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MauricioCarneiro / batch_gamgee_data_structures.cpp
Last active August 29, 2015 14:05
Data structures design example for batch SAM processing in gamgee
/*
Here are the alignment data structures we covered during today’s call. The storage for alignment data looks like this:
*/
template <typename system_tag>
struct BAM_alignment_batch_storage
{
uint32 num_reads;
nvbio::vector<system_tag, cigar_op> cigars;
@MauricioCarneiro
MauricioCarneiro / hts_test.c
Created June 6, 2014 16:52
Quick test for vcf/bcf loading using htslib
#include <stdlib.h>
#include <unistd.h>
#include <stdio.h>
#include "htslib/vcf.h"
int main(int argc, char *argv[])
{
int c, is_sam = 0, is_copy = 0;
long cnt = 0;
vcfFile *fp;
@MauricioCarneiro
MauricioCarneiro / .vimrc
Last active March 12, 2016 09:13
C++11 vim development environment configuration (vimrc)
" Vundle configuration
set nocompatible " be iMproved, required
filetype off " required
set rtp+=~/.vim/bundle/vundle/ " set the runtime path to include Vundle and initialize
call vundle#begin()
" Plugins
Bundle 'gmarik/vundle'
Bundle 'Valloric/YouCompleteMe'
Bundle 'a.vim'