From d381f56b34de95775027ca27b8d855f494e73ff2 Mon Sep 17 00:00:00 2001
From: Michael Wykes <michael.wykes@nanoporetech.com>
Date: Fri, 1 May 2020 17:12:59 +0100
Subject: [PATCH 1/4] bump version and update changelog

---
 CHANGELOG.md       | 10 ++++++++++
 medaka/__init__.py |  2 +-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8ee7f005..b0d8d2d0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,13 @@
+v1.0.0
+-------
+Models, features and fixes release
+
+* Consensus models for Guppy 3.6.0.
+* Fast consensus models for Guppy 3.4.4.
+* Fix to methylation aggregation.
+* VCF annotation tool.
+
+
 v0.12.1
 -------
 Minor release harmonising versions of htslib/samtools dependencies.
diff --git a/medaka/__init__.py b/medaka/__init__.py
index 00e8f3f1..7b2b1f1e 100644
--- a/medaka/__init__.py
+++ b/medaka/__init__.py
@@ -4,7 +4,7 @@
 import os
 import subprocess
 
-__version__ = 'v0.12.2-rc.1'
+__version__ = '1.0.0'
 
 
 def check_minimap2_version():

From 2c8261d9720e135d8987f7a0ee53b65165a74d55 Mon Sep 17 00:00:00 2001
From: Michael Wykes <michael.wykes@nanoporetech.com>
Date: Mon, 4 May 2020 17:39:33 +0100
Subject: [PATCH 2/4] remove guppy 3.4.4 fast models

---
 medaka/data/r941_min_fast_g344_model.hdf5  | 3 ---
 medaka/data/r941_prom_fast_g344_model.hdf5 | 3 ---
 medaka/options.py                          | 6 ++----
 3 files changed, 2 insertions(+), 10 deletions(-)
 delete mode 100644 medaka/data/r941_min_fast_g344_model.hdf5
 delete mode 100644 medaka/data/r941_prom_fast_g344_model.hdf5

diff --git a/medaka/data/r941_min_fast_g344_model.hdf5 b/medaka/data/r941_min_fast_g344_model.hdf5
deleted file mode 100644
index afe1c112..00000000
--- a/medaka/data/r941_min_fast_g344_model.hdf5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:ff96ecee28bd1cb97f9b85694d494d16460f36295c7e94d4d9f5ef47db836ba9
-size 3299554
diff --git a/medaka/data/r941_prom_fast_g344_model.hdf5 b/medaka/data/r941_prom_fast_g344_model.hdf5
deleted file mode 100644
index bd8b1900..00000000
--- a/medaka/data/r941_prom_fast_g344_model.hdf5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:136813ba5a8d0d40a1ed06e13c372d037c6c2253c40d3c3b47c1bfae3aba3bab
-size 3299554
diff --git a/medaka/options.py b/medaka/options.py
index 870ce7fd..99667b38 100644
--- a/medaka/options.py
+++ b/medaka/options.py
@@ -30,10 +30,8 @@
     'r103_prom_snp_g3210', 'r103_prom_variant_g3210']
 archived_models = [
     # r9 consensus
-    'r941_min_fast_g303', 'r941_min_fast_g344',
-    'r941_min_high_g303', 'r941_min_high_g330',
-    'r941_prom_fast_g303', 'r941_prom_fast_g344',
-    'r941_prom_high_g303', 'r941_prom_high_g330',
+    'r941_min_fast_g303', 'r941_min_high_g303', 'r941_min_high_g330',
+    'r941_prom_fast_g303', 'r941_prom_high_g303', 'r941_prom_high_g330',
     # r10 consensus
     'r10_min_high_g303', 'r10_min_high_g340',
     # snp and variant

From c421234b0febe1d713068c49768d1fbb7f8064de Mon Sep 17 00:00:00 2001
From: Michael Wykes <michael.wykes@nanoporetech.com>
Date: Mon, 4 May 2020 18:26:32 +0100
Subject: [PATCH 3/4] Apply suggestion to CHANGELOG.md

---
 CHANGELOG.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0d8d2d0..7229c54b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,6 @@ v1.0.0
 Models, features and fixes release
 
 * Consensus models for Guppy 3.6.0.
-* Fast consensus models for Guppy 3.4.4.
 * Fix to methylation aggregation.
 * VCF annotation tool.
 

From 8264996601367aab6b0af7795d108026147bca03 Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Mon, 4 May 2020 18:28:59 +0100
Subject: [PATCH 4/4] Apply suggestion to CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7229c54b..51bde392 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@ v1.0.0
 Models, features and fixes release
 
 * Consensus models for Guppy 3.6.0.
+* Add functionality for auto-download of older models.
 * Fix to methylation aggregation.
 * VCF annotation tool.