bicycle1885

" General
syntax enable
set nocompatible
set noswapfile
if executable("rg")
    set grepprg=rg\ --vimgrep\ --no-heading
    set grepformat=%f:%l:%c:%m,%f:%l:%m
endif
autocmd QuickFixCmdPost * copen
nnoremap <silent> <C-n> :cn<CR>

bicycle1885

# Randomized SVD
# --------------
#
# H. Li, G. C. Linderman, et al. "Algorithm 971: An Implementation of a
# Randomized Algorithm for Principal Component Analysis", ACM Transactions on
# Mathematical Software (TOMS), 2017
# DOI: https://doi.org/10.1145/3004053
#
# N. Halko, P. G. Martinsson, and J. A. Tropp, "Finding Structure with
# Randomness: Probabilistic Algorithms for Constructing Approximate Matrix

bicycle1885

quote 
    if p > p_end
        @goto exit
    end
    ##667 = (Automa.SizedMemory)(data)
    if cs == 1
        @goto state_case_1
    else 
        if cs == 2
            @goto state_case_2

bicycle1885

# License: MIT

module Base64

export
    Base64EncodePipe,
    base64encode

# Data buffer for pipes.
mutable struct Buffer

bicycle1885

import NamedTuples: NamedTuples, @NT

# Atom
# ----

# NOTE: This must be synchronized with `AtomCoords`.
struct Atom
    id::Int32
    x::Float32
    y::Float32

bicycle1885

using CodecZlib
using BioSequences

function readfasta(filepath)
    open(GzipDecompressionStream, filepath) do stream
        reader = FASTA.Reader(stream)
        for record in reader
            id  = FASTA.identifier(record)
            seq = FASTA.sequence(record)
            @show id, seq

bicycle1885

using Bio.Seq
import DataStructures: SortedSet

immutable MinHashSketch
    sketch::Vector{UInt64}
    kmersize::Int

    function MinHashSketch(sketch::Vector, kmersize::Int)
        length(sketch) > 0 || error("Sketch cannot be empty")
        kmersize > 0 || error("Kmersize must be greater than 0")

bicycle1885

import Automa
import Automa.RegExp: @re_str
import BufferedStreams
import BufferedStreams: BufferedInputStream
import Bio

const fastq_machine = (function ()
    re   = Automa.RegExp
    cat  = re.cat
    rep  = re.rep

bicycle1885

import Automa
import Automa.RegExp: @re_str
const re = Automa.RegExp

# VCF v4.2
const vcf_machine = (function ()
    delim(x, sep) = re.opt(re.cat(x, re.rep(re.cat(sep, x))))

    nl = re"\n"
    newline = re"\r?" * nl

bicycle1885

using Automa
using Automa.RegExp
const re = Automa.RegExp

length = re"[0-9]+\.[0-9]+"
name = re.rep1(re"[!-~]" \ re"[,:;()[\]]")
spaces = re" +"

const newick = compile(
    re"\(" => :(emit(:lparen)),