Add Project.toml

Also fixed deprecation warnings.

.gitignore

@@ -1 +1,5 @@
 .DS_Store
+*.jl.*.cov
+*.jl.cov
+*.jl.mem
+Manifest.toml

.travis.yml

@@ -3,8 +3,8 @@ os:
   - linux
   - osx
 julia:
-  - 0.7
   - 1.0
+  - 1.5
   - nightly
 notifications:
   email:

CHANGELOG.md

@@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Added
+- :arrow_up: Added Project.toml
 
 ## [0.4.0] - 2018-11-22
 ### Added

Project.toml

@@ -0,0 +1,32 @@
+name = "GeneticVariation"
+uuid = "9bc6ac9d-e6b2-5f70-b0a8-242a01662520"
+authors = ["Ben J. Ward <[email protected]>"]
+version = "0.4.1"
+
+[deps]
+Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
+BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
+BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
+Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
+IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
+Twiddle = "7200193e-83a8-5a55-b20d-5d36d44a0795"
+
+[compat]
+Automa = "0.8"
+BGZFStreams = "0.3"
+BioCore = "2.0.5"
+BioSequences = "1.1"
+BufferedStreams = "1"
+Combinatorics = "0.7"
+IntervalTrees = "1"
+Twiddle = "1.1"
+julia = "1"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+
+[targets]
+test = ["Test","YAML"]

appveyor.yml

@@ -1,6 +1,6 @@
 environment:
   matrix:
-  - julia_version: 1
+  - julia_version: 1.5
   - julia_version: nightly
 
 platform:

src/GeneticVariation.jl

@@ -73,11 +73,9 @@ import IntervalTrees: Interval, IntervalValue
 import Twiddle:
     enumerate_nibbles,
     nibble_mask,
-    count_zero_nibbles,
+    count_0000_nibbles,
     count_nonzero_nibbles,
-    count_one_nibbles,
-    count_zero_bitpairs,
-    count_nonzero_bitpairs
+    count_1111_nibbles
 
 include("vcf/vcf.jl")
 include("bcf/bcf.jl")

src/site_counting.jl

@@ -77,16 +77,16 @@ for A in (DNAAlphabet, RNAAlphabet)
         @inline function bp_chunk_count(::Type{Mutated}, ::Type{$A{4}}, a::UInt64, b::UInt64)
             m = nibble_mask(Certain, a, b)
             d = (a ⊻ b) & m
-            return count_nonzero_nibbles(d), count_one_nibbles(m)
+            return count_nonzero_nibbles(d), count_1111_nibbles(m)
         end
 
         # TODO Finish transitions and transversions
         # Transition
         @inline function bp_chunk_count(::Type{Transition}, ::Type{$A{4}}, a::UInt64, b::UInt64)
             m = nibble_mask(Certain, a, b)
             d = (a ⊻ b) & m
-            remcount = count_zero_nibbles(d) # Count of the identical nucleotides.
-            tve = count_one_nibbles(nibble_mask(0x9999999999999999, d)) # Count the 1001 transversion edge case.
+            remcount = count_0000_nibbles(d) # Count of the identical nucleotides.
+            tve = count_1111_nibbles(nibble_mask(0x9999999999999999, d)) # Count the 1001 transversion edge case.
             d &= (d >> 1)
             d &= 0x7777777777777777
             tvc = count_ones(d)