nixpkgs/pkgs/by-name/ha/hap-py/python3.patch

diff --git a/src/c++/lib/tools/Roc.cpp b/src/c++/lib/tools/Roc.cpp
index fabe2be..2c6bb49 100644
--- a/src/c++/lib/tools/Roc.cpp
+++ b/src/c++/lib/tools/Roc.cpp
@@ -34,6 +34,9 @@
  */
 
 #include "helpers/Roc.hh"
+#include <stdexcept>
+#include <limits>
+
 
 #include <algorithm>
 #include <cmath>
diff --git a/src/cmake/cxx.cmake b/src/cmake/cxx.cmake
old mode 100755
new mode 100644
diff --git a/src/python/Haplo/happyroc.py b/src/python/Haplo/happyroc.py
index 152bd18..e439957 100644
--- a/src/python/Haplo/happyroc.py
+++ b/src/python/Haplo/happyroc.py
@@ -97,7 +97,7 @@ def roc(roc_table, output_path,
                 header = l.split("\t")
             else:
                 rec = {}
-                for k, v in itertools.izip(header, l.split("\t")):
+                for k, v in zip(header, l.split("\t")):
                     rec[k] = v
 
                 if filter_handling:
@@ -160,11 +160,11 @@ def roc(roc_table, output_path,
 
     if "all" not in result:
         # minimal empty DF
-        minidata = [{"Type": "SNP", "Subtype": "*", "Filter": "ALL", "Genotype": "*", "Subset": "*", "QQ": "*"} for _ in xrange(2)]
+        minidata = [{"Type": "SNP", "Subtype": "*", "Filter": "ALL", "Genotype": "*", "Subset": "*", "QQ": "*"} for _ in range(2)]
         minidata[1]["Type"] = "INDEL"
         result["all"] = pandas.DataFrame(minidata, columns=RESULT_ALLCOLUMNS)
         for i, c in enumerate(RESULT_ALLCOLUMNS):
-            result["all"][c] = result["all"][c].astype(RESULT_ALLDTYPES[i], raise_on_error=False)
+            result["all"][c] = result["all"][c].astype(RESULT_ALLDTYPES[i], errors="ignore")
 
     for k, v in result.items():
         result[k] = _postprocessRocData(pandas.DataFrame(v, columns=RESULT_ALLCOLUMNS))
diff --git a/src/python/Haplo/partialcredit.py b/src/python/Haplo/partialcredit.py
index d9e22bb..0f2b2cf 100644
--- a/src/python/Haplo/partialcredit.py
+++ b/src/python/Haplo/partialcredit.py
@@ -202,7 +202,7 @@ def partialCredit(vcfname,
     try:
         res = runParallel(pool,
                           preprocessWrapper,
-                          itertools.izip(itertools.repeat(vcfname), locations),
+                          zip(itertools.repeat(vcfname), locations),
                           {"reference": reference,
                            "decompose": decompose,
                            "leftshift": leftshift,
diff --git a/src/python/Haplo/quantify.py b/src/python/Haplo/quantify.py
index 042d13e..b1d362e 100755
--- a/src/python/Haplo/quantify.py
+++ b/src/python/Haplo/quantify.py
@@ -152,7 +152,7 @@ def run_quantify(filename,
         run_str += " -v %s" % pipes.quote(write_vcf)
 
     if regions:
-        for k, v in regions.iteritems():
+        for k, v in regions.items():
             run_str += " -R '%s:%s'" % (k, v)
 
     if roc_regions:
diff --git a/src/python/Somatic/Mutect.py b/src/python/Somatic/Mutect.py
index 7ac923c..81f08b5 100755
--- a/src/python/Somatic/Mutect.py
+++ b/src/python/Somatic/Mutect.py
@@ -148,7 +148,7 @@ def extractMutectSNVFeatures(vcfname, tag, avg_depth=None):
                 n_allele_alt_count = 0
             else:
                 n_allele_alt_count = 0
-                for a in xrange(0, len(alleles_alt)):
+                for a in range(0, len(alleles_alt)):
                     n_allele_alt_count += float(rec[n_sample + "AD"][a + 1])
 
