weinstockj

import os
output_vcf_dir = "output_vcfs"
bcf_dir = "freeze.8/phased/"
nwd_file = "vcf-split/10-samples.txt"
vcf_split_binary = "vcf-split/bin/vcf-split"
ad2vcf_binary = "ad2vcf/bin/ad2vcf"
cram_path_binary="bin/topmedpath.pl"

if not os.path.exists(bcf_dir):
    IOError(f"{bcf_dir} does not exist")

weinstockj

ADMM_box_eq_QP = function(Dmat, dvec, Amat, bvec, 
                          lb, ub, rho = 1, max.iter = 1e5, tol = 1e-8) {
  
  n <- length(dvec)
  m <- length(bvec)
  stopifnot(dim(Amat) == c(m,n) && dim(Dmat) == c(n, n)) ## sanity checking
  x0 = rep(0, n)
  
  x <- x0 ## initial value of 
  z <- x0 ## initial value of z

weinstockj

task subset_vcf {
    File vcf
    File tabix
    File bed
    String basename
    Int disk_size
    Int preemptible_tries

    command <<<
        echo "basename is: ${basename}"