diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a8fe223..d319b22 100644 --- a/.gitlab-ci.yml +++ b/.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:]]+$/' - diff --git a/CHANGELOG.md b/CHANGELOG.md index dc8d5dd..0fb0082 100755 --- a/CHANGELOG.md +++ b/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. diff --git a/medaka/__init__.py b/medaka/__init__.py index c1c5ef9..b8f297b 100755 --- a/medaka/__init__.py +++ b/medaka/__init__.py @@ -5,7 +5,7 @@ import subprocess import sys -__version__ = "1.9.0" +__version__ = "1.9.1" try: import parasail diff --git a/src/medaka_counts.c b/src/medaka_counts.c index a87b5a5..7d63100 100644 --- a/src/medaka_counts.c +++ b/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);