Update to version 1.3.1

docs/conf.py

@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '1.3'
 # The full version, including alpha/beta/rc tags.
-release = '1.3.0'
+release = '1.3.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -45,29 +45,18 @@ tools:
 New in version |version|
 ------------------------
 
-This version adds a few features and updates:
-
-- pVACvector now accepts a list of spacers to use when testing junction
-  epitopes. These can be specified using the ``--spacers`` parameter with a
-  comma-separated list of spacer peptides. Including the string ``None`` will
-  also test each junction without spacers. The default is
-  ``None,HH,HHC,HHH,HHHD,HHHC,AAY,HHHH,HHAA,HHL,AAL``
-- The ``--expn-val`` cutoff parameter has been updated to be a float instead
-  of an integer. This allows the user to provide a decimal
-  cuttoff for the filtering on gene and transcript expression values.
-  Previously, only whole numbers were accepted.
-- Decimal numbers in the pVACseq reports are now rounded to three decimal
-  places. Previously, they were not rounded.
-
-In addition, this version also fixes a few bugs:
-
-- The ``--normal-vaf`` cutoff value was incorrectly defaulting to 0.2 instead
-  of 0.02. This resulted in the coverage filter not being as stringent as it
-  should've been.
-- There were a number of bugs in pVACapi and pVACviz that would prevent a user
-  from submitting jobs using the interface in certain conditions. These have been resolved.
-- pVACseq would previsouly not support SVs in the input VCF where the alt had
-  a value of ``<DEL>``. These kinds of variants are now supported.
+This version is a hotfix release. It fixes the following issues:
+
+- Some prediction algorithms might predict a binding affinity of 0 which could
+  lead to division by 0 errors when calculating the fold change. In this
+  situation we now set the fold change to ``inf`` (infinity).
+- Previously the ``--maximum-transcript-support-level`` threshold was not
+  getting propagated to the main pipeline step correctly, resulting in errors
+  in the transcript support level filter.
+- There was a bug in the multithreading logic that would result in
+  certain steps getting executed more than once, which in turn would lead to
+  FileNotFound errors when these duplicate executions were happening at the
+  same time.
 
 Past release notes can be found on our :ref:`releases` page.
 

docs/releases/1_3.rst

@@ -27,3 +27,19 @@ In addition, this version also fixes a few bugs:
   from submitting jobs using the interface in certain conditions. These have been resolved.
 - pVACseq would previsouly not support SVs in the input VCF where the alt had
   a value of ``<DEL>``. These kinds of variants are now supported.
+
+1.3.1
+-----
+
+This version is a hotfix release. It fixes the following issues:
+
+- Some prediction algorithms might predict a binding affinity of 0 which could
+  lead to division by 0 errors when calculating the fold change. In this
+  situation we now set the fold change to ``inf`` (infinity).
+- Previously the ``--maximum-transcript-support-level`` threshold was not
+  getting propagated to the main pipeline step correctly, resulting in errors
+  in the transcript support level filter.
+- There was a bug in the multithreading logic that would result in
+  certain steps getting executed more than once, which in turn would lead to
+  FileNotFound errors when these duplicate executions were happening at the
+  same time.

setup.py

@@ -56,7 +56,7 @@
 
 setup(
     name="pvactools",
-    version="1.3.0",
+    version="1.3.1",
     packages=[
         "tools",
         "tools.pvacfuse",