             if n_allele_alt_count + n_allele_ref_count == 0:
@@ -163,7 +163,7 @@ def extractMutectSNVFeatures(vcfname, tag, avg_depth=None):
                 t_allele_alt_count = 0
             else:
                 t_allele_alt_count = 0
-                for a in xrange(0, len(alleles_alt)):
+                for a in range(0, len(alleles_alt)):
                     t_allele_alt_count += float(rec[t_sample + "AD"][a + 1])
 
             if t_allele_alt_count + t_allele_ref_count == 0:
@@ -344,7 +344,7 @@ def extractMutectIndelFeatures(vcfname, tag, avg_depth=None):
                 n_allele_alt_count = 0
             else:
                 n_allele_alt_count = 0
-                for a in xrange(0, len(alleles_alt)):
+                for a in range(0, len(alleles_alt)):
                     n_allele_alt_count += float(rec[n_sample + "AD"][a + 1])
 
             if n_allele_alt_count + n_allele_ref_count == 0:
@@ -359,7 +359,7 @@ def extractMutectIndelFeatures(vcfname, tag, avg_depth=None):
                 t_allele_alt_count = 0
             else:
                 t_allele_alt_count = 0
-                for a in xrange(0, len(alleles_alt)):
+                for a in range(0, len(alleles_alt)):
                     t_allele_alt_count += float(rec[t_sample + "AD"][a + 1])
 
             if t_allele_alt_count + t_allele_ref_count == 0:
diff --git a/src/python/Tools/bcftools.py b/src/python/Tools/bcftools.py
index 6146b7a..6d80d14 100755
--- a/src/python/Tools/bcftools.py
+++ b/src/python/Tools/bcftools.py
@@ -128,8 +128,8 @@ def concatenateParts(output, *args):
             to_delete.append(tf2.name)
             to_delete.append(tf1.name + ".csi")
             to_delete.append(tf2.name + ".csi")
-            half1 = [tf1.name] + list(args[:len(args)/2])
-            half2 = [tf2.name] + list(args[len(args)/2:])
+            half1 = [tf1.name] + list(args[:len(args)//2])
+            half2 = [tf2.name] + list(args[len(args)//2:])
             concatenateParts(*half1)
             runBcftools("index", tf1.name)
             concatenateParts(*half2)
diff --git a/src/python/Tools/metric.py b/src/python/Tools/metric.py
index 71ccc99..372626d 100755
--- a/src/python/Tools/metric.py
+++ b/src/python/Tools/metric.py
@@ -115,7 +115,7 @@ def replaceNaNs(xobject):
             if type(xobject[k]) is dict or type(xobject[k]) is list or type(xobject[k]) is float:
                 xobject[k] = replaceNaNs(xobject[k])
     elif type(xobject) is list:
-        for k in xrange(0, len(xobject)):
+        for k in range(0, len(xobject)):
             if type(xobject[k]) is dict or type(xobject[k]) is list or type(xobject[k]) is float:
                 xobject[k] = replaceNaNs(xobject[k])
     elif type(xobject) is float:
diff --git a/src/python/Tools/parallel.py b/src/python/Tools/parallel.py
index 9d49760..5fcb37e 100755
--- a/src/python/Tools/parallel.py
+++ b/src/python/Tools/parallel.py
@@ -17,9 +17,9 @@ import logging
 import traceback
 import subprocess
 import multiprocessing
-import cPickle
+import pickle
 import tempfile
-from itertools import islice, izip, repeat
+from itertools import islice, repeat
 
 from . import LoggingWriter
 
@@ -93,7 +93,7 @@ def runParallel(pool, fun, par, *args, **kwargs):
 
