Merge branch 'v43_models' into 'dev'

V43 models See merge request research/medaka!571
nanoporetech · Dec 5, 2023 · 9dffdee · 9dffdee
2 parents 159ada1 + fdd876e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.11.3]
+### Added
+- Consensus and variant models for v4.3.0 dorado models.
+
+
 ## [v1.11.2]
 ### Added
 - Parsing model information from fastq headers output by Guppy and MinKNOW.

diff --git a/medaka/__init__.py b/medaka/__init__.py
@@ -5,7 +5,7 @@
 import subprocess
 import sys
 
-__version__ = "1.11.2"
+__version__ = "1.11.3"
 
 try:
     import pyabpoa as abpoa

diff --git a/medaka/data/r1041_e82_400bps_hac_v4.3.0_model.tar.gz b/medaka/data/r1041_e82_400bps_hac_v4.3.0_model.tar.gz
diff --git a/medaka/data/r1041_e82_400bps_hac_variant_v4.3.0_model.tar.gz b/medaka/data/r1041_e82_400bps_hac_variant_v4.3.0_model.tar.gz
diff --git a/medaka/data/r1041_e82_400bps_sup_v4.3.0_model.tar.gz b/medaka/data/r1041_e82_400bps_sup_v4.3.0_model.tar.gz
diff --git a/medaka/data/r1041_e82_400bps_sup_variant_v4.3.0_model.tar.gz b/medaka/data/r1041_e82_400bps_sup_variant_v4.3.0_model.tar.gz
diff --git a/medaka/options.py b/medaka/options.py
@@ -9,18 +9,18 @@
 
 # the models used by default for CLI entry points
 default_models = {
-    'consensus': 'r1041_e82_400bps_sup_v4.2.0',
-    'variant': 'r1041_e82_400bps_sup_variant_v4.2.0'
+    'consensus': 'r1041_e82_400bps_sup_v4.3.0',
+    'variant': 'r1041_e82_400bps_sup_variant_v4.3.0'
 }
 
 # current models are those included in PyPI packages
 current_models = [
     # r1041 e82 (kit14) consensus
-    'r1041_e82_400bps_hac_v4.2.0',
-    'r1041_e82_400bps_sup_v4.2.0',
+    'r1041_e82_400bps_hac_v4.3.0',
+    'r1041_e82_400bps_sup_v4.3.0',
     # r1041 variant calling
-    'r1041_e82_400bps_hac_variant_v4.2.0',
-    'r1041_e82_400bps_sup_variant_v4.2.0',
+    'r1041_e82_400bps_hac_variant_v4.3.0',
+    'r1041_e82_400bps_sup_variant_v4.3.0',
 ]
 
 # mapping from basecaller model names to medaka models.
@@ -56,6 +56,8 @@
         ('r1041_e82_400bps_hac_v4.1.0', 'r1041_e82_400bps_hac_variant_v4.1.0'),
     '[email protected]':
         ('r1041_e82_400bps_hac_v4.2.0', 'r1041_e82_400bps_hac_variant_v4.2.0'),
+    '[email protected]':
+        ('r1041_e82_400bps_hac_v4.3.0', 'r1041_e82_400bps_hac_variant_v4.3.0'),
     'dna_r10.4.1_e8.2_400bps_hac_prom':
         ('r1041_e82_400bps_hac_g632', 'r1041_e82_400bps_hac_variant_g632'),
     '[email protected]':
@@ -66,6 +68,8 @@
         ('r1041_e82_400bps_sup_v4.1.0', 'r1041_e82_400bps_sup_variant_v4.1.0'),
     '[email protected]':
         ('r1041_e82_400bps_sup_v4.2.0', 'r1041_e82_400bps_sup_variant_v4.2.0'),
+    '[email protected]':
+        ('r1041_e82_400bps_sup_v4.3.0', 'r1041_e82_400bps_sup_variant_v4.3.0'),
     # R9.4.1 This is a little dodgy
     # note: 'dna_r9.4.1_450bps_hac' is not present here as there is not a
     #       injective mapping.
@@ -106,6 +110,7 @@
     'r1041_e82_260bps_hac_v4.0.0', 'r1041_e82_260bps_sup_v4.0.0',
     'r1041_e82_260bps_hac_v4.1.0', 'r1041_e82_260bps_sup_v4.1.0',
     'r1041_e82_400bps_hac_v4.1.0', 'r1041_e82_400bps_sup_v4.1.0',
+    'r1041_e82_400bps_hac_v4.2.0', 'r1041_e82_400bps_sup_v4.2.0',
     # r1041 e82 variant calling
     'r1041_e82_400bps_hac_variant_g615',
     'r1041_e82_400bps_fast_variant_g615',