi)
+            elif var.POS == 1234567:
+                self.assertEqual(None, pi)
+
+    def test_is_snp(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            is_snp = var.is_snp
+            if var.POS == 14370:
+                self.assertEqual(True, is_snp)
+            if var.POS == 17330:
+                self.assertEqual(True, is_snp)
+            if var.POS == 1110696:
+                self.assertEqual(True, is_snp)
+            if var.POS == 1230237:
+                self.assertEqual(False, is_snp)
+            elif var.POS == 1234567:
+                self.assertEqual(False, is_snp)
+
+    def test_is_indel(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            is_indel = var.is_indel
+            if var.POS == 14370:
+                self.assertEqual(False, is_indel)
+            if var.POS == 17330:
+                self.assertEqual(False, is_indel)
+            if var.POS == 1110696:
+                self.assertEqual(False, is_indel)
+            if var.POS == 1230237:
+                self.assertEqual(True, is_indel)
+            elif var.POS == 1234567:
+                self.assertEqual(True, is_indel)
+
+    def test_is_transition(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            is_trans = var.is_transition
+            if var.POS == 14370:
+                self.assertEqual(True, is_trans)
+            if var.POS == 17330:
+                self.assertEqual(False, is_trans)
+            if var.POS == 1110696:
+                self.assertEqual(False, is_trans)
+            if var.POS == 1230237:
+                self.assertEqual(False, is_trans)
+            elif var.POS == 1234567:
+                self.assertEqual(False, is_trans)
+
+    def test_is_deletion(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            is_del = var.is_deletion
+            if var.POS == 14370:
+                self.assertEqual(False, is_del)
+            if var.POS == 17330:
+                self.assertEqual(False, is_del)
+            if var.POS == 1110696:
+                self.assertEqual(False, is_del)
+            if var.POS == 1230237:
+                self.assertEqual(True, is_del)
+            elif var.POS == 1234567:
+                self.assertEqual(False, is_del)
+
+    def test_var_type(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            type = var.var_type
+            if var.POS == 14370:
+                self.assertEqual("snp", type)
+            if var.POS == 17330:
+                self.assertEqual("snp", type)
+            if var.POS == 1110696:
+                self.assertEqual("snp", type)
+            if var.POS == 1230237:
+                self.assertEqual("indel", type)
+            elif var.POS == 1234567:
+                self.assertEqual("indel", type)
+        # SV tests
+        reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
+        for var in reader:
+            type = var.var_type
+            if var.POS == 2827693:
+                self.assertEqual("sv", type)
+            if var.POS == 321682:
+                self.assertEqual("sv", type)
+            if var.POS == 14477084:
+                self.assertEqual("sv", type)
+            if var.POS == 9425916:
+                self.assertEqual("sv", type)
+            elif var.POS == 12665100:
+                self.assertEqual("sv", type)
+            elif var.POS == 18665128:
+                self.assertEqual("sv", type)
+
+
+    def test_var_subtype(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            subtype = var.var_subtype
+            if var.POS == 14370:
+                self.assertEqual("ts", subtype)
+            if var.POS == 17330:
+                self.assertEqual("tv", subtype)
+            if var.POS == 1110696:
+                self.assertEqual("unknown", subtype)
+            if var.POS == 1230237:
+                self.assertEqual("del", subtype)
+            elif var.POS == 1234567:
+                self.assertEqual("unknown", subtype)
+        # SV tests
+        reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
+        for var in reader:
+            subtype = var.var_subtype
+            if var.POS == 2827693:
+                self.assertEqual("DEL", subtype)
+            if var.POS == 321682:
+                self.assertEqual("DEL", subtype)
+            if var.POS == 14477084:
+                self.assertEqual("DEL:ME:ALU", subtype)
+            if var.POS == 9425916:
+                self.assertEqual("INS:ME:L1", subtype)
+            elif var.POS == 12665100:
+                self.assertEqual("DUP", subtype)
+            elif var.POS == 18665128:
