From 046f166544ef4bcf312849ba4366e071b89742bd Mon Sep 17 00:00:00 2001
From: Kemal Eren <kemal@kemaleren.com>
Date: Sun, 31 Jul 2016 20:32:41 +0200
Subject: [PATCH] Fix fastq quality encoding inference (#243)

* FASTQ parser actually uses given `quality_encoding` argument.

`infer_quality_encoding()` was overwriting the given `encodings`
argument.

* FASTQParser requires exactly one quality encoding

* make `quality_encoding` a required argument to `open(filename, FASTQ)`

* update tests to use new fastq parsing api
---
 src/precompile.jl    |  4 ++--
 src/seq/fastq.jl     | 11 +++++++++--
 src/seq/quality.jl   |  1 -
 test/seq/runtests.jl | 12 ++++++------
 4 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/src/precompile.jl b/src/precompile.jl
index 7872899e0..fa04d2bc2 100644
--- a/src/precompile.jl
+++ b/src/precompile.jl
@@ -6,11 +6,11 @@
 
 if VERSION < v"0.5-"
     precompile(Base.open, (ASCIIString, Type{Seq.FASTA},))
-    precompile(Base.open, (ASCIIString, Type{Seq.FASTQ},))
+    precompile(Base.open, (ASCIIString, Type{Seq.FASTQ}, Type{Seq.QualityEncoding},))
     precompile(Base.open, (ASCIIString, Type{Intervals.BED},))
 else
     precompile(Base.open, (String, Type{Seq.FASTA},))
-    precompile(Base.open, (String, Type{Seq.FASTQ},))
+    precompile(Base.open, (String, Type{Seq.FASTQ}, Type{Seq.QualityEncoding},))
     precompile(Base.open, (String, Type{Intervals.BED},))
 end
 precompile(Base.read, (Seq.FASTAParser{Seq.BioSequence},))
diff --git a/src/seq/fastq.jl b/src/seq/fastq.jl
index 229c9bf00..0d860533b 100644
--- a/src/seq/fastq.jl
+++ b/src/seq/fastq.jl
@@ -59,7 +59,7 @@ function Base.open(
         ascii_offset::Integer=typemin(Int))
     io = open(filepath, mode)
     if mode[1] == 'r'
-        return open(BufferedInputStream(io), FASTQ; quality_encoding=quality_encoding)
+        return open(BufferedInputStream(io), FASTQ, quality_encoding)
     elseif mode[1] ∈ ('w', 'a')
         return FASTQWriter(io, quality_header, ascii_offset)
     end
@@ -67,8 +67,8 @@ function Base.open(
 end
 
 function Base.open{S}(input::BufferedInputStream, ::Type{FASTQ},
+                      quality_encoding::QualityEncoding,
                       ::Type{S}=DNASequence;
-                      quality_encoding::QualityEncoding=EMPTY_QUAL_ENCODING,
                       # TODO: remove this option after v0.2
                       qualenc=quality_encoding)
     return FASTQParser{S}(input, quality_encoding)
@@ -90,6 +90,13 @@ type FASTQParser{S<:Sequence} <: AbstractParser
 
     function FASTQParser(input::BufferedInputStream,
                          quality_encodings::QualityEncoding)
+        if quality_encodings == EMPTY_QUAL_ENCODING
+            error("The `quality_encodings` argument is required when parsing FASTQ.")
+        elseif count_ones(convert(UInt16, quality_encodings)) > 1
+            error("The `quality_encodings` argument must specify exactly one encoding.")
+        elseif count_ones(convert(UInt16, quality_encodings & ALL_QUAL_ENCODINGS)) != 1
+            error("Unknown quality encoding.")
+        end
         return new(Ragel.State(fastqparser_start, input),
                    BufferedOutputStream(), BufferedOutputStream(),
                    StringField(), StringField(), 0, quality_encodings)
diff --git a/src/seq/quality.jl b/src/seq/quality.jl
index 8da4d44cf..b2ae380f9 100644
--- a/src/seq/quality.jl
+++ b/src/seq/quality.jl
@@ -90,7 +90,6 @@ giving the set of compatible encodings.
 function infer_quality_encoding(data::Vector{UInt8}, start, stop,
                                 encodings::QualityEncoding=ALL_QUAL_ENCODINGS,
                                 default::QualityEncoding=EMPTY_QUAL_ENCODING)
-    encodings = ALL_QUAL_ENCODINGS
     @inbounds for i in start:stop
         c = data[i]
         if '!' <= c <= '~'
diff --git a/test/seq/runtests.jl b/test/seq/runtests.jl
index 3789824d3..91b85d872 100644
--- a/test/seq/runtests.jl
+++ b/test/seq/runtests.jl
@@ -2764,15 +2764,15 @@ end
 
         function check_fastq_parse(filename)
             # Reading from a stream
-            for seqrec in open(filename, FASTQ)
+            for seqrec in open(filename, FASTQ, Seq.SANGER_QUAL_ENCODING)
             end
 
             # Reading from a memory mapped file
-            for seqrec in open(filename, FASTQ, memory_map=true)
+            for seqrec in open(filename, FASTQ, Seq.SANGER_QUAL_ENCODING, memory_map=true)
             end
 
             # in-place parsing
-            stream = open(filename, FASTQ)
+            stream = open(filename, FASTQ, Seq.SANGER_QUAL_ENCODING)
             entry = eltype(stream)()
             while !eof(stream)
                 read!(stream, entry)
@@ -2782,14 +2782,14 @@ end
             output = IOBuffer()
             writer = Seq.FASTQWriter(output, false, typemin(Int))
             expected_entries = Any[]
-            for seqrec in open(filename, FASTQ)
+            for seqrec in open(filename, FASTQ, Seq.SANGER_QUAL_ENCODING)
                 write(writer, seqrec)
                 push!(expected_entries, seqrec)
             end
             flush(writer)
 
             read_entries = Any[]
-            for seqrec in open(takebuf_array(output), FASTQ)
+            for seqrec in open(takebuf_array(output), FASTQ, Seq.SANGER_QUAL_ENCODING)
                 push!(read_entries, seqrec)
             end
 
@@ -2822,7 +2822,7 @@ end
             """)
             for A in (DNAAlphabet{2}, DNAAlphabet{4})
                 seekstart(input)
-                seq = first(open(input, FASTQ, BioSequence{A})).seq
+                seq = first(open(input, FASTQ, Seq.SANGER_QUAL_ENCODING, BioSequence{A})).seq
                 @test typeof(seq) == BioSequence{A}
             end
         end