Phrap is a program for assembling shotgun DNA sequence data.
Among other features, it allows use of the entire read and not just the
trimmed high quality part, it uses a combination of user-supplied and
internally computed data quality information to improve assembly accuracy
in the presence of repeats, it constructs the contig sequence as a mosaