From 533a2ac19d3643f1dadb3f5051e143921ff5be15 Mon Sep 17 00:00:00 2001 From: Jonathan Margoliash Date: Mon, 20 Mar 2023 12:22:21 -0700 Subject: [PATCH] Bump version number --- PUBLISHING.rst | 2 +- RELEASE_NOTES.rst | 8 ++++++++ setup.py | 2 +- trtools/mergeSTR/README.rst | 2 +- trtools/version.py | 2 +- 5 files changed, 12 insertions(+), 4 deletions(-) diff --git a/PUBLISHING.rst b/PUBLISHING.rst index 85a45384..a27ae5ed 100644 --- a/PUBLISHING.rst +++ b/PUBLISHING.rst @@ -42,7 +42,7 @@ Once changes have been made to develop that are ready to be published, first cho Then go through the steps of merging the changes into the master branch: -#. Run pytest and make sure all the tests pass. Then run :code:`./test/cmdline_tests.sh` and make sure those tests pass. +#. Run :code:`pytest` and make sure all the tests pass. Then run :code:`./test/cmdline_tests.sh` and make sure those tests pass. #. Change the 'Unreleased Changes' section of :code:`RELEASE_NOTES.rst` to the new version number. #. Check if any changes have been made that have not yet been documented in the release notes. If so, document them. #. Update the version number in setup.py diff --git a/RELEASE_NOTES.rst b/RELEASE_NOTES.rst index 16e993f6..619e9179 100644 --- a/RELEASE_NOTES.rst +++ b/RELEASE_NOTES.rst @@ -1,3 +1,11 @@ +5.0.2 +----- + +Bug fixes: + +* MergeSTR now will no longer sometimes emit an alternate allele identical to the ref allele when + dealing with flanking base pairs. + 5.0.1 ----- diff --git a/setup.py b/setup.py index 41fb66e3..bfb4deb8 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ curdir = os.path.abspath(os.path.dirname(__file__)) MAJ = 5 MIN = 0 -REV = 1 +REV = 2 VERSION = '%d.%d.%d' % (MAJ, MIN, REV) with open(os.path.join(curdir, 'trtools/version.py'), 'w') as fout: fout.write( diff --git a/trtools/mergeSTR/README.rst b/trtools/mergeSTR/README.rst index 045fa91c..3ffc0883 100644 --- a/trtools/mergeSTR/README.rst +++ b/trtools/mergeSTR/README.rst @@ -9,7 +9,7 @@ MergeSTR If TR genotyping was performed separately on different samples or batches of samples, mergeSTR can be used to combine the resulting VCFs into one file. This is often necessary for downstream steps such as: computing per-locus statistics, performing per-locus filtering, and association testing. -While other VCF libraries have capabilities to merge VCF files, they do not always handle multi-allelic TRs properly, especially if the allele definitions are different across files. MergeSTR is TR-aware and currently handles VCF files obtained by: GangSTR, HipSTR, ExpansionHunter, popSTR, or adVNTR. See below for specific VCF fields supported for each genotyper. +While other VCF libraries have capabilities to merge VCF files, they do not always handle multi-allelic TRs properly, especially if the allele definitions are different across files. MergeSTR is TR-aware. See below for specific VCF fields supported for each genotyper. mergeSTR does not support merging VCFs produced by different TR genotypers - that is a more complex usecase, and we are designing a separate tool to do that. diff --git a/trtools/version.py b/trtools/version.py index adac3ff1..e4741ae5 100644 --- a/trtools/version.py +++ b/trtools/version.py @@ -1,4 +1,4 @@ # THIS FILE IS GENERATED FROM SETUP.PY -version = '5.0.1' +version = '5.0.2' __version__ = version \ No newline at end of file