     """
     if pool:
-        result = pool.map(parMapper, izip(par, repeat( { "fun": fun, "args": args, "kwargs": kwargs } )))
+        result = pool.map(parMapper, zip(par, repeat( { "fun": fun, "args": args, "kwargs": kwargs } )))
     else:
         result = []
         for c in par:
diff --git a/src/python/Tools/sessioninfo.py b/src/python/Tools/sessioninfo.py
index 75650ec..b49bf59 100644
--- a/src/python/Tools/sessioninfo.py
+++ b/src/python/Tools/sessioninfo.py
@@ -34,7 +34,6 @@ def sessionInfo():
               'version': version,
               'runInfo': [{"key": "commandline", "value": " ".join(sys.argv)}],
               'uname': " / ".join(platform.uname()),
-              'dist': " / ".join(platform.dist()),
               'mac_ver': " / ".join([platform.mac_ver()[0], platform.mac_ver()[2]]),
               'python_implementation': platform.python_implementation(),
               'python_version': platform.python_version(),
diff --git a/src/python/Tools/vcfcallerinfo.py b/src/python/Tools/vcfcallerinfo.py
index eb7e86e..947f2c4 100755
--- a/src/python/Tools/vcfcallerinfo.py
+++ b/src/python/Tools/vcfcallerinfo.py
@@ -33,8 +33,8 @@ class CallerInfo(object):
 
     def asDict(self):
         kvd = ["name", "version", "parameters"]
-        return {"aligners": [dict(y for y in itertools.izip(kvd, x)) for x in self.aligners],
-                "callers": [dict(y for y in itertools.izip(kvd, x)) for x in self.callers]}
+        return {"aligners": [dict(y for y in zip(kvd, x)) for x in self.aligners],
+                "callers": [dict(y for y in zip(kvd, x)) for x in self.callers]}
 
     def addVCF(self, vcfname):
         """ Add caller versions from a VCF
diff --git a/src/python/hap.py b/src/python/hap.py
index 8045936..93279a4 100755
--- a/src/python/hap.py
+++ b/src/python/hap.py
@@ -188,7 +188,7 @@ def main():
         parser.print_help()
         exit(1)
 
-    print "Hap.py %s" % Tools.version        
+    print("Hap.py %s" % Tools.version)
     if args.version:
         exit(0)
 
diff --git a/src/python/ovc.py b/src/python/ovc.py
index 2837255..20b4442 100755
--- a/src/python/ovc.py
+++ b/src/python/ovc.py
@@ -34,7 +34,7 @@ lines = 1
 for line in f:
 	l = line.split("\t")
 	if len(l) > 3 and (last-1) > int(l[1]):
-		print "Overlap at %s:%i (line %i)" % (l[0], int(l[1]), lines)
+		print(Overlap at %s:%i (line %i)) % (l[0], int(l[1]), lines)
 		exit(1)
 	elif len(l) > 3:
 		last = int(l[2])
diff --git a/src/python/pre.py b/src/python/pre.py
index 5ca1644..a37a4b2 100755
--- a/src/python/pre.py
+++ b/src/python/pre.py
@@ -47,8 +47,8 @@ import Haplo.partialcredit
 def hasChrPrefix(chrlist):
     """ returns if list of chr names has a chr prefix or not """
 
-    noprefix = map(str, range(23)) + ["X", "Y", "MT"]
-    withprefix = ["chr" + x for x in map(str, range(23)) + ["X", "Y", "M"]]
+    noprefix = [str(x) for x in range(23)] + ["X", "Y", "MT"]
+    withprefix = ["chr" + str(x) for x in range(23)] + ["X", "Y", "M"]
 
     count_noprefix = len(list(set(noprefix) & set(chrlist)))
     count_prefix = len(list(set(withprefix) & set(chrlist)))
@@ -126,7 +126,7 @@ def preprocess(vcf_input,
 
         if gender == "auto":
             logging.info(mf)
-            if "female" in mf:
+            if b"female" in mf:
                 gender = "female"
             else:
                 gender = "male"
@@ -392,7 +392,7 @@ def main():
         exit(0)
 
     if args.version:
-        print "pre.py %s" % Tools.version  # noqa:E999
+        print(pre.py %s) % Tools.version  # noqa:E999
         exit(0)
 
     args.input = args.input[0]
diff --git a/src/python/qfy.py b/src/python/qfy.py
index 4f247ee..59ed68a 100755
--- a/src/python/qfy.py
+++ b/src/python/qfy.py
@@ -203,8 +203,8 @@ def quantify(args):
 
