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" Vim syntax file
" Language: VCF v4.3
" Filetypes: .vcf
" Maintainer: bioSyntax
" Version: v0
"TODO
" Set vim sync mode so it can deal with long lines
if exists("syntax_on")
syntax reset
" VCF syntax is per-line so restrict context to one line
syntax sync minlines=1
colorscheme bioSyntax
" VCF are wide files; remove word-wrapping
set nowrap
endif
" Syntax Organization
" Use 'containedin=' when a syntax defintion must only be matched within only one region
" Use 'contained' when a syntax definition may be matched from two or more regions
" All region definitions are limited to 'oneline' in VCF
" VCF DATA Selection
" =========================================================
"
" Column 1: LONG LINE FAILSAFE (no highlight)
syntax region FAILSAFE start='^' end='$' contains=COL2
" Column 1: CHROM
syntax region chr start='^[^#]' end='$' oneline contains=COL2
" Column 2: POS
syntax region COL2 matchgroup=COL2 start='\t' end='\n\@=' oneline contained contains=COL3
syntax region chrStart start='\t\@<=[0-9]' end='[\n\t]\@=' contained containedin=COL2
" Column 3: ID
syntax region COL3 matchgroup=COL3 start='\t' end='\n\@=' oneline contained contains=COL4,nt_
syntax region ID start='\t\@<=\S' end='[\n\t]\@=' containedin=COL3
" Column 4: REF
syntax region COL4 matchgroup=COL4 start='\t' end='\n\@=' oneline contained contains=COL5,ntA,ntT,ntG,ntC,ntN,nt_
syntax match ntA '[Aa]' contained
syntax match ntT '[Tt]' contained
syntax match ntG '[Gg]' contained
syntax match ntC '[Cc]' contained
syntax match ntN '[Nn]' contained
syntax match nt_ '\.' contained
" Column 5: ALT
syntax region COL5 matchgroup=COL5 start='\t' end='\n\@=' oneline contained contains=COL6,ntA,ntT,ntG,ntC,ntN,nt_
" Column 6: QUAL
syntax region COL6 matchgroup=COL6 start='\t' end='\n\@=' oneline contained contains=COL7
syntax region QUAL start='\t\@<=[0-9]' end='[\n\t]\@=' oneline containedin=COL6
" Column 7: FILTER
syntax region COL7 matchgroup=COL7 start='\t' end='\n\@=' oneline contained contains=COL8,bon,mal,nt_
" Column 8: INFO
syntax region COL8 matchgroup=COL8 start='\t' end='\n\@=' oneline contained contains=COL9
syntax region INFOtag start='\t\@<=[A-Za-z]' end='[\n\t]\@=' oneline containedin=COL8 contains=numeric,string
" Column 9: FORMAT
syntax region COL9 matchgroup=COL9 start='\t' end='\n\@=' oneline contained contains=COL10
syntax region FORMATtag start='\t\@<=[A-Za-z]' end='[\n\t]\@=' oneline containedin=COL9
" Column 10+: DATA
syntax region COL10 matchgroup=COL10 start='\t' end='\n\@=' oneline contained
" Data Start Header Lines
syntax match header '^#CHROM.\+'
" VCF Header Selection
" =========================================================
"
syntax region comment start='^##' end='\n' oneline contains=header,FILTER,FORMAT,INFO,reference
" First Line Header
syntax region header start='fileformat' end='\n' oneline contained
" FILTER Lines
syntax region FILTER start='FILTER' end='\n' oneline contained contains=string,stringQuote,numeric
" FORMAT Lines
syntax region FORMAT start='FORMAT' end='\n' oneline contained contains=string,stringQuote,numeric
" INFO Lines
syntax region INFO start='INFO' end='\n' oneline contained contains=string,stringQuote,numeric
" Non-specification Lines
syntax region reference start='\(contig=\|reference=\)' end='\n' oneline contained
" Header Submatches (ID, Other Tags, Quote Strings)
syntax region numeric start='=\@<=[^<\"]\@=' end='[,;\t]\@=' oneline contained
syntax region string start='\(ID=\)\@<=' end='[,;\t]\@=' oneline contained
syntax region stringQuote start='\"' end='\"' oneline contained
" Highlighting / Local Link Controls
" =========================================================
highlight link FILTERtag FILTER
highlight link FORMATtag FORMAT
highlight link INFOtag INFO
highlight link QUAL numeric
highlight link ID string
highlight link FILTER keyword1
highlight link FORMAT keyword2
highlight link INFO keyword3
highlight link reference chrStart
highlight link nt_ ntX
highlight link stringQuote quoteString
" Highlighting / Global Theme Control
" =========================================================
" (TO CHANGE THEME COLORS, MODIFY VALUES BELOW ONLY)
"
"highlight numeric ctermfg=31
"highlight string ctermfg=160
"highlight stringQuote ctermfg=160 cterm=italic
"highlight comment ctermfg=08
"highlight header ctermfg=08 ctermbg=250 cterm=bold
"highlight keyword1 ctermfg=130 " Orange
"highlight keyword2 ctermfg=89 " Purple Dark
"highlight keyword3 ctermfg=172 " Yellow
"highlight chr ctermfg=28 cterm=bold
"highlight chrStart ctermfg=28
"highlight ntA ctermfg=Black ctermbg=10 guibg=#272822
"highlight ntG ctermfg=Black ctermbg=214 guibg=#FF8C00
"highlight ntC ctermfg=Black ctermbg=9 guibg=#2A0AFD
"highlight ntT ctermfg=Black ctermbg=33 guibg=#FD0A0A
"highlight ntN ctermfg=Black ctermbg=255 guibg=#FD0A0A
"highlight nt_ ctermfg=Black ctermbg=255 guibg=#000000
|
