Update to version 5.1.0

docs/conf.py

@@ -24,9 +24,9 @@
 author = 'Susanna Kiwala, Chris Miller'
 
 # The short X.Y version
-version = '5.0'
+version = '5.1'
 # The full version, including alpha/beta/rc tags
-release = '5.0.1'
+release = '5.1.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/vcf_expression_annotator.rst

@@ -11,8 +11,9 @@ be specified. This will result in the expression value to be written to the
 ``GX`` or ``TX`` field, respectively.
 
 The input VCF needs to be annotated with VEP with gene and transcript information so
-that the VCF Expression Annotator can match a variant's gene and transcript
-identifier in the VCF to the one in the expression file. Depending on the
+that the VCF Expression Annotator can match a variant's Ensembl gene and transcript
+identifier in the VCF to the one in the expression file. When running in
+``gene`` mode, Ensembl IDs - not gene names - are used. Depending on the
 expression software used, the transcript identifiers might contain version
 numbers. To add transcript version numbers to your VEP annotation, use the
 ``--transcript_version`` when running VEP. You can also use the

docs/vcf_readcount_annotator.rst

@@ -7,11 +7,13 @@ and add its data to your VCF. It supports both DNA and RNA readcounts.
 
 DNA readcounts are identified by specifying ``DNA`` in the list of
 positional arguments. Depth, allele counts, and VAFs are then written to the
-DP, AD, and AF fields, respectively.
+DP, AD, and AF fields, respectively. Forward and reverse strand allele counts
+are written in the ADF and ADR fields, respectively.
 
 RNA readcounts are identified by specifying ``RNA`` in the list of positional
 arguments. Depth, allele counts, and VAFs are then written tot he RDP, RAD,
-and RAF fields, respectively.
+and RAF fields, respectively. Forward and reverse strand allele counts
+are written in the RADF and RADR fields, respectively.
 
 If your VCF is a multi-sample VCF, you have to pick one of the sample in
 your VCF by setting the ``--sample-name`` option. This is the sample that the

docs/vep_annotation_reporter.rst

@@ -19,7 +19,10 @@ values. This is the default behavior unless VEP was run with
 one of the ``--flag_pick`` options, all possible transcript consequences will be
 reported by VEP but only one of these consequences will be picked by VEP as the
 "best" consequence. This is denoted in the ``PICK`` field. If this field is
-available, then the values for that transcript will be reported.
+available, then the values for that transcript will be reported. For some
+variants, VCFs annotated with the ``PICK`` field might not report any of the
+consequences as picked. In that case, the values for all transcript consequences are
+reported.
 
 VEP annotations can also be added to an existing TSV with variant
 information by using the ``--input-tsv`` option. In order to match

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="vatools",
-    version="5.0.1",
+    version="5.1.0",
     packages=["vatools"],
     entry_points={
         "console_scripts":[