lh3

#include <unistd.h>
#include <assert.h>
#include <stdlib.h>
#include <stdio.h>
#include "kstring.h"
#include "sam.h"
#include "kbtree.h"

typedef struct {
	int pos, n, sum;

lh3

#include <stddef.h>
#include <stdio.h>
#include <string.h>
#include "getopt.h"

char *optarg;
int optind=1, opterr=1, optopt, __optpos, optreset=0;

#define optpos __optpos

lh3

#!/usr/bin/env perl

use strict;
use warnings;
use Getopt::Std;

my %opts = ();
getopts('fd:', \%opts);

die("Usage: pexe.pl [options] <exe1> [exe2 [...]]

lh3

# OUTSIDE VM: launch an instance
gcloud compute instances create lh3test --machine-type n1-standard-1 --image-project ubuntu-os-cloud --image-family ubuntu-1604-lts

#
# INSIDE VM!!!
#

# install dependencies
sudo apt-get update
sudo apt-get install libboost-all-dev cmake libstdc++6 clang-3.8 cmake git-all python3 zlib1g-dev

lh3

Table of Contents

• Introduction
• Terminologies
• GFA: Mandatory Fields
  • Segment line
  • Link line
  • Gap line
  • Match line
• TODO

lh3

#!/usr/bin/perl

use strict;
use warnings;
use Getopt::Std;

my %opts = (t=>'ct', m=>50);
getopts('t:m:3', \%opts);

my $type;

lh3

var getopt = function(args, ostr) {
	var oli; // option letter list index
	if (typeof(getopt.place) == 'undefined')
		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
	if (getopt.place == -1) { // update scanning pointer
		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
			getopt.place = -1;
			return null;
		}
		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"

lh3

#!/usr/bin/env perl

use strict;
use warnings;
use Getopt::Std;

my %opts = (g=>37, l=>2, L=>100);
getopts('g:l:L:o:Huc', \%opts);

# check path

lh3

Source	Dst. file type	Protocol	Time (s)	Command Line
NCBI	.sra	ftp	296	wget
NCBI	.fastq.gz	sra toolkit	~23000	fastq-dump -Z --gzip --split-spot
local file	sra=>fastq.gz	sra toolkit	~15000	fastq-dump --gzip --split-spot --split-3
EBI	.fastq.gz	aspera	513+492	aspera -QT -l 300m
EBI	.fastq.gz	ftp	1876+1946	wget

Notes:

lh3

This gist demonstrates fast BAM slicing without re-compressing the alignment data. It only works for BAMs generated by samtools-0.1.8+ and htslib, as it requires the BAM to be block aligned.

To use this gist, you need to first acquire and compile htslib. After that:

cd htslib; gcc -g -O2 -Wall -o fsi -I. /path/to/fsi.c libhts.a -lz
./fsi aln.bam > aln.fsi
perl fsi-get.pl aln.bam aln.fsi chr11:1000000-1200000 > slice.bam