From e2877c22933d3d3f8c50a6576c110dd71f2ad435 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 29 Mar 2018 09:26:32 -0500 Subject: [PATCH] Update version --- docs/conf.py | 2 +- docs/index.rst | 30 +++++++++++------------------- setup.py | 2 +- 3 files changed, 13 insertions(+), 21 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 28eaeeedb..ce0c88c94 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -69,7 +69,7 @@ # The short X.Y version. version = '1.0' # The full version, including alpha/beta/rc tags. -release = '1.0.2' +release = '1.0.3' # 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 4aaa88e2a..69d186276 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -38,25 +38,17 @@ New in version |release| This is a hotfix release. It fixes the following issues: -- The epitope length used for generating the peptide fasta when running with - multiple epitope lengths was incorrect. This would potentially result in including - fasta sequences that were shorter than the largest epitope length which - would cause an error during calls to IEDB. -- pVACseq would fail with a nondescript error message if the input VCF was not - annotated with VEP before running. A more descriptive error message has been - added. -- IEDB changed the format of class II IEDB alleles which would cause an error - when running with those alleles. pVACtools will now handle transposing the - affected alleles into the new format. -- The standalone binding filters had a few bugs that would result in syntax - errors during runtime. -- The indexes created for each fusion entry with pVACfuse had the potential to - not be unique which would result in parsing errors downstream. -- pVACseq had the potential to use the incorrect VEP allele for positions with - multiple alternate alleles which would result in the incorrect CSQ entry - getting used for some of those alternate alleles. -- pVACseq would throw an error if the chosen peptide sequence length exceeds - the wildtype protein sequence length of a transcript. +- Stop-gain mutation were previously not handled correctly. If a mutation had + a \* (stop gain) in the VEP Amino_acids field, pVACseq would throw an error. + We now ensure that those cases are handled. pVACseq will also skip stop-gain + mutations if the resulting mutant peptide sequence is not novel. +- pVACseq would previously throw an error if multiple mutations resulted + in the same consequence. This is now handled by assigning a unique + identifier to each mutation. +- We added a better warning messages if the chosen prediction algorithms and + alleles MHC classes are mutually exclusive, e.g., if only class I prediction + algorithms were chosen with only class II alleles. Previously, pVACseq would + simply finish without producing any output or errors. Coming soon ----------- diff --git a/setup.py b/setup.py index c54e825db..2ca8e0f85 100644 --- a/setup.py +++ b/setup.py @@ -45,7 +45,7 @@ setup( name="pvactools", - version="1.0.2", + version="1.0.3", packages=["tools", "tools.pvacfuse", "tools.pvacvector", "tools.pvacseq", "lib", "utils.pvacapi", "utils.pvacapi.controllers"], entry_points={ "console_scripts":[