extract BigBed types from .rl (#241)

BioJulia · Jul 30, 2016 · b8e991b · b8e991b
1 parent d1c6071
commit b8e991b
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Showing 3 changed files with 39 additions and 97 deletions.
diff --git a/src/intervals/bigbed-parser.jl b/src/intervals/bigbed-parser.jl
@@ -1,22 +1,4 @@
 # WARNING: This file was generated from bigbed-parser.rl using ragel. Do not edit!
-type BigBedData <: IntervalStream{BEDMetadata}
-stream::BufferedInputStream
-header::BigBedHeader
-zoom_headers::Vector{BigBedZoomHeader}
-autosql::AbstractString
-summary::BigBedTotalSummary
-btree_header::BigBedBTreeHeader
-rtree_header::BigBedRTreeHeader
-data_count::UInt32
-
-# preallocated space for reading and searching the B-tree
-btree_internal_nodes::Vector{BigBedBTreeInternalNode}
-btree_leaf_nodes::Vector{BigBedBTreeLeafNode}
-key::Vector{UInt8}
-node_keys::Vector{Vector{UInt8}}
-uncompressed_data::Vector{UInt8}
-end
-
 
 	# Parser for data blocks in a BigBed file. This is very similar
 	# to the BED parser in bed.rl, with the following exceptions:
@@ -33,35 +15,6 @@ const __bigbedparser_nfa_targs = Int8[ 0, 0 ,  ]
 const __bigbedparser_nfa_offsets = Int8[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ,  ]
 const __bigbedparser_nfa_push_actions = Int8[ 0, 0 ,  ]
 const __bigbedparser_nfa_pop_trans = Int8[ 0, 0 ,  ]
-typealias StringFieldVector Vector{StringField}
-typealias NullableStringFieldVector Nullable{StringFieldVector}
-typealias NullableStringField Nullable{StringField}
-
-type BigBedDataParser <: AbstractParser
-state::Ragel.State
-
-# intermediate values used during parsing
-chrom_id::UInt32
-red::Float32
-green::Float32
-blue::Float32
-block_size_idx::Int
-block_first_idx::Int
-seq_names::Nullable{StringFieldVector}
-assumed_seqname::Nullable{StringField}
-
-function BigBedDataParser(input::BufferedInputStream;
-seq_names::NullableStringFieldVector=NullableStringFieldVector(),
-assumed_seqname::NullableStringField=NullableStringField())
-
-begin
-cs = convert( Int , _bigbedparser_start );
-
-end
-return new(Ragel.State(cs, input), 0, 0.0, 0.0, 0.0, 1, 1, seq_names, assumed_seqname)
-end
-end
-
 
 Ragel.@generate_read!_function("_bigbedparser", BigBedDataParser, BEDInterval,
 begin

diff --git a/src/intervals/bigbed-parser.rl b/src/intervals/bigbed-parser.rl
@@ -1,23 +1,3 @@
-
-type BigBedData <: IntervalStream{BEDMetadata}
-    stream::BufferedInputStream
-    header::BigBedHeader
-    zoom_headers::Vector{BigBedZoomHeader}
-    autosql::AbstractString
-    summary::BigBedTotalSummary
-    btree_header::BigBedBTreeHeader
-    rtree_header::BigBedRTreeHeader
-    data_count::UInt32
-
-    # preallocated space for reading and searching the B-tree
-    btree_internal_nodes::Vector{BigBedBTreeInternalNode}
-    btree_leaf_nodes::Vector{BigBedBTreeLeafNode}
-    key::Vector{UInt8}
-    node_keys::Vector{Vector{UInt8}}
-    uncompressed_data::Vector{UInt8}
-end
-
-
 # Parser for data blocks in a BigBed file. This is very similar
 # to the BED parser in bed.rl, with the following exceptions:
 #
@@ -122,38 +102,8 @@ end
     main := (bed_entry %finish_match)*;
 }%%
 
-
 %%write data;
 
-# because brackets can fuck with ragel's parsing in unpredictable ways
-typealias StringFieldVector Vector{StringField}
-typealias NullableStringFieldVector Nullable{StringFieldVector}
-typealias NullableStringField Nullable{StringField}
-
-type BigBedDataParser <: AbstractParser
-    state::Ragel.State
-
-    # intermediate values used during parsing
-    chrom_id::UInt32
-    red::Float32
-    green::Float32
-    blue::Float32
-    block_size_idx::Int
-    block_first_idx::Int
-    seq_names::Nullable{StringFieldVector}
-    assumed_seqname::Nullable{StringField}
-
-    function BigBedDataParser(input::BufferedInputStream;
-                              seq_names::NullableStringFieldVector=NullableStringFieldVector(),
-                              assumed_seqname::NullableStringField=NullableStringField())
-
-        %% write init;
-
-        return new(Ragel.State(cs, input), 0, 0.0, 0.0, 0.0, 1, 1, seq_names, assumed_seqname)
-    end
-end
-
-
 Ragel.@generate_read!_function("_bigbedparser", BigBedDataParser, BEDInterval,
     begin
         %%write exec;

diff --git a/src/intervals/bigbed.jl b/src/intervals/bigbed.jl
@@ -348,6 +348,45 @@ end
 immutable BigBed <: FileFormat end
 immutable BigWig <: FileFormat end
 
+type BigBedData <: IntervalStream{BEDMetadata}
+    stream::BufferedInputStream
+    header::BigBedHeader
+    zoom_headers::Vector{BigBedZoomHeader}
+    autosql::AbstractString
+    summary::BigBedTotalSummary
+    btree_header::BigBedBTreeHeader
+    rtree_header::BigBedRTreeHeader
+    data_count::UInt32
+
+    # preallocated space for reading and searching the B-tree
+    btree_internal_nodes::Vector{BigBedBTreeInternalNode}
+    btree_leaf_nodes::Vector{BigBedBTreeLeafNode}
+    key::Vector{UInt8}
+    node_keys::Vector{Vector{UInt8}}
+    uncompressed_data::Vector{UInt8}
+end
+
+type BigBedDataParser <: AbstractParser
+    state::Ragel.State
+
+    # intermediate values used during parsing
+    chrom_id::UInt32
+    red::Float32
+    green::Float32
+    blue::Float32
+    block_size_idx::Int
+    block_first_idx::Int
+    seq_names::Nullable{Vector{StringField}}
+    assumed_seqname::Nullable{StringField}
+
+    function BigBedDataParser(input::BufferedInputStream;
+                              seq_names::Nullable{Vector{StringField}}=Nullable{Vector{StringField}}(),
+                              assumed_seqname::Nullable{StringField}=Nullable{StringField}())
+        cs = _bigbedparser_start
+        return new(Ragel.State(cs, input), 0, 0.0, 0.0, 0.0, 1, 1, seq_names, assumed_seqname)
+    end
+end
+
 include("bigbed-parser.jl")
 
 """