+                self.assertEqual("DUP:TANDEM", subtype)
+
+    def test_is_sv(self):
+        reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
+        for var in reader:
+            is_sv = var.is_sv
+            if var.POS == 2827693:
+                self.assertEqual(True, is_sv)
+            if var.POS == 321682:
+                self.assertEqual(True, is_sv)
+            if var.POS == 14477084:
+                self.assertEqual(True, is_sv)
+            if var.POS == 9425916:
+                self.assertEqual(True, is_sv)
+            elif var.POS == 12665100:
+                self.assertEqual(True, is_sv)
+            elif var.POS == 18665128:
+                self.assertEqual(True, is_sv)
+
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            is_sv = var.is_sv
+            if var.POS == 14370:
+                self.assertEqual(False, is_sv)
+            if var.POS == 17330:
+                self.assertEqual(False, is_sv)
+            if var.POS == 1110696:
+                self.assertEqual(False, is_sv)
+            if var.POS == 1230237:
+                self.assertEqual(False, is_sv)
+            elif var.POS == 1234567:
+                self.assertEqual(False, is_sv)
+
+    def test_is_sv_precise(self):
+        reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
+        for var in reader:
+            is_precise = var.is_sv_precise
+            if var.POS == 2827693:
+                self.assertEqual(True, is_precise)
+            if var.POS == 321682:
+                self.assertEqual(False, is_precise)
+            if var.POS == 14477084:
+                self.assertEqual(False, is_precise)
+            if var.POS == 9425916:
+                self.assertEqual(False, is_precise)
+            elif var.POS == 12665100:
+                self.assertEqual(False, is_precise)
+            elif var.POS == 18665128:
+                self.assertEqual(False, is_precise)
+
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            is_precise = var.is_sv_precise
+            if var.POS == 14370:
+                self.assertEqual(False, is_precise)
+            if var.POS == 17330:
+                self.assertEqual(False, is_precise)
+            if var.POS == 1110696:
+                self.assertEqual(False, is_precise)
+            if var.POS == 1230237:
+                self.assertEqual(False, is_precise)
+            elif var.POS == 1234567:
+                self.assertEqual(False, is_precise)
+
+    def test_sv_end(self):
+        reader = cyvcf.Reader(fh('example-4.1-sv.vcf'))
+        for var in reader:
+            sv_end = var.sv_end
+            if var.POS == 2827693:
+                self.assertEqual(2827680, sv_end)
+            if var.POS == 321682:
+                self.assertEqual(321887, sv_end)
+            if var.POS == 14477084:
+                self.assertEqual(14477381, sv_end)
+            if var.POS == 9425916:
+                self.assertEqual(9425916, sv_end)
+            elif var.POS == 12665100:
+                self.assertEqual(12686200, sv_end)
+            elif var.POS == 18665128:
+                self.assertEqual(18665204, sv_end)
+
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            sv_end = var.sv_end
+            if var.POS == 14370:
+                self.assertEqual(None, sv_end)
+            if var.POS == 17330:
+                self.assertEqual(None, sv_end)
+            if var.POS == 1110696:
+                self.assertEqual(None, sv_end)
+            if var.POS == 1230237:
+                self.assertEqual(None, sv_end)
+            elif var.POS == 1234567:
+                self.assertEqual(None, sv_end)
+
+
+class TestCall(unittest.TestCase):
+
+    def test_phased(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            phases = var.gt_phases
+            print var
+            if var.POS == 14370:
+                self.assertEqual([True, True, False], phases)
+            if var.POS == 17330:
+                self.assertEqual([True, True, False], phases)
+            if var.POS == 1110696:
+                self.assertEqual([True, True, False], phases)
+            if var.POS == 1230237:
+                self.assertEqual([True, True, False], phases)
+            elif var.POS == 1234567:
+                self.assertEqual([False, False, False], phases)
+
+    def test_gt_bases(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            gt_bases = [s.gt_bases for s in var.samples]
+            if var.POS == 14370:
+                self.assertEqual(['G|G', 'A|G', 'A/A'], gt_bases)
+            elif var.POS == 17330:
+                self.assertEqual(['T|T', 'T|A', 'T/T'], gt_bases)
