From 9956ae5c989d753eec72a2eda1d905ff135150ea Mon Sep 17 00:00:00 2001
From: Michael Wykes <michael.wykes@nanoporetech.com>
Date: Wed, 6 May 2020 10:35:33 +0100
Subject: [PATCH] restore ability of medaka_variant to show help when run with
 no args

---
 CHANGELOG.md           |  8 ++++++++
 medaka/__init__.py     |  2 +-
 medaka/medaka.py       | 15 +++++++++------
 medaka/models.py       |  1 -
 medaka/options.py      |  2 +-
 scripts/medaka_variant |  8 +++++---
 6 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 51bde392..9be3c0b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,11 @@
+v1.0.1
+-------
+Minor fixes release, resolving issues introduced in v1.0.0.
+
+* Fix default model for SNP calling. 
+* Fix issue causing medaka_consensus to crash. 
+ 
+
 v1.0.0
 -------
 Models, features and fixes release
diff --git a/medaka/__init__.py b/medaka/__init__.py
index 7b2b1f1e..76dff04b 100644
--- a/medaka/__init__.py
+++ b/medaka/__init__.py
@@ -4,7 +4,7 @@
 import os
 import subprocess
 
-__version__ = '1.0.0'
+__version__ = '1.0.1'
 
 
 def check_minimap2_version():
diff --git a/medaka/medaka.py b/medaka/medaka.py
index 611eab5a..1c92f15b 100644
--- a/medaka/medaka.py
+++ b/medaka/medaka.py
@@ -152,8 +152,9 @@ def _log_level():
 def _model_arg():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter, add_help=False)
-    parser.add_argument('--model', action=ResolveModel, default=medaka.options.default_models['consensus'],
-            help='Model definition, default is equivalent to {}.'.format(medaka.options.default_models['consensus']))
+    parser.add_argument('--model', action=ResolveModel,
+            default=medaka.options.default_models['consensus'],
+            help='Model to use.')
     parser.add_argument('--allow_cudnn', dest='allow_cudnn', default=True, action='store_true', help=argparse.SUPPRESS)
     parser.add_argument('--disable_cudnn', dest='allow_cudnn', default=False, action='store_false',
             help='Disable use of cuDNN model layers.')
@@ -200,9 +201,9 @@ def is_rle_encoder(model_name):
 
 def get_alignment_params(args):
     if is_rle_encoder(args.model):
-        align_params = alignment_params['rle']
+        align_params = medaka.options.alignment_params['rle']
     else:
-        align_params = alignment_params['non-rle']
+        align_params = medaka.options.alignment_params['non-rle']
 
     print(align_params)
 
@@ -389,10 +390,9 @@ def main():
     # Consensus from features input
     cfparser = subparsers.add_parser('consensus_from_features',
         help='Run inference from a trained model on existing features.',
-        parents=[_log_level()],
+        parents=[_log_level(), _model_arg()],
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     cfparser.add_argument('features', nargs='+', help='Pregenerated features (from medaka features).')
-    cfparser.add_argument('--model', action=ResolveModel, default=medaka.options.default_models['consensus'], help='Model definition.')
 
     # Compression of fasta/q to quality-RLE fastq
     rleparser = subparsers.add_parser('fastrle',
@@ -637,4 +637,7 @@ def main():
             if RG is not None:
                 msg = "Reads will be filtered to only those with RG tag: {}"
                 logger.info(msg.format(RG))
+        # if model is default, resolve to file, save mess in help text
+        if hasattr(args, 'model'):
+            args.model = medaka.models.resolve_model(args.model)
         args.func(args)
diff --git a/medaka/models.py b/medaka/models.py
index e7bfa15b..4d2b263c 100644
--- a/medaka/models.py
+++ b/medaka/models.py
@@ -64,7 +64,6 @@ def resolve_model(model):
                     pathlib.Path(d).mkdir(parents=True, exist_ok=True)
                     with open(fp, 'wb') as fh:
                         fh.write(data)
-                    print("returning ", fp)
                     return fp
                 except Exception:  # we might not have write access
                     pass
diff --git a/medaka/options.py b/medaka/options.py
index 99667b38..7b27effc 100644
--- a/medaka/options.py
+++ b/medaka/options.py
@@ -39,7 +39,7 @@
 allowed_models = sorted(current_models + archived_models)
 default_models = {
     'consensus': 'r941_min_high_g351',
-    'snp': 'r941_min_high_g351',
+    'snp': 'r941_prom_snp_g322',
     'variant': 'r941_prom_variant_g322'}
 
 alignment_params = {
diff --git a/scripts/medaka_variant b/scripts/medaka_variant
index ee0528b8..57954b86 100755
--- a/scripts/medaka_variant
+++ b/scripts/medaka_variant
@@ -1,7 +1,9 @@
 #!/usr/bin/env bash
 set -eo pipefail
 
-myInvocation="CL=\"$(printf %q "$BASH_SOURCE")$((($#)) && printf ' %q' "$@")\""
+printf -v args ' %q' $@
+src=${BASH_SOURCE}
+INVOCATION=$([ $# -ne 0 ] && echo $src $args || echo $src)
 
 medaka_version=$(medaka --version)
 modeldata=()
@@ -388,8 +390,8 @@ else
         ${REF} ${UNFILTERED}
 
     # Add invocation of this script to VCF header
-    INVOCATION_DATE="##${myInvocation}; $(date)"
-    sed -i "/^#CHROM.*/i $INVOCATION_DATE" ${UNFILTERED} 
+    INVOCATION_DATE="##CL=${INVOCATION}; $(date)"
+    sed -i "/^#CHROM.*/i ${INVOCATION_DATE}" ${UNFILTERED} 
 
     if $FILTER_FLAG; then
         # Filter resulting vcf