millironx/XAM.jl
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Align emission symbols for TranscodingStreams

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This commit is contained in:
Ciarán O'Mara 2019-11-30 21:18:34 +11:00
parent 6cd89aba08
commit 12db2c4ea8
1 changed files with 47 additions and 47 deletions
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94
src/sam/readrecord.jl
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@ -185,79 +185,79 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
metainfo = let metainfo = let
tag = re"[A-Z][A-Z]" \ cat("CO") tag = re"[A-Z][A-Z]" \ cat("CO")
tag.actions[:enter] = [:mark1] tag.actions[:enter] = [:pos1]
tag.actions[:exit] = [:metainfo_tag] tag.actions[:exit] = [:metainfo_tag]
dict = let dict = let
key = re"[A-Za-z][A-Za-z0-9]" key = re"[A-Za-z][A-Za-z0-9]"
key.actions[:enter] = [:mark2] key.actions[:enter] = [:pos2]
key.actions[:exit] = [:metainfo_dict_key] key.actions[:exit] = [:metainfo_dict_key]
val = re"[ -~]+" val = re"[ -~]+"
val.actions[:enter] = [:mark2] val.actions[:enter] = [:pos2]
val.actions[:exit] = [:metainfo_dict_val] val.actions[:exit] = [:metainfo_dict_val]
keyval = cat(key, ':', val) keyval = cat(key, ':', val)
cat(keyval, rep(cat('\t', keyval))) cat(keyval, rep(cat('\t', keyval)))
end end
dict.actions[:enter] = [:mark1] dict.actions[:enter] = [:pos1]
dict.actions[:exit] = [:metainfo_val] dict.actions[:exit] = [:metainfo_val]
co = cat("CO") co = cat("CO")
co.actions[:enter] = [:mark1] co.actions[:enter] = [:pos1]
co.actions[:exit] = [:metainfo_tag] co.actions[:exit] = [:metainfo_tag]
comment = re"[^\r\n]*" comment = re"[^\r\n]*"
comment.actions[:enter] = [:mark1] comment.actions[:enter] = [:pos1]
comment.actions[:exit] = [:metainfo_val] comment.actions[:exit] = [:metainfo_val]
cat('@', alt(cat(tag, '\t', dict), cat(co, '\t', comment))) cat('@', alt(cat(tag, '\t', dict), cat(co, '\t', comment)))
end end
metainfo.actions[:enter] = [:anchor] metainfo.actions[:enter] = [:mark]
metainfo.actions[:exit] = [:metainfo] metainfo.actions[:exit] = [:metainfo]
record = let record = let
qname = re"[!-?A-~]+" qname = re"[!-?A-~]+"
qname.actions[:enter] = [:mark] qname.actions[:enter] = [:pos]
qname.actions[:exit] = [:record_qname] qname.actions[:exit] = [:record_qname]
flag = re"[0-9]+" flag = re"[0-9]+"
flag.actions[:enter] = [:mark] flag.actions[:enter] = [:pos]
flag.actions[:exit] = [:record_flag] flag.actions[:exit] = [:record_flag]
rname = re"\*|[!-()+-<>-~][!-~]*" rname = re"\*|[!-()+-<>-~][!-~]*"
rname.actions[:enter] = [:mark] rname.actions[:enter] = [:pos]
rname.actions[:exit] = [:record_rname] rname.actions[:exit] = [:record_rname]
pos = re"[0-9]+" pos = re"[0-9]+"
pos.actions[:enter] = [:mark] pos.actions[:enter] = [:pos]
pos.actions[:exit] = [:record_pos] pos.actions[:exit] = [:record_pos]
mapq = re"[0-9]+" mapq = re"[0-9]+"
mapq.actions[:enter] = [:mark] mapq.actions[:enter] = [:pos]
mapq.actions[:exit] = [:record_mapq] mapq.actions[:exit] = [:record_mapq]
cigar = re"\*|([0-9]+[MIDNSHPX=])+" cigar = re"\*|([0-9]+[MIDNSHPX=])+"
cigar.actions[:enter] = [:mark] cigar.actions[:enter] = [:pos]
