From 7fa1eb1eef9af94089ca1e7f2ea177d9acc0c12e Mon Sep 17 00:00:00 2001
From: Nick Croucher <n.croucher@imperial.ac.uk>
Date: Sat, 20 Apr 2024 09:57:10 +0100
Subject: [PATCH] Update ordering of file with new function implementation

---
 ...ecombinations.tre.branch_snps.expected.tab | 286 +++++++++---------
 ...ecombinations.tre.branch_snps.expected.tab |  12 +-
 2 files changed, 149 insertions(+), 149 deletions(-)

diff --git a/tests/data/multiple_recombinations.tre.branch_snps.expected.tab b/tests/data/multiple_recombinations.tre.branch_snps.expected.tab
index 26f61f5e..eb4e3b9e 100644
--- a/tests/data/multiple_recombinations.tre.branch_snps.expected.tab
+++ b/tests/data/multiple_recombinations.tre.branch_snps.expected.tab
@@ -1,3 +1,15 @@
+FT   variation       35
+FT                   /node="Node_5->sequence_2"
+FT                   /colour="4"
+FT                   /taxa="sequence_2"
+FT                   /parent_base="T"
+FT                   /replace="A"
+FT   variation       41
+FT                   /node="Node_5->sequence_4"
+FT                   /colour="4"
+FT                   /taxa="sequence_4"
+FT                   /parent_base="A"
+FT                   /replace="G"
 FT   variation       28
 FT                   /node="Node_2->sequence_9"
 FT                   /colour="4"
@@ -136,394 +148,382 @@ FT                   /colour="4"
 FT                   /taxa="  sequence_7 sequence_8 sequence_9"
 FT                   /parent_base="A"
 FT                   /replace="G"
-FT   variation       28
-FT                   /node="Node_4->Node_3"
+FT   variation       22
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="   sequence_7 sequence_8 sequence_9 sequence_6"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
+FT   variation       35
+FT                   /node="Node_7->Node_6"
+FT                   /colour="4"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /parent_base="A"
+FT                   /replace="T"
 FT   variation       51
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       53
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       54
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       55
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       56
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       57
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       58
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       59
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       60
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       61
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       62
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       63
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       64
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       65
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       66
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       67
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       69
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       70
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       71
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       73
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       74
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       75
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       76
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       77
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       78
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       79
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       80
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       81
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       82
-FT                   /node="Node_4->sequence_5"
+FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
-FT                   /taxa="sequence_5"
+FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       84
-FT                   /node="Node_4->sequence_5"
-FT                   /colour="4"
-FT                   /taxa="sequence_5"
-FT                   /parent_base="A"
-FT                   /replace="C"
-FT   variation       35
-FT                   /node="Node_5->sequence_2"
-FT                   /colour="4"
-FT                   /taxa="sequence_2"
-FT                   /parent_base="T"
-FT                   /replace="A"
-FT   variation       41
-FT                   /node="Node_5->sequence_4"
-FT                   /colour="4"
-FT                   /taxa="sequence_4"
-FT                   /parent_base="A"
-FT                   /replace="G"
-FT   variation       22
 FT                   /node="Node_7->Node_6"
 FT                   /colour="4"
 FT                   /taxa=" sequence_3  sequence_2 sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="C"
-FT   variation       35
-FT                   /node="Node_7->Node_6"
+FT   variation       28
+FT                   /node="Node_4->Node_3"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="   sequence_7 sequence_8 sequence_9 sequence_6"
 FT                   /parent_base="A"
-FT                   /replace="T"
+FT                   /replace="C"
 FT   variation       51
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       53
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       54
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       55
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       56
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       57
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       58
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       59
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       60
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       61
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       62
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       63
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       64
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       65
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       66
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       67
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       69
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       70
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       71
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       73
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       74
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       75
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       76
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       77
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       78
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       79
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       80
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       81
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       82
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       84
-FT                   /node="Node_7->Node_6"
+FT                   /node="Node_4->sequence_5"
 FT                   /colour="4"
-FT                   /taxa=" sequence_3  sequence_2 sequence_4"
+FT                   /taxa="sequence_5"
 FT                   /parent_base="A"
 FT                   /replace="C"
 FT   variation       16
diff --git a/tests/data/no_recombinations.tre.branch_snps.expected.tab b/tests/data/no_recombinations.tre.branch_snps.expected.tab
index 985bc620..8c768cd4 100644
--- a/tests/data/no_recombinations.tre.branch_snps.expected.tab
+++ b/tests/data/no_recombinations.tre.branch_snps.expected.tab
@@ -1,15 +1,15 @@
-FT   variation       23
-FT                   /node="N2->sequence_6"
-FT                   /colour="4"
-FT                   /taxa="sequence_6"
-FT                   /parent_base="G"
-FT                   /replace="A"
 FT   variation       40
 FT                   /node="N6->sequence_4"
 FT                   /colour="4"
 FT                   /taxa="sequence_4"
 FT                   /parent_base="A"
 FT                   /replace="G"
+FT   variation       23
+FT                   /node="N2->sequence_6"
+FT                   /colour="4"
+FT                   /taxa="sequence_6"
+FT                   /parent_base="G"
+FT                   /replace="A"
 FT   variation       34
 FT                   /node="N5->sequence_2"
 FT                   /colour="4"