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Genomicsplc · Jun 19, 2018 · 4e6f2ca · 4e6f2ca
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Showing 8 changed files with 31 additions and 11 deletions.
diff --git a/LICENSE b/LICENSE
@@ -1,10 +1,7 @@
-This project contains several third-party libraries all released under the
-same license. The copyrights of each library is detailed below.
-
 MIT LICENSE
 
-Copyright (c) 2017 GENOMICS plc (variantkey, rsidvar)
-Copyright (c) 2017 Nicola Asuni - Tecnick.com (binsearch)
+Copyright (c) 2017-2018 GENOMICS plc
+Copyright (c) 2017-2018 Nicola Asuni - Tecnick.com (binsearch)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.6.1
+2.6.2
diff --git a/c/src/genoref.c b/c/src/genoref.c
@@ -43,6 +43,29 @@ inline char get_genoref_seq(const unsigned char *src, const uint32_t idx[], uint
     return (char)src[offset];
 }
 
+/*
+    Abbreviation codes for degenerate bases
+    (http://www.sbcs.qmul.ac.uk/iubmb/misc/naseq.html)
+
+    SYMBOL   DESCRIPTION                     BASES REPRESENTED
+    ----------------------------------------------------------
+    A        adenine                         A
+    C        cytosine                         C
+    G        guanine                           G
+    T        thymine                            T
+    W        weak                            A  T
+    S        strong                           CG
+    M        amino                           AC
+    K        keto                              GT
+    R        purine                          A G
+    Y        pyrimidine                       C T
+    B        not A (B comes after A)          CGT
+    D        not C (D comes after C)         A GT
+    H        not G (H comes after G)         AC T
+    V        not T (V comes after T and U)   ACG
+    N        any base (not a gap)            ACGT
+*/
+
 inline int check_reference(const unsigned char *src, const uint32_t idx[], uint8_t chrom, uint32_t pos, const char *ref, size_t sizeref)
 {
     uint32_t offset = (idx[chrom] + pos);

diff --git a/conda/c.vk/meta.yaml b/conda/c.vk/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: vk
-  version: 2.6.0
+  version: 2.6.2
 
 source:
   path: ../..

diff --git a/conda/python/meta.yaml b/conda/python/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: variantkey
-  version: 2.6.0
+  version: 2.6.2
 
 source:
   path: ../..

diff --git a/conda/r/meta.yaml b/conda/r/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-variantkey
-  version: 2.6.0
+  version: 2.6.2
 
 source:
   path: ../..

diff --git a/python/setup.py b/python/setup.py
@@ -30,7 +30,7 @@ def run(self):
 
 setup(
     name='variantkey',
-    version='2.6.0',
+    version='2.6.2',
     keywords=('variantkey variant key genetic genomics'),
     description="VariantKey Bindings for Python",
     long_description=read('../README.md'),

diff --git a/r/variantkey/DESCRIPTION b/r/variantkey/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: variantkey
 Title: Genetic VariantKey
-Version: 2.6.0.1
+Version: 2.6.2.1
 Authors@R: person("Nicola", "Asuni", email = "info@genomicsplc.com", role = c("aut", "cre"))
 Description: Tools to generate and process a 64 bit Unsigned Integer Keys for Human Genetic Variants.
     The VariantKey is sortable for chromosome and position,