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

#!/usr/bin/env perl

use strict;
use warnings;

die("Usage: gem2sam.pl <gem.map>\n") if (@ARGV == 0 && -t STDIN);

while (<>) {
	chomp;
	my @t = split("\t");

lh3

#!/usr/bin/env perl

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

my %opts = (t=>8, k=>17, m=>0.6, s=>200, p=>'wtasm');
getopts('t:p:k:m:s:', \%opts);
die (qq/Usage: smartdenovo.pl [options] <reads.fa>
Options:

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

Writing a program for efficient matrix multiplication is tricky. A naive implementation usually looks like this (I will use a square matrix for simplicity):

for (i = 0; i < n; ++i)
  for (j = 0; j < n; ++i)
    for (k = 0, m[i][j] = 0.; k < n; ++i)
      m[i][j] += a[i][k] * b[k][j];

The problem is the inner loop a[i][k] * b[k][j] where b[k][j] and b[k+1][j] are not adjacent in memory. This leads to frequent cache misses for large matrices. The better implementation is to transpose matrix b. The implementation will look like:

for (i = 0; i < n; ++i) // transpose

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

Table of Contents

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

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

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