Pall Melsted pmelsted

## measure-memory.pl
#!/usr/bin/perl

my $cmd = 'strace -e trace=mmap,munmap,brk ';
for my $arg (@ARGV) {
    $arg =~ s/'/'\\''/g;
    $cmd .= " '$arg'";
}
$cmd .= ' 2>&1 >/dev/null';
open( PIPE, "$cmd|" ) or die "Cannot execute command \"$cmd\"\n";

## DebuggingKallisto.md

      
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                pmelsted
                / DebuggingKallisto.md
            
            
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              November 2, 2015 15:03
            
              
                Debugging kallisto with gdb
              
          
    You can debug kallisto with gdb and valgrind even if you can't compile it on your machine.
In order to do this you need to download the Debuggable binary, which is found on this gist.
You also need to place the source code in the same directory as where you will be debugging
wget https://github.com/pachterlab/kallisto/archive/v0.42.4.tar.gz
tar xzvf v0.42.4.tar.gz


## gist:4721991
De Bruijn graph toy example

Genome:
ATGAAGTGGGTAAC

Reads:
ATGAAGTGGG
   TAGTGGGTAA
    AGTGCGTAAC
	#!/usr/bin/perl

	my $cmd = 'strace -e trace=mmap,munmap,brk ';
	for my $arg (@ARGV) {
	$arg =~ s/'/'\\''/g;
	$cmd .= " '$arg'";
	}
	$cmd .= ' 2>&1 >/dev/null';
	open( PIPE, "$cmd\|" ) or die "Cannot execute command \"$cmd\"\n";
	De Bruijn graph toy example

	Genome:
	ATGAAGTGGGTAAC

	Reads:
	ATGAAGTGGG
	TAGTGGGTAA
	AGTGCGTAAC