From 2626cc59fd0c6f23a16c36479d4202416a4894f1 Mon Sep 17 00:00:00 2001
From: EricWilliam Buehler <buehlere@selene.cbio.private>
Date: Tue, 22 Nov 2022 16:18:02 -0500
Subject: [PATCH 1/2] update version for pysam and change to pyvcf3

---
 requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index d250250..8c58cc5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,8 +2,8 @@ networkx
 numpy
 pandas
 plotly
-pysam==0.16.0.1
-PyVCF==0.6.8
+pysam
+pyvcf3
 python-dateutil
 pytz
 retrying

From 54936b6ad13eea3de0b8f659d926cdb1f10c9368 Mon Sep 17 00:00:00 2001
From: EricWilliam Buehler <buehlere@selene.cbio.private>
Date: Tue, 22 Nov 2022 16:23:13 -0500
Subject: [PATCH 2/2] change delimitor in cluster column, causing issues in ch
 qc

---
 biometrics/cluster.py               |   2 +-
 tests/test_data/test_sample1.pickle | Bin 0 -> 1436 bytes
 tests/test_data/test_sample2.pickle | Bin 0 -> 1436 bytes
 3 files changed, 1 insertion(+), 1 deletion(-)
 create mode 100644 tests/test_data/test_sample1.pickle
 create mode 100644 tests/test_data/test_sample2.pickle

diff --git a/biometrics/cluster.py b/biometrics/cluster.py
index 9d7f0e3..8dae9db 100644
--- a/biometrics/cluster.py
+++ b/biometrics/cluster.py
@@ -44,7 +44,7 @@ def cluster(self, comparisons):
             max_occurence = occurences.most_common()
             max_occurence_val = max_occurence[0][1]
             most_common_group = list(filter(lambda x: x[1] == max_occurence_val, max_occurence))
-            most_common_group = ','.join([i[0] for i in most_common_group])
+            most_common_group = ':'.join([i[0] for i in most_common_group])
 
             for i, sample in enumerate(samples_in_group):
 
diff --git a/tests/test_data/test_sample1.pickle b/tests/test_data/test_sample1.pickle
new file mode 100644
index 0000000000000000000000000000000000000000..adc374fbbd065165714ba773a71accbdf62781e7
GIT binary patch
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diff --git a/tests/test_data/test_sample2.pickle b/tests/test_data/test_sample2.pickle
new file mode 100644
index 0000000000000000000000000000000000000000..0ecb7c698ab871bbebca47e1aa034b266e31c0d3
GIT binary patch
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