cboursnell

java -ea -Xmx31g -Dsamjdk.create_index=true -Dsamjdk.use_async_io_read_samtools=true -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=true -Dsamjdk.compression_level=1 -cp gridss-1.4.1-jar-with-dependencies.jar gridss.CallVariants TMP_DIR=. WORKING_DIR=. REFERENCE_SEQUENCE=genome.fa INPUT=normal.sort.bam INPUT=tumour.sort.bam OUTPUT=test04 ASSEMBLY=assembly_output | tee -a gridss.log
[Mon Aug 07 15:11:00 BST 2017] gridss.CallVariants OUTPUT=test04 ASSEMBLY=assembly_output INPUT=[normal.sort.bam, tumour.sort.bam] WORKING_DIR=. TMP_DIR=[.] REFERENCE_SEQUENCE=genome.fa    READ_PAIR_CONCORDANT_PERCENT=0.995 WORKER_THREADS=8 IGNORE_DUPLICATES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=1 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Mon Aug 07 15:11:00 BST 2017] Executing as boursn01@nm16bs014739 on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-2ubuntu1.16.04.3-

cboursnell

var sets = new Array();

function run() {
  put_things_in_array();
  print_things_from_array();
}

function put_things_in_array() {
  for(var i = 0 ; i < 10; i++) {
    var obj = new Array();

cboursnell

#!/usr/bin/env ruby

# simulate paired end reads from a reference

require 'trollop'
require 'rubystats'

ARGV[0] = "--help" if ARGV.length() == 0

opts = Trollop::options do

cboursnell

def segment seq, k, path
  if k==0
    path << seq
    p path
    # puts "k==0\t#{seq}"
  else
    (0..seq.length-k-1).each do |i|
      # puts "seq = #{seq}, k == #{k}, i == #{i}"
      pa = path.clone
      left = seq[0..i]

cboursnell

#!/usr/bin/env	ruby

require 'helper'

class TestBetterSam < Test::Unit::TestCase

  context "BetterSam" do

    setup do
      # this is run before each test