Update version

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.

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
 -----------

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":[