Merge branch 'zerodivide' into 'dev'

Fix a divide-by-zero

See merge request research/medaka!552

.gitlab-ci.yml

@@ -5,10 +5,6 @@ stages:
     - build
     - deploy
 
-variables:
-    DOCKERTAG: "medaka/medaka:latest"
-
-
 # Install a particular Python and set PYTHON envvar for Makefile 
 .install-pyenv: &install-pyenv |
     git clone https://github.com/pyenv/pyenv.git ~/.pyenv
@@ -76,14 +72,6 @@ test-mem-check:
         - make mem_check
 
 
-test-docker:
-    image: ${DOCKERDEV_IMAGE} 
-    stage: test
-    script:
-        - apk --no-cache add make
-        - DOCKERTAG=$DOCKERTAG make docker
-        - docker run --rm -v $PWD:/data $DOCKERTAG medaka_consensus -x -i /data/medaka/test/data/test_reads.fasta.gz -d /data/medaka/test/data/draft_ref.fasta -o /data/dockertest
-
 ###
 # Source distribution
 #
@@ -209,19 +197,3 @@ push-github:
     rules:
         - if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'
 
-push-dockerhub:
-    image: ${DOCKERDEV_IMAGE} 
-    stage: deploy
-    script:
-        - apk --no-cache add make
-        - echo ${DOCKERHUB_TOKEN} | docker login --username ${DOCKERHUB_USER} --password-stdin
-        - DOCKERTAG=$DOCKERTAG make docker
-        - LATEST="ontresearch/medaka:latest"
-        - TAG="ontresearch/medaka:$CI_COMMIT_TAG"
-        - docker tag $DOCKERTAG $LATEST 
-        - docker tag $DOCKERTAG $TAG
-        - docker push ${LATEST}
-        - docker push ${TAG}
-    rules:
-        - if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'
-

CHANGELOG.md

@@ -4,6 +4,10 @@ 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).
 
+## [v1.9.1]
+### Fixed
+- A long-standing bug in pileup_counts that manifests for single-position pileups on ARM64.
+
 ## [v1.9.0]
 ### Added
 - Added `medaka tandem` targeted tandem repeat variant calling.

medaka/__init__.py

@@ -5,7 +5,7 @@
 import subprocess
 import sys
 
-__version__ = "1.9.0"
+__version__ = "1.9.1"
 
 try:
     import parasail

src/medaka_counts.c

@@ -352,7 +352,7 @@ plp_data calculate_pileup(
 
         // reallocate output if necessary
         if (n_cols + max_ins > pileup->buffer_cols) {
-            float cols_per_pos = (float) (n_cols + max_ins) / (pos - start);
+            float cols_per_pos = (float) (n_cols + max_ins) / (1 + pos - start);
             // max_ins can dominate so add at least that
             buffer_cols = max_ins + max(2 * pileup->buffer_cols, (int) cols_per_pos * (end - start));
             enlarge_plp_data(pileup, buffer_cols);