Merge pull request #237 from bicycle1885/backports-0.2

Backports for 0.2

REQUIRE

@@ -5,6 +5,6 @@ Compat
 IndexableBitVectors 0.1.1
 IntervalTrees
 Iterators
-Libz 0.1.1
+Libz 0.2
 LightGraphs
 LightXML

src/align/pairwise/alignment.jl

@@ -128,6 +128,14 @@ function count_aligned(aln::PairwiseAlignment)
     return n
 end
 
+function ref2seq(i::Integer, aln::PairwiseAlignment)
+    return ref2seq(i, aln.a)
+end
+
+function seq2ref(i::Integer, aln::PairwiseAlignment)
+    return seq2ref(i, aln.a)
+end
+
 
 # Printers
 # --------

src/intervals/bigbed.jl

@@ -512,7 +512,7 @@ function Base.start(bb::BigBedData)
     parser_isdone = isnull(tryread!(parser, next_interval))
 
     return BigBedIteratorState(seq_names, data_count, 1,
-                               getindex(zlib_stream.source.zstream).total_in,
+                               zlib_stream.source.zstream.total_in,
                                parser, parser_isdone, next_interval)
 end
 
@@ -535,7 +535,7 @@ function Base.next(bb::BigBedData, state::BigBedIteratorState)
         state.parser = BigBedDataParser(
              BufferedInputStream(bb.uncompressed_data, unc_block_size),
              seq_names=Nullable(state.seq_names))
-        state.data_offset += getindex(zlib_stream.source.zstream).total_in
+        state.data_offset += zlib_stream.source.zstream.total_in
 
         state.parser_isdone = isnull(tryread!(state.parser, state.next_interval))
         @assert !state.parser_isdone

test/align/runtests.jl

@@ -461,6 +461,25 @@ end
         @test count_aligned(aln) == 16
     end
 
+    @testset "Interfaces" begin
+        seq = dna"ACGTATAGT"
+        ref = dna"ATCGTATTGGT"
+        # seq:  1 A-CGTATAG-T  9
+        #         | ||||| | |
+        # ref:  1 ATCGTATTGGT 11
+        model = AffineGapScoreModel(EDNAFULL, gap_open=-4, gap_extend=-1)
+        result = pairalign(GlobalAlignment(), seq, ref, model)
+        @test isa(result, PairwiseAlignmentResult)
+        aln = alignment(result)
+        @test isa(aln, PairwiseAlignment)
+        @test seq2ref(1, aln) == (1, OP_SEQ_MATCH)
+        @test seq2ref(2, aln) == (3, OP_SEQ_MATCH)
+        @test seq2ref(3, aln) == (4, OP_SEQ_MATCH)
+        @test ref2seq(1, aln) == (1, OP_SEQ_MATCH)
+        @test ref2seq(2, aln) == (1, OP_DELETE)
+        @test ref2seq(3, aln) == (2, OP_SEQ_MATCH)
+    end
+
     @testset "GlobalAlignment" begin
         affinegap = AffineGapScoreModel(
             match=0,

test/tools/runtests.jl

@@ -7,13 +7,16 @@ else
     const Test = BaseTestNext
 end
 
+using Compat
 using Bio.Seq,
       Bio.Tools.BLAST,
       TestFunctions
 
 get_bio_fmt_specimens()
 path = Pkg.dir("Bio", "test", "BioFmtSpecimens")
 
+if !is_windows()  # temporarily disable the BLAST tests on Windows (issue: #197)
+
 @testset "BLAST+ blastn" begin
     na1 = dna"""
     CGGACCAGACGGACACAGGGAGAAGCTAGTTTCTTTCATGTGATTGANAT
@@ -35,7 +38,6 @@ path = Pkg.dir("Bio", "test", "BioFmtSpecimens")
     @test typeof(blastn(na1, nucldb, db=true)) == Array{BLASTResult, 1}
     @test typeof(blastn(na1, fna)) == Array{BLASTResult, 1}
     @test typeof(blastn(fna, nucldb, db=true)) == Array{BLASTResult, 1}
-
 end
 
 @testset "BLAST+ blastp" begin
@@ -61,4 +63,6 @@ end
     @test typeof(blastp(faa, protdb, db=true)) == Array{BLASTResult, 1}
 end
 
+end  # if !is_windows()
+
 end # TestTools