cigar.actions[:exit] = [:record_cigar] cigar.actions[:exit] = [:record_cigar]
rnext = re"\*|=|[!-()+-<>-~][!-~]*" rnext = re"\*|=|[!-()+-<>-~][!-~]*"
rnext.actions[:enter] = [:mark] rnext.actions[:enter] = [:pos]
rnext.actions[:exit] = [:record_rnext] rnext.actions[:exit] = [:record_rnext]
pnext = re"[0-9]+" pnext = re"[0-9]+"
pnext.actions[:enter] = [:mark] pnext.actions[:enter] = [:pos]
pnext.actions[:exit] = [:record_pnext] pnext.actions[:exit] = [:record_pnext]
tlen = re"[-+]?[0-9]+" tlen = re"[-+]?[0-9]+"
tlen.actions[:enter] = [:mark] tlen.actions[:enter] = [:pos]
tlen.actions[:exit] = [:record_tlen] tlen.actions[:exit] = [:record_tlen]
seq = re"\*|[A-Za-z=.]+" seq = re"\*|[A-Za-z=.]+"
seq.actions[:enter] = [:mark] seq.actions[:enter] = [:pos]
seq.actions[:exit] = [:record_seq] seq.actions[:exit] = [:record_seq]
qual = re"[!-~]+" qual = re"[!-~]+"
qual.actions[:enter] = [:mark] qual.actions[:enter] = [:pos]
qual.actions[:exit] = [:record_qual] qual.actions[:exit] = [:record_qual]
field = let field = let
@ -272,7 +272,7 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
cat(tag, ':', val) cat(tag, ':', val)
end end
field.actions[:enter] = [:mark] field.actions[:enter] = [:pos]
field.actions[:exit] = [:record_field] field.actions[:exit] = [:record_field]
cat( cat(
@ -289,7 +289,7 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
qual, qual,
rep(cat('\t', field))) rep(cat('\t', field)))
end end
record.actions[:enter] = [:anchor] record.actions[:enter] = [:mark]
record.actions[:exit] = [:record] record.actions[:exit] = [:record]
newline = let newline = let
@ -309,23 +309,23 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
end)() end)()
const sam_metainfo_actions = Dict( const sam_metainfo_actions = Dict(
:metainfo_tag => :(record.tag = (mark1:p-1) .- offset), :metainfo_tag => :(record.tag = (pos1:p-1) .- offset),
:metainfo_val => :(record.val = (mark1:p-1) .- offset), :metainfo_val => :(record.val = (pos1:p-1) .- offset),
:metainfo_dict_key => :(push!(record.dictkey, (mark2:p-1) .- offset)), :metainfo_dict_key => :(push!(record.dictkey, (pos2:p-1) .- offset)),
:metainfo_dict_val => :(push!(record.dictval, (mark2:p-1) .- offset)), :metainfo_dict_val => :(push!(record.dictval, (pos2:p-1) .- offset)),
:metainfo => quote :metainfo => quote
resize_and_copy!(record.data, data, offset+1:p-1) resize_and_copy!(record.data, data, offset+1:p-1)
record.filled = (offset+1:p-1) .- offset record.filled = (offset+1:p-1) .- offset
end, end,
:anchor => :(), :mark => :(),
:mark1 => :(mark1 = p), :pos1 => :(pos1 = p),
:mark2 => :(mark2 = p) :pos2 => :(pos2 = p)
) )
generate_index_function( generate_index_function(
MetaInfo, MetaInfo,
sam_metainfo_machine, sam_metainfo_machine,
:(mark1 = mark2 = offset = 0), :(pos1 = pos2 = offset = 0),
sam_metainfo_actions sam_metainfo_actions
) |> eval ) |> eval
@ -333,7 +333,7 @@ generate_readheader_function(
Reader, Reader,
MetaInfo, MetaInfo,
sam_header_machine, sam_header_machine,
:(mark1 = mark2 = offset = 0), :(pos1 = pos2 = offset = 0),
merge(sam_metainfo_actions, Dict( merge(sam_metainfo_actions, Dict(
:metainfo => quote :metainfo => quote
resize_and_copy!(record.data, data, upanchor!(stream):p-1) resize_and_copy!(record.data, data, upanchor!(stream):p-1)
@ -345,7 +345,7 @@ generate_readheader_function(
end, end,
:header => :(finish_header = true; @escape), :header => :(finish_header = true; @escape),
:countline => :(linenum += 1), :countline => :(linenum += 1),
:anchor => :(anchor!(stream, p); offset = p - 1))), :mark => :(anchor!(stream, p); offset = p - 1))),
quote quote
if !eof(stream) if !eof(stream)
stream.position -= 1 # cancel look-ahead stream.position -= 1 # cancel look-ahead
@ -354,37 +354,37 @@ generate_readheader_function(
) |> eval ) |> eval
const sam_record_actions = Dict( const sam_record_actions = Dict(
:record_qname => :(record.qname = (mark:p-1) .- offset), :record_qname => :(record.qname = (pos:p-1) .- offset),
:record_flag => :(record.flag = (mark:p-1) .- offset), :record_flag => :(record.flag = (pos:p-1) .- offset),
:record_rname => :(record.rname = (mark:p-1) .- offset), :record_rname => :(record.rname = (pos:p-1) .- offset),
:record_pos => :(record.pos = (mark:p-1) .- offset), :record_pos => :(record.pos = (pos:p-1) .- offset),
:record_mapq => :(record.mapq = (mark:p-1) .- offset), :record_mapq => :(record.mapq = (pos:p-1) .- offset),
:record_cigar => :(record.cigar = (mark:p-1) .- offset), :record_cigar => :(record.cigar = (pos:p-1) .- offset),
:record_rnext => :(record.rnext = (mark:p-1) .- offset), :record_rnext => :(record.rnext = (pos:p-1) .- offset),
:record_pnext => :(record.pnext = (mark:p-1) .- offset), :record_pnext => :(record.pnext = (pos:p-1) .- offset),
:record_tlen => :(record.tlen = (mark:p-1) .- offset), :record_tlen => :(record.tlen = (pos:p-1) .- offset),
:record_seq => :(record.seq = (mark:p-1) .- offset), :record_seq => :(record.seq = (pos:p-1) .- offset),
:record_qual => :(record.qual = (mark:p-1) .- offset), :record_qual => :(record.qual = (pos:p-1) .- offset),
:record_field => :(push!(record.fields, (mark:p-1) .- offset)), :record_field => :(push!(record.fields, (pos:p-1) .- offset)),
:record => quote :record => quote
resize_and_copy!(record.data, data, 1:p-1) resize_and_copy!(record.data, data, 1:p-1)
record.filled = (offset+1:p-1) .- offset record.filled = (offset+1:p-1) .- offset
end, end,
:anchor => :(), :mark => :(),
:mark => :(mark = p) :pos => :(pos = p)
) )
generate_index_function( generate_index_function(
Record, Record,
sam_record_machine, sam_record_machine,
:(mark = offset = 0), :(pos = offset = 0),
sam_record_actions sam_record_actions
) |> eval ) |> eval
generate_read_function( generate_read_function(
Reader, Reader,
sam_body_machine, sam_body_machine,
:(mark = offset = 0), :(pos = offset = 0),
merge(sam_record_actions, Dict( merge(sam_record_actions, Dict(
:record => quote :record => quote
resize_and_copy!(record.data, data, upanchor!(stream):p-1) resize_and_copy!(record.data, data, upanchor!(stream):p-1)
@ -393,6 +393,6 @@ generate_read_function(
@escape @escape
end, end,
:countline => :(linenum += 1), :countline => :(linenum += 1),
:anchor => :(anchor!(stream, p); offset = p - 1)) :mark => :(anchor!(stream, p); offset = p - 1))
) )
) |> eval ) |> eval