+            elif var.POS == 1110696:
+                self.assertEqual(['G|T', 'T|G', 'T/T'], gt_bases)
+            elif var.POS == 1230237:
+                self.assertEqual(['T|T', 'T|T', 'T/T'], gt_bases)
+            elif var.POS == 1234567:
+                self.assertEqual([None, 'GTCT/GTACT', 'G/G'], gt_bases)
+
+    def test_gt_types(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            for s in var:
+                print s.data
+            gt_types = [s.gt_type for s in var.samples]
+            if var.POS == 14370:
+                self.assertEqual([0,1,3], gt_types)
+            elif var.POS == 17330:
+                self.assertEqual([0,1,0], gt_types)
+            elif var.POS == 1110696:
+                self.assertEqual([1,1,3], gt_types)
+            elif var.POS == 1230237:
+                self.assertEqual([0,0,0], gt_types)
+            elif var.POS == 1234567:
+                self.assertEqual([None,1,3], gt_types)
+
+    def test_gt_depths(self):
+        reader = cyvcf.Reader(fh('example-4.0.vcf'))
+        for var in reader:
+            for s in var:
+                print s.data
+            gt_depths = [s.gt_depth for s in var.samples]
+            if var.POS == 14370:
+                self.assertEqual([1,8,5], gt_depths)
+            elif var.POS == 17330:
+                self.assertEqual([3,5,3], gt_depths)
+            elif var.POS == 1110696:
+                self.assertEqual([6,0,4], gt_depths)
+            elif var.POS == 1230237:
+                self.assertEqual([7,4,2], gt_depths)
+            elif var.POS == 1234567:
+                self.assertEqual([4,2,3], gt_depths)
+
+    def test_gt_ref_depths(self):
+
+        reader = cyvcf.Reader(fh('gatk.vcf'))
+        for var in reader:
+            gt_ref_depths = [s.gt_ref_depth for s in var.samples]
+            if var.POS == 42522392:
+                self.assertEqual([6,138,169,249,248,250,250], gt_ref_depths)
+            elif var.POS == 42522613:
+                self.assertEqual([13,118,241,161,110,106,116], gt_ref_depths)
+            elif var.POS == 42527891:
+                self.assertEqual([-1,238,246,239,232,233,238], gt_ref_depths)
+
+    def test_gt_alt_depths(self):
+
+        reader = cyvcf.Reader(fh('gatk.vcf'))
+        for var in reader:
+            gt_alt_depths = [s.gt_alt_depth for s in var.samples]
+            if var.POS == 42522392:
+                self.assertEqual([0,107,77,0,1,0,0], gt_alt_depths)
+            elif var.POS == 42522613:
+                self.assertEqual([4,127,0,85,132,135,126], gt_alt_depths)
+            elif var.POS == 42527891:
+                self.assertEqual([-1,7,3,11,16,14,11], gt_alt_depths)
+
+    def test_gt_quals(self):
+
+        reader = cyvcf.Reader(fh('gatk.vcf'))
+        for var in reader:
+            gt_quals = [s.gt_qual for s in var.samples]
+            if var.POS == 42522392:
+                self.assertEqual([18.04,99,99,99,99,99,99], gt_quals)
+            elif var.POS == 42522613:
+                self.assertEqual([62.64,99,99,99,99,99,99], gt_quals)
+            elif var.POS == 42527891:
+                self.assertEqual([-1,13.70,5.97,31.42,49.09,52.10,12.71], gt_quals)
+
+
+class TestTabix(unittest.TestCase):
+
+    def setUp(self):
+        self.reader = cyvcf.Reader(fh('tb.vcf.gz'))
+
+        self.run = cyvcf.parser.pysam is not None
+
+
+    def testFetchRange(self):
+        if not self.run:
+            return
+        lines = list(self.reader.fetch('20', 14370, 14370))
+        self.assertEquals(len(lines), 1)
+        self.assertEqual(lines[0].POS, 14370)
+
+        lines = list(self.reader.fetch('20', 14370, 17330))
+        self.assertEquals(len(lines), 2)
+        self.assertEqual(lines[0].POS, 14370)
+        self.assertEqual(lines[1].POS, 17330)
+
+
+        lines = list(self.reader.fetch('20', 1110695, 1234567))
+        self.assertEquals(len(lines), 3)
+
+    def testFetchSite(self):
+        if not self.run:
+            return
+        site = self.reader.fetch('20', 14370)
+        assert site.POS == 14370
+
+        site = self.reader.fetch('20', 14369)
+        assert site is None
+
+
+
+
+class TestOpenMethods(unittest.TestCase):
+
+    samples = 'NA00001 NA00002 NA00003'.split()
+
+    def testOpenFilehandle(self):
+        r = cyvcf.Reader(fh('example-4.0.vcf'))
+        self.assertEqual(self.samples, r.samples)
+        self.assertEqual('example-4.0.vcf', os.path.split(r.filename)[1])
+
+    def testOpenFilename(self):
+        r = cyvcf.Reader(filename='test/example-4.0.vcf')
+        self.assertEqual(self.samples, r.samples)
+
