From fdd876ec92b273e85d3223fadfa0dc5209db870b Mon Sep 17 00:00:00 2001 From: David Newman Date: Tue, 5 Dec 2023 17:16:40 +0000 Subject: [PATCH] V43 models --- CHANGELOG.md | 5 +++++ medaka/__init__.py | 2 +- .../r1041_e82_400bps_hac_v4.3.0_model.tar.gz | 3 +++ ...1_e82_400bps_hac_variant_v4.3.0_model.tar.gz | 3 +++ .../r1041_e82_400bps_sup_v4.3.0_model.tar.gz | 3 +++ ...1_e82_400bps_sup_variant_v4.3.0_model.tar.gz | 3 +++ medaka/options.py | 17 +++++++++++------ 7 files changed, 29 insertions(+), 7 deletions(-) create mode 100755 medaka/data/r1041_e82_400bps_hac_v4.3.0_model.tar.gz create mode 100755 medaka/data/r1041_e82_400bps_hac_variant_v4.3.0_model.tar.gz create mode 100755 medaka/data/r1041_e82_400bps_sup_v4.3.0_model.tar.gz create mode 100755 medaka/data/r1041_e82_400bps_sup_variant_v4.3.0_model.tar.gz diff --git a/CHANGELOG.md b/CHANGELOG.md index 226eae9..9c5048a 100755 --- 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 index 5fc7cae..8e4460a 100755 --- 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 new file mode 100755 index 0000000..8008887 --- /dev/null +++ b/medaka/data/r1041_e82_400bps_hac_v4.3.0_model.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e4bcf64b998236ec5faaf543843287c62181fe6247f1bc4e5d386dcafbd726e1 +size 3316419 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 new file mode 100755 index 0000000..e417911 --- /dev/null +++ b/medaka/data/r1041_e82_400bps_hac_variant_v4.3.0_model.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:548de1695c7aaa30236a5f0a429065e8a6bb26e08057266beee369c9cac7967c +size 3334828 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 new file mode 100755 index 0000000..0900534 --- /dev/null +++ b/medaka/data/r1041_e82_400bps_sup_v4.3.0_model.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:17f852af3af41fb1a37fca64b1493a80e2a45be88224ec7d0a0b2303aeb0d1e9 +size 3331823 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 new file mode 100755 index 0000000..2036bb3 --- /dev/null +++ b/medaka/data/r1041_e82_400bps_sup_variant_v4.3.0_model.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4f90db21d85b65f7cd340cc56ea9572a43bf4f13ee136ca1f5a00ca38fc41f27 +size 3338143 diff --git a/medaka/options.py b/medaka/options.py index 6a37d6f..a1e1cff 100755 --- 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'), 'dna_r10.4.1_e8.2_400bps_hac@v4.2.0': ('r1041_e82_400bps_hac_v4.2.0', 'r1041_e82_400bps_hac_variant_v4.2.0'), + 'dna_r10.4.1_e8.2_400bps_hac@v4.3.0': + ('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'), 'dna_r10.4.1_e8.2_400bps_sup@v3.5.2': @@ -66,6 +68,8 @@ ('r1041_e82_400bps_sup_v4.1.0', 'r1041_e82_400bps_sup_variant_v4.1.0'), 'dna_r10.4.1_e8.2_400bps_sup@v4.2.0': ('r1041_e82_400bps_sup_v4.2.0', 'r1041_e82_400bps_sup_variant_v4.2.0'), + 'dna_r10.4.1_e8.2_400bps_sup@v4.3.0': + ('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',