Upgrade to version 4.0.7

Author: susannasiebert

docs/conf.py

@@ -70,7 +70,7 @@
 # The short X.Y version.
 version = '4.0'
 # The full version, including alpha/beta/rc tags.
-release = '4.0.6'
+release = '4.0.7'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/index.rst

@@ -56,9 +56,32 @@ New in Release |release|
 
 This is a bugfix release. It fixes the following problem(s):
 
-- A bug in the aggregate report creation incorrectly evaluated the Transcript
-  Support Level and resulted in picking the wrong Best Transcript in some
-  cases.
+- The multithreading capabilities in pVACtools are not available for Mac OSX.
+  Attempting to use the -t parameter would result in the forked processes
+  crashing but the run would still complete successfully leading to results
+  with incomplete data. This release will result in an error when multithreading is
+  used under Mac OSX.
+- We've observed issues with IEDB's API sometimes returning incorrect or
+  incomplete data. This results in downstream errors. This release updates the prediction
+  calling to log such occurrences and to retry the API when they are observed.
+- MHCflurry sometimes returns no binding affinity percentile data. This
+  resulted in errors when parsing such prediction data. This release fixes our
+  parsing logic to handle this case.
+- TSL parsing of the input VCF in pVACseq used to be limited to human data
+  only. This release adds support for TSL parsing in mouse data.
+- When running with the --noncanonical flag, the exons.csv file will contain
+  exon postions for all possible transcript combinations. However, the transcripts
+  weren't being taken into account when parsing this file to determine the fusion
+  positions. This release fixes this issue by looking up the positions for the
+  specific transcripts of the record currently being parsed.
+- When using BLASTp for the reference proteome match step, we applied the word-size
+  parameter in order to only return perfect matches. However, for short sequences,
+  word-size must be less than half the query length, or reliable hits can be missed.
+  This release updates how the word-size parameter is calculated in order to
+  meet this criteria.
+- This release addresses in error in pVACview that would occur in the
+  Transcripts in Set window when there are
+  no peptides passing the aggregate inclusion binding threshold.
 
 New in Version |version|
 ------------------------

docs/releases/4_0.rst

@@ -133,11 +133,43 @@ This is a bugfix release. It fixes the following problem(s):
   resulting in the observed behavior. This release reverts the change from PR
   988.
 
-This is a bugfix release. It fixes the following problem(s):
-
 Version 4.0.6
 -------------
 
+This is a bugfix release. It fixes the following problem(s):
+
 - A bug in the aggregate report creation incorrectly evaluated the Transcript
   Support Level and resulted in picking the wrong Best Transcript in some
   cases.
+
+Version 4.0.7
+-------------
+
+This is a bugfix release. It fixes the following problem(s):
+
+- The multithreading capabilities in pVACtools are not available for Mac OSX.
+  Attempting to use the -t parameter would result in the forked processes
+  crashing but the run would still complete successfully leading to results
+  with incomplete data. This release will result in an error when multithreading is
+  used under Mac OSX.
+- We've observed issues with IEDB's API sometimes returning incorrect or
+  incomplete data. This results in downstream errors. This release updates the prediction
+  calling to log such occurrences and to retry the API when they are observed.
+- MHCflurry sometimes returns no binding affinity percentile data. This
+  resulted in errors when parsing such prediction data. This release fixes our
+  parsing logic to handle this case.
+- TSL parsing of the input VCF in pVACseq used to be limited to human data
+  only. This release adds support for TSL parsing in mouse data.
+- When running with the --noncanonical flag, the exons.csv file will contain
+  exon postions for all possible transcript combinations. However, the transcripts
+  weren't being taken into account when parsing this file to determine the fusion
+  positions. This release fixes this issue by looking up the positions for the
+  specific transcripts of the record currently being parsed.
+- When using BLASTp for the reference proteome match step, we applied the word-size
+  parameter in order to only return perfect matches. However, for short sequences,
+  word-size must be less than half the query length, or reliable hits can be missed.
+  This release updates how the word-size parameter is calculated in order to
+  meet this criteria.
+- This release addresses in error in pVACview that would occur in the
+  Transcripts in Set window when there are
+  no peptides passing the aggregate inclusion binding threshold.

setup.py

@@ -51,7 +51,7 @@
 
 setup(
     name="pvactools",
-    version="4.0.6",
+    version="4.0.7",
     packages=[
         "pvactools.tools",
         "pvactools.tools.pvacbind",