+    def testOpenFilehandleGzipped(self):
+        r = cyvcf.Reader(fh('tb.vcf.gz'))
+        self.assertEqual(self.samples, r.samples)
+
+    def testOpenFilenameGzipped(self):
+        r = cyvcf.Reader(filename='test/tb.vcf.gz')
+        self.assertEqual(self.samples, r.samples)
+
+
+class TestFilter(unittest.TestCase):
+
+
+    def testApplyFilter(self):
+        s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq')
+        #print out
+        assert s == 0
+        buf = StringIO()
+        buf.write(out)
+        buf.seek(0)
+
+        print buf.getvalue()
+        reader = cyvcf.Reader(buf)
+
+
+        # check filter got into output file
+        assert 'sq30' in reader.filters
+
+        print reader.filters
+
+        # check sites were filtered
+        n = 0
+        for r in reader:
+            if r.QUAL < 30:
+                assert 'sq30' in r.FILTER
+                n += 1
+            else:
+                assert r.FILTER is None or 'sq30' not in r.FILTER
+        assert n == 2
+
+
+    def testApplyMultipleFilters(self):
+        s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 '
+        '--genotype-quality 50 test/example-4.0.vcf sq mgq')
+        assert s == 0
+        #print out
+        buf = StringIO()
+        buf.write(out)
+        buf.seek(0)
+        reader = cyvcf.Reader(buf)
+
+        print reader.filters
+
+        assert 'mgq50' in reader.filters
+        assert 'sq30' in reader.filters
+
+
+class TestRegression(unittest.TestCase):
+
+    def test_issue_16(self):
+        reader = cyvcf.Reader(fh('issue-16.vcf'))
+        assert reader.next().QUAL == None
+
+    def test_null_mono(self):
+        # null qualities were written as blank, causing subsequent parse to fail
+        print os.path.abspath(os.path.join(os.path.dirname(__file__),  'null_genotype_mono.vcf'))
+        p = cyvcf.Reader(fh('null_genotype_mono.vcf'))
+        assert p.samples
+        out = StringIO()
+        writer = cyvcf.Writer(out, p)
+        map(writer.write_record, p)
+        out.seek(0)
+        print out.getvalue()
+        p2 = cyvcf.Reader(out)
+        rec = p2.next()
+        assert rec.samples
+
+
+class TestUtils(unittest.TestCase):
+
+    def test_walk(self):
+        # easy case: all same sites
+        reader1 = cyvcf.Reader(fh('example-4.0.vcf'))
+        reader2 = cyvcf.Reader(fh('example-4.0.vcf'))
+        reader3 = cyvcf.Reader(fh('example-4.0.vcf'))
+
+        n = 0
+        for x in utils.walk_together(reader1, reader2, reader3):
+            assert len(x) == 3
+            assert (x[0] == x[1]) and (x[1] == x[2])
+            n+= 1
+        assert n == 5
+
+        # artificial case 2 from the left, 2 from the right, 2 together, 1 from the right, 1 from the left
+
+        expected = 'llrrttrl'
+        reader1 = cyvcf.Reader(fh('walk_left.vcf'))
+        reader2 = cyvcf.Reader(fh('example-4.0.vcf'))
+
+        for ex, recs in zip(expected, utils.walk_together(reader1, reader2)):
+
+            if ex == 'l':
+                assert recs[0] is not None
+                assert recs[1] is None
+            if ex == 'r':
+                assert recs[1] is not None
+                assert recs[0] is None
+            if ex == 't':
+                assert recs[0] is not None
+                assert recs[1] is not None
+
+
+class TestAD(unittest.TestCase):
+    def setUp(self):
+        self.reader = cyvcf.Reader(fh('test.vcf'))
+
+    def testRefDepth(self):
+        v = self.reader.next()
+        self.assertEqual(v.samples[0].gt_ref_depth, -1)
+
+class TestGLInt(unittest.TestCase):
+    def setUp(self):
+        self.reader = cyvcf.Reader(fh('test-gl.vcf'))
+    def testGLInt(self):
+        v = next(self.reader)
+        self.assertEqual(v.samples[0].gt_phred_likelihoods, None)
+
+
+
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestAD))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestGatkOutput))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestFreebayesOutput))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestSamtoolsOutput))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestWriter))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestTabix))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestOpenMethods))
+#suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestFilter))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(Test1kg))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestRecord))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestCall))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestRegression))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestGLInt))