mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-11-23 02:09:55 +00:00
Align emission symbols for TranscodingStreams
This commit is contained in:
Ciarán O'Mara
parent
6cd89aba08
commit
12db2c4ea8
1 changed files with 47 additions and 47 deletions
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@ -185,79 +185,79 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
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metainfo = let
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tag = re"[A-Z][A-Z]" \ cat("CO")
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tag.actions[:enter] = [:mark1]
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tag.actions[:enter] = [:pos1]
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tag.actions[:exit] = [:metainfo_tag]
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dict = let
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key = re"[A-Za-z][A-Za-z0-9]"
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key.actions[:enter] = [:mark2]
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key.actions[:enter] = [:pos2]
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key.actions[:exit] = [:metainfo_dict_key]
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val = re"[ -~]+"
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val.actions[:enter] = [:mark2]
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val.actions[:enter] = [:pos2]
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val.actions[:exit] = [:metainfo_dict_val]
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keyval = cat(key, ':', val)
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cat(keyval, rep(cat('\t', keyval)))
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end
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dict.actions[:enter] = [:mark1]
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dict.actions[:enter] = [:pos1]
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dict.actions[:exit] = [:metainfo_val]
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co = cat("CO")
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co.actions[:enter] = [:mark1]
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co.actions[:enter] = [:pos1]
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co.actions[:exit] = [:metainfo_tag]
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comment = re"[^\r\n]*"
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comment.actions[:enter] = [:mark1]
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comment.actions[:enter] = [:pos1]
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comment.actions[:exit] = [:metainfo_val]
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cat('@', alt(cat(tag, '\t', dict), cat(co, '\t', comment)))
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end
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metainfo.actions[:enter] = [:anchor]
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metainfo.actions[:enter] = [:mark]
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metainfo.actions[:exit] = [:metainfo]
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record = let
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qname = re"[!-?A-~]+"
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qname.actions[:enter] = [:mark]
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qname.actions[:enter] = [:pos]
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qname.actions[:exit] = [:record_qname]
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flag = re"[0-9]+"
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flag.actions[:enter] = [:mark]
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flag.actions[:enter] = [:pos]
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flag.actions[:exit] = [:record_flag]
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rname = re"\*|[!-()+-<>-~][!-~]*"
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rname.actions[:enter] = [:mark]
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rname.actions[:enter] = [:pos]
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rname.actions[:exit] = [:record_rname]
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pos = re"[0-9]+"
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pos.actions[:enter] = [:mark]
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pos.actions[:enter] = [:pos]
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pos.actions[:exit] = [:record_pos]
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mapq = re"[0-9]+"
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mapq.actions[:enter] = [:mark]
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mapq.actions[:enter] = [:pos]
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mapq.actions[:exit] = [:record_mapq]
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cigar = re"\*|([0-9]+[MIDNSHPX=])+"
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cigar.actions[:enter] = [:mark]
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cigar.actions[:enter] = [:pos]
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cigar.actions[:exit] = [:record_cigar]
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rnext = re"\*|=|[!-()+-<>-~][!-~]*"
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rnext.actions[:enter] = [:mark]
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rnext.actions[:enter] = [:pos]
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rnext.actions[:exit] = [:record_rnext]
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pnext = re"[0-9]+"
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pnext.actions[:enter] = [:mark]
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pnext.actions[:enter] = [:pos]
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pnext.actions[:exit] = [:record_pnext]
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tlen = re"[-+]?[0-9]+"
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tlen.actions[:enter] = [:mark]
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tlen.actions[:enter] = [:pos]
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tlen.actions[:exit] = [:record_tlen]
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seq = re"\*|[A-Za-z=.]+"
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seq.actions[:enter] = [:mark]
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seq.actions[:enter] = [:pos]
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seq.actions[:exit] = [:record_seq]
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qual = re"[!-~]+"
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qual.actions[:enter] = [:mark]
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qual.actions[:enter] = [:pos]
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qual.actions[:exit] = [:record_qual]
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field = let
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@ -272,7 +272,7 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
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cat(tag, ':', val)
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end
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field.actions[:enter] = [:mark]
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field.actions[:enter] = [:pos]
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field.actions[:exit] = [:record_field]
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cat(
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@ -289,7 +289,7 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
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qual,
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rep(cat('\t', field)))
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end
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record.actions[:enter] = [:anchor]
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record.actions[:enter] = [:mark]
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record.actions[:exit] = [:record]
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newline = let
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@ -309,23 +309,23 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
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end)()
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const sam_metainfo_actions = Dict(
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:metainfo_tag => :(record.tag = (mark1:p-1) .- offset),
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:metainfo_val => :(record.val = (mark1:p-1) .- offset),
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:metainfo_dict_key => :(push!(record.dictkey, (mark2:p-1) .- offset)),
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:metainfo_dict_val => :(push!(record.dictval, (mark2:p-1) .- offset)),
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:metainfo_tag => :(record.tag = (pos1:p-1) .- offset),
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:metainfo_val => :(record.val = (pos1:p-1) .- offset),
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:metainfo_dict_key => :(push!(record.dictkey, (pos2:p-1) .- offset)),
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:metainfo_dict_val => :(push!(record.dictval, (pos2:p-1) .- offset)),
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:metainfo => quote
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resize_and_copy!(record.data, data, offset+1:p-1)
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record.filled = (offset+1:p-1) .- offset
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end,
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:anchor => :(),
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:mark1 => :(mark1 = p),
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:mark2 => :(mark2 = p)
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:mark => :(),
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:pos1 => :(pos1 = p),
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:pos2 => :(pos2 = p)
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)
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generate_index_function(
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MetaInfo,
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sam_metainfo_machine,
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:(mark1 = mark2 = offset = 0),
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:(pos1 = pos2 = offset = 0),
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sam_metainfo_actions
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) |> eval
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@ -333,7 +333,7 @@ generate_readheader_function(
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Reader,
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MetaInfo,
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sam_header_machine,
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:(mark1 = mark2 = offset = 0),
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:(pos1 = pos2 = offset = 0),
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merge(sam_metainfo_actions, Dict(
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:metainfo => quote
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resize_and_copy!(record.data, data, upanchor!(stream):p-1)
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@ -345,7 +345,7 @@ generate_readheader_function(
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end,
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:header => :(finish_header = true; @escape),
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:countline => :(linenum += 1),
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:anchor => :(anchor!(stream, p); offset = p - 1))),
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:mark => :(anchor!(stream, p); offset = p - 1))),
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quote
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if !eof(stream)
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stream.position -= 1 # cancel look-ahead
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@ -354,37 +354,37 @@ generate_readheader_function(
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) |> eval
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const sam_record_actions = Dict(
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:record_qname => :(record.qname = (mark:p-1) .- offset),
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:record_flag => :(record.flag = (mark:p-1) .- offset),
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:record_rname => :(record.rname = (mark:p-1) .- offset),
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:record_pos => :(record.pos = (mark:p-1) .- offset),
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:record_mapq => :(record.mapq = (mark:p-1) .- offset),
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:record_cigar => :(record.cigar = (mark:p-1) .- offset),
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:record_rnext => :(record.rnext = (mark:p-1) .- offset),
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:record_pnext => :(record.pnext = (mark:p-1) .- offset),
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:record_tlen => :(record.tlen = (mark:p-1) .- offset),
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:record_seq => :(record.seq = (mark:p-1) .- offset),
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:record_qual => :(record.qual = (mark:p-1) .- offset),
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:record_field => :(push!(record.fields, (mark:p-1) .- offset)),
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:record_qname => :(record.qname = (pos:p-1) .- offset),
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:record_flag => :(record.flag = (pos:p-1) .- offset),
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:record_rname => :(record.rname = (pos:p-1) .- offset),
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:record_pos => :(record.pos = (pos:p-1) .- offset),
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:record_mapq => :(record.mapq = (pos:p-1) .- offset),
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:record_cigar => :(record.cigar = (pos:p-1) .- offset),
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:record_rnext => :(record.rnext = (pos:p-1) .- offset),
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:record_pnext => :(record.pnext = (pos:p-1) .- offset),
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:record_tlen => :(record.tlen = (pos:p-1) .- offset),
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:record_seq => :(record.seq = (pos:p-1) .- offset),
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:record_qual => :(record.qual = (pos:p-1) .- offset),
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:record_field => :(push!(record.fields, (pos:p-1) .- offset)),
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:record => quote
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resize_and_copy!(record.data, data, 1:p-1)
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record.filled = (offset+1:p-1) .- offset
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end,
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:anchor => :(),
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:mark => :(mark = p)
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:mark => :(),
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:pos => :(pos = p)
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)
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generate_index_function(
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Record,
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sam_record_machine,
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:(mark = offset = 0),
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:(pos = offset = 0),
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sam_record_actions
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) |> eval
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generate_read_function(
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Reader,
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sam_body_machine,
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:(mark = offset = 0),
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:(pos = offset = 0),
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merge(sam_record_actions, Dict(
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:record => quote
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resize_and_copy!(record.data, data, upanchor!(stream):p-1)
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@ -393,6 +393,6 @@ generate_read_function(
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@escape
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end,
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:countline => :(linenum += 1),
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:anchor => :(anchor!(stream, p); offset = p - 1))
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:mark => :(anchor!(stream, p); offset = p - 1))
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)
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) |> eval
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