Merge pull request #1200 from griffithlab/pvacvector_bug

Fix pVACvector bug that would result in not all junctional epitopes getting tested on clipping

docs/index.rst

@@ -91,8 +91,8 @@ It also fixes the following problem(s):
   associated with incorrect variants. Additionally, it fixes several
   deprecation warnings and typos. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173
 
-New in Version |version|
-------------------------
+New in Version 5
+----------------
 
 This is a major version release. Please note that pVACtools 5.0 is not guaranteed to be
 backwards-compatible and certain changes could break old workflows.

docs/releases.rst

@@ -22,3 +22,4 @@ Release Notes
    releases/4_3
    releases/4_4
    releases/5_0
+   releases/5_1

docs/releases/5_1.rst

@@ -0,0 +1,36 @@
+Version 5.1
+===========
+
+Version 5.1.0
+-------------
+
+This is a minor feature release. It adds the following features:
+
+- This update allows pVACvector to remove peptides in order to find a partial solution if a full solution cannot be found.
+  The number of peptides permitted to be removed can be controlled by the ``--allow-n-peptide-exclusion`` parameter. by
+  @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1168
+- This update adds functionalities to pVACvector to prevent the core neoantigen candidate from getting clipped. by
+  @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1174
+- When only elution algorithms are chosen and no binding affinity algorithms,
+  the pipelines will now output a warning message that no aggregated report
+  can be created. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1165
+- When creating the aggregated report, the Best Peptide for some variants
+  may not match the aggregate inclusion criteria and no detail information
+  would be available for this peptide when investigating the variant. This
+  update ensures that the Best Peptide is always included in the metrics file
+  and counted toward the Num Included Peptides count. by @susannasiebert in
+  https://github.com/griffithlab/pVACtools/pull/1177
+- The evaluation buttons in pVACview will now be colored green for Accept, red
+  for Reject, and orange for Review to visually differentiate the different
+  statuses. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173
+
+It also fixes the following problem(s):
+
+- This release removes two parameters from pVACvector: ``--aggregate-inclusion-binding-threshold`` and ``--aggregate-inclusion-count-limit``
+  which are not applicable to this pipeline. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1180
+- This release fixes various pVACview bugs. Specifically, it fixes a bug that
+  would result in pVACview crashing when a variant with a Num Included
+  Peptides of 0 was selected. It also fixes a bug where re-tiering the
+  candidates before selecting evaluations would result in evaluations being
+  associated with incorrect variants. Additionally, it fixes several
+  deprecation warnings and typos. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173

pvactools/lib/fasta_generator.py

@@ -402,8 +402,8 @@ def execute(self):
                             if right_clip_length > first_position:
                                 warnings.add("Clipping {} amino acids off the start of peptide {} would clip the best peptide. Skipping.".format(right_clip_length, seq2))
                                 continue
-                        trunc_seq1 = seq1_seq[(len(seq1_seq) - wingspan_length):(len(seq1_seq) - left_clip_length)]
-                        trunc_seq2 = seq2_seq[(0 + right_clip_length):wingspan_length]
+                        trunc_seq1 = seq1_seq[(len(seq1_seq) - wingspan_length - left_clip_length):(len(seq1_seq) - left_clip_length)]
+                        trunc_seq2 = seq2_seq[(0 + right_clip_length):wingspan_length + right_clip_length]
 
                         if self.spacer != 'None':
                             seq_ID = "{}|{}|{}|{}|{}".format(seq1, left_clip_length, self.spacer, right_clip_length, seq2)