noporpoise

#!/usr/bin/env python
# coding=utf-8
# License: Public domain (CC0)
# Isaac Turner 2016/12/05

from __future__ import print_function

import difflib
import re

panzi

// "License": Public Domain
// I, Mathias Panzenböck, place this file hereby into the public domain. Use it at your own risk for whatever you like.
// In case there are jurisdictions that don't support putting things in the public domain you can also consider it to
// be "dual licensed" under the BSD, MIT and Apache licenses, if you want to. This code is trivial anyway. Consider it
// an example on how to get the endian conversion functions on different platforms.

#ifndef PORTABLE_ENDIAN_H__
#define PORTABLE_ENDIAN_H__

#if (defined(_WIN16) || defined(_WIN32) || defined(_WIN64)) && !defined(__WINDOWS__)

cschin

(1) If we use Celera Assembler's bogart unitiger, it will generate a file called "bests.edges" in the "4-unitigger" as one of its output directories.

(2) I wrote a simple script converting the edge list to a GML. The script can be downloaded https://github.com/PacificBiosciences/HBAR-DTK/blob/master/src/CA_best_edge_to_GML.py  

(3) Load the graph into gephi (https://gephi.org/)

(4) I typically use the following steps of different layout algorithms in Gephi to get a good layout, 

1) "YifanHu's Multilevel" to get a rough layout, the output usually catches good large scale structure and detangle the graph reasonably one so I can start to see features of the assembly overlap graph (or the string graph.)

adamjohnson

"Help, I keep getting a 'Permission Denied (publickey)' error when I push!"

This means, on your local machine, you haven't made any SSH keys. Not to worry. Here's how to fix:

1. Open git bash (Use the Windows search. To find it, type "git bash") or the Mac Terminal. Pro Tip: You can use any *nix based command prompt (but not the default Windows Command Prompt!)
2. Type cd ~/.ssh. This will take you to the root directory for Git (Likely C:\Users\[YOUR-USER-NAME]\.ssh\ on Windows)
3. Within the .ssh folder, there should be these two files: id_rsa and id_rsa.pub. These are the files that tell your computer how to communicate with GitHub, BitBucket, or any other Git based service. Type ls to see a directory listing. If those two files don't show up, proceed to the next step. NOTE: Your SSH keys must be named id_rsa and id_rsa.pub in order for Git, GitHub, and BitBucket to recognize them by default.
4. To create the SSH keys, type ssh-keygen -t rsa -C "your_email@example.com". Th

ashelly

//Copyright (c) 2011 ashelly.myopenid.com under <http://www.opensource.org/licenses/mit-license>
 
#include <stdlib.h>
 
//Customize for your data Item type
typedef int Item;
#define ItemLess(a,b)  ((a)<(b))
#define ItemMean(a,b)  (((a)+(b))/2)
 
typedef struct Mediator_t

churchofthought

void strrev(char *strStart, const int len){
    
    char* strEnd = strStart + len;
    
    while (strStart <= (strEnd -= 8)){
        
        __uint64_t buf = *(__uint64_t*)strStart;
        
        *(__uint64_t*)strStart = *(__uint64_t*)strEnd;
        __asm__ ("bswap %0" : "=r" (*(__uint64_t*)strStart) : "0" (*(__uint64_t*)strStart));

willwade

#!/usr/bin/env python
# Contact: Will Wade willwa.de
# Date: April 2013
# Needs mechanize and pybtex
#
# NB: Little error checking going on in this script
# TO-DO: Check last-download-date of bibtex file later than last-modified date on CUL. ? possible
# 
# With thanks to https://pypi.python.org/pypi/citeulike_api/0.1.3dev for the login part 
import mechanize

kconragan

# Mac OS X Lion introduced a new, iOS-like context menu when you press and hold a key
# that enables you to choose a character from a menu of options. If you are on Lion
# try it by pressing and holding down 'e' in any app that uses the default NSTextField
# for input.
#
# It's a nice feature and continues the blending of Mac OS X and iOS features. However,
# it's a nightmare to deal with in Sublime Text if you're running Vintage (Vim) mode,
# as it means you cannot press and hold h/j/k/l to move through your file. You have
# to repeatedly press the keys to navigate.