From b91e136f91b660ee11268edb4d02f4d111643152 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Fri, 25 Oct 2019 09:18:46 -0500 Subject: [PATCH] Upgrade to version 1.5.3 --- docs/conf.py | 2 +- docs/index.rst | 18 +++++++++++++++--- setup.py | 2 +- 3 files changed, 17 insertions(+), 5 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 67eed9b3c..085169234 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -69,7 +69,7 @@ # The short X.Y version. version = '1.5' # The full version, including alpha/beta/rc tags. -release = '1.5.2' +release = '1.5.3' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/docs/index.rst b/docs/index.rst index d1bbea50c..837f08874 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -52,9 +52,21 @@ New in release |release| This is a hotfix release. It fixes the following issues: -- AGFusion exon files may be comma-delimited. Previously, the file parser - assumed the files were tab-delimited. This release now allows AGFusion - inputs that are comma- or tab-delimited. +- pVACbind would previously throw an error if a peptide sequence in the input + fasta was shorter than one of the chosen epitope lengths. This issue has + been fixed by first parsing the input fasta and creating individual fasta + files for each epitope length that enforce a minimum length of the peptide + sequences matching the respective epitope length. +- Previous versions of pVACtools resolved an issue where IEDB would output a + warning line if one of the epitope sequences only contained A, C, G, or T + amino acids, since those sequences could also be nuclotide sequences. + However, this issue was only fixed in pVACseq, not pVACbind, or pVACvector. + This release fixes this issue for all tools. +- The wrappers for NetChop or NetMHCstabpan split the set of input epitopes + into chunks of 100 before processing. Due to a bug in the file splitting + logic, one epitope for each chunk over 100 would be errenously dropped. This + effectively would result in less epitopes being returned in the filtered + report than if running the pipelines without NetChop or NetMHCstabpan. New in version |version| ------------------------ diff --git a/setup.py b/setup.py index 1f902bec4..83d6757c2 100644 --- a/setup.py +++ b/setup.py @@ -61,7 +61,7 @@ setup( name="pvactools", - version="1.5.2", + version="1.5.3", packages=[ "tools", "tools.pvacbind",