     # in default mode, print result summary to stdout
     if not args.quiet and not args.verbose:
-        print "Benchmarking Summary:"
-        print essential_numbers.to_string(index=False)
+        print("Benchmarking Summary:")
+        print(essential_numbers.to_string(index=False))
 
     # keep this for verbose output
     if not args.verbose:
@@ -213,12 +213,12 @@ def quantify(args):
         except:
             pass
 
-    for t in res.iterkeys():
+    for t in res.keys():
         metrics_output["metrics"].append(dataframeToMetricsTable("roc." + t, res[t]))
 
     # gzip JSON output
     if args.write_json:
         with gzip.open(args.reports_prefix + ".metrics.json.gz", "w") as fp:
-            json.dump(metrics_output, fp)
+            fp.write(json.dumps(metrics_output, default=np_encoder).encode('ascii'))
 
 
@@ -362,7 +363,7 @@ def main():
         exit(0)
 
     if args.version:
-        print "qfy.py %s" % Tools.version
+        print(qfy.py %s) % Tools.version
         exit(0)
 
     if args.fp_bedfile and args.preprocessing_truth_confregions:
diff --git a/src/python/som.py b/src/python/som.py
index e942351..c01d522 100755
--- a/src/python/som.py
+++ b/src/python/som.py
@@ -640,7 +640,7 @@ def main():
                              "overlap):\n" + ambie.to_string(index=False))
                 # in default mode, print result summary to stdout
                 if not args.quiet and not args.verbose:
-                    print "FP/ambiguity classes with info (multiple classes can " \
+                    print(FP/ambiguity classes with info (multiple classes can ) \
                           "overlap):\n" + ambie.to_string(index=False)
                 ambie.to_csv(args.output + ".ambiclasses.csv")
                 metrics_output["metrics"].append(dataframeToMetricsTable("ambiclasses", ambie))
@@ -659,7 +659,7 @@ def main():
                     formatters={'reason': '{{:<{}s}}'.format(ambie['reason'].str.len().max()).format}, index=False))
                 # in default mode, print result summary to stdout
                 if not args.quiet and not args.verbose:
-                    print "Reasons for defining as ambiguous (multiple reasons can overlap):\n" + ambie.to_string(
+                    print(Reasons for defining as ambiguous (multiple reasons can overlap):\n) + ambie.to_string(
                         formatters={'reason': '{{:<{}s}}'.format(ambie['reason'].str.len().max()).format}, index=False)
                 ambie.to_csv(args.output + ".ambireasons.csv")
                 metrics_output["metrics"].append(dataframeToMetricsTable("ambireasons", ambie))
@@ -936,7 +936,7 @@ def main():
         logging.info("\n" + res.to_string())
         # in default mode, print result summary to stdout
         if not args.quiet and not args.verbose:
-            print "\n" + res.to_string()
+            print(\n) + res.to_string()
 
         res["sompyversion"] = vstring
 
diff --git a/src/python/qfy.py b/src/python/qfy.py
index 59ed68a..be8d7e1 100755
--- a/src/python/qfy.py
+++ b/src/python/qfy.py
@@ -33,6 +33,7 @@ import pandas
 import json
 import tempfile
 import gzip
+import numpy as np
 
 scriptDir = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
 sys.path.append(os.path.abspath(os.path.join(scriptDir, '..', 'lib', 'python27')))
@@ -45,6 +46,10 @@ import Haplo.happyroc
 import Haplo.gvcf2bed
 from Tools import fastasize
 
+# Cannot convert data to json without a custom enconder
+def np_encoder(object):
+    if isinstance(object, np.generic):
+        return object.item()
 
 def quantify(args):
     """ Run quantify and write tables """