faidx.sublime-syntax

%YAML 1.2
---
# Fasta Index (faidx) syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: faidx
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions: [fai,fai]
scope: source.faidx

# Fasta Index Filetype Description
# NAME  Name of this reference sequence
# LENGTH  Total length of this reference sequence, in bases
# OFFSET  Offset within the FASTA file of this sequence's first base
# LINEBASES The number of bases on each line
# LINEWIDTH The number of bytes in each line, including the newline

contexts:
  main:
    # COLUMN 1
    - match: '^[\S]*\t'
      scope: chr.faidx
      push: contig.length

    # COLUMN 3
    - match: '(?<=\t)[\S]*\t'
      scope: numeric.faidx
      push: genomic.offset

    # COLUMN 5
    - match: '[\S]*$'
      scope: comment.faidx

  contig.length:
    # COLUMN 2
    - match: '[\S]*'
      scope: chrStart.faidx
    - match: \t
      pop: true

  genomic.offset:
    # COLUMN 4
    - match: '[\S]*'
      scope: comment.faidx
    - match: \t
      pop: true