Merge pull request #48 from MillironX/feature/BioAlignmentsv2.2

Upgrade BioAlignments to v2.2 & BioSequences to v3

.github/workflows/UnitTests.yml

@@ -13,7 +13,6 @@ jobs:
       fail-fast: false
       matrix:
         julia-version:
-          - '1.0' # LTS
           - '1.6' # LTS
           - '1'
         julia-arch: [x64, x86]

Project.toml

@@ -17,13 +17,13 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 [compat]
 Automa = "0.7, 0.8"
 BGZFStreams = "0.3"
-BioAlignments = "2"
+BioAlignments = "2.2"
 BioGenerics = "0.1"
-BioSequences = "2.0.4"
+BioSequences = "3"
 GenomicFeatures = "2"
 Indexes = "0.1"
 TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
-julia = "1"
+julia = "1.6"
 
 [extras]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

src/bam/record.jl

@@ -91,7 +91,7 @@ function Base.empty!(record::Record)
     record.tlen       = 0
 
     #Note: data will be overwritten and indexed using data_size.
-    
+
     return record
 end
 
@@ -505,7 +505,7 @@ function hastemplength(record::Record)
 end
 
 """
-    sequence(record::Record)::BioSequences.LongDNASeq
+    sequence(record::Record)::BioSequences.LongDNA{4}
 
 Get the segment sequence of `record`.
 """
@@ -522,7 +522,7 @@ function sequence(record::Record)
         x = unsafe_load(src, i)
         data[i] = (x & 0x0f0f0f0f0f0f0f0f) << 4 | (x & 0xf0f0f0f0f0f0f0f0) >> 4
     end
-    return BioSequences.LongDNASeq(data, 1:seqlen, false)
+    return BioSequences.LongDNA{4}(data, UInt(seqlen))
 end
 
 function hassequence(record::Record)

src/sam/record.jl

@@ -387,7 +387,7 @@ function hastemplength(record::Record)
 end
 
 """
-    sequence(record::Record)::BioSequences.LongDNASeq
+    sequence(record::Record)::BioSequences.LongDNA{4}
 
 Get the segment sequence of `record`.
 """
@@ -398,7 +398,7 @@ function sequence(record::Record)
         return nothing
     end
     seqlen = length(record.seq)
-    ret = BioSequences.LongDNASeq(seqlen)
+    ret = BioSequences.LongDNA{4}(undef, seqlen)
     copyto!(ret, 1, record.data, first(record.seq), seqlen)
     return ret
 end