Merge branch 'hotfix'

docs/conf.py

@@ -62,9 +62,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '4.0.3'
+version = '4.0.4'
 # The full version, including alpha/beta/rc tags.
-release = '4.0.3'
+release = '4.0.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -23,12 +23,7 @@ pVAC-Seq is a cancer immunotherapy pipeline for the identification of **p**\ ers
 New in version |version|
 ------------------------
 
-We added an :ref:`optional downstream analysis tool<optional_downstream_analysis_tools_label>` to generate an annotated fasta file from a VCF with protein sequences of mutations and matching wildtypes. This tool can be run with the ``pvacseq generate_protein_fasta`` command.
-
-This release fixes a couple of errors that were introduced in the previous version which would occur during the processing of certain inframe indels.
-
-This version also fixes an error that would occur if the number of variants to
-process was a multiple of the chosen ``--fasta-size``.
+This release fixes a couple of minor bugs. Firstly, the pipeline will now skip variants that result in the loss of a start codon. Secondly, this release fixes a bug that would result in an error when the input VCF doesn't contain any sample genotype information. VCFs with no samples will now be fully processed through the pipeline.
 
 Citation
 --------

pvacseq/lib/convert_vcf.py

@@ -87,7 +87,9 @@ def parse_csq_entries_for_allele(csq_entries, csq_format, csq_allele):
 
 def resolve_consequence(consequence_string):
     consequences = {consequence.lower() for consequence in consequence_string.split('&')}
-    if 'frameshift_variant' in consequences:
+    if 'start_lost' in consequences:
+        consequence = None
+    elif 'frameshift_variant' in consequences:
         consequence = 'FS'
     elif 'missense_variant' in consequences:
         consequence = 'missense'
@@ -186,10 +188,11 @@ def main(args_input = sys.argv[1:]):
         reference  = entry.REF
         alts       = entry.ALT
 
-        genotype = entry.genotype(vcf_reader.samples[0])
-        if genotype.gt_type is None or genotype.gt_type == 0:
-            #The genotype is uncalled or hom_ref
-            continue
+        if len(vcf_reader.samples) == 1:
+            genotype = entry.genotype(vcf_reader.samples[0])
+            if genotype.gt_type is None or genotype.gt_type == 0:
+                #The genotype is uncalled or hom_ref
+                continue
 
         alleles_dict = resolve_alleles(entry)
         for alt in alts:

setup.py

@@ -29,7 +29,7 @@
 
 setup(
     name="pvacseq",
-    version="4.0.3",
+    version="4.0.4",
     packages=["pvacseq", "pvacseq.lib", "pvacseq.server"],
     entry_points={
         "console_scripts":[