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Vang Le biocyberman

  • Aalborg University
  • Aalborg, Denmark
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View bcbio_nextgen_debug.py
[2013-08-18 09:34] INFO 11:34:24,077 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34] INFO 11:34:24,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34] INFO 11:34:24,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34] INFO 11:34:24,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34] INFO 11:34:24,081 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpn8kdHQ/WES01_WES01_SQ1_FT2-chr19-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-calla
View callable-callableblocks.bed
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1 15669 15990
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@biocyberman
biocyberman / build-emacs.sh
Last active Jul 26, 2019 — forked from favadi/build-emacs.sh
Compile latest emacs version in Ubuntu Precise, Trusty ...
View build-emacs.sh
#!/bin/bash
# Build latest version of Emacs, version management with stow
# OS: Tested on Ubuntu 12.04 LTS onward
# version: 25.1
# Toolkit: lucid
set -e
readonly version="26.2"
View emacs byobu ssh true color setup
running ediff over byobu ssh sessions has poor colors. I can't see color markings, therefore it's difficult to do diff and merge.
For emacs itself
https://gist.github.com/choppsv1/e8198df70cb1778b04d6 (Managed to improved color without this patch)
remove ubuntu tmux
tmux upgrade from github https://github.com/tmux/tmux. Also need to compile and install http://libevent.org/ for tmux
For bybou
View QDNAseq.R
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
# test if there is at least one argument: if not, return an error
if (length(args)==0) {
stop("Please provide prefix for output", call.=FALSE)
} else if (length(args)==1) {
## default bin size
args[2] = 500
}
@biocyberman
biocyberman / mixinbenchmark.d
Last active Sep 20, 2018
An example of function bechmarking in D for various ways of emplementing mixins
View mixinbenchmark.d
import std.stdio;
import std.conv : to;
import std.datetime.stopwatch: benchmark, Duration;
mixin template kroundup32(T) {
// string mstr = "String from template";
void kroundup32(ref T x){
// pragma(inline, true);
--x;
x|=x>>1;
View annotateBed.R
#!/usr/bin/env Rscript
## Date: Tue Aug 7 10:43:27 2018
## Last modified Time-stamp: <2018-08-10 12:54:38 CEST (vql)>
## Author: Vang Quy Le
## Organization: Aalborg University Hospital
## Copyright 2018 Vang Quy Le
##
## This file is free software: you may copy, redistribute and/or modify it
## under the terms of the GNU General Public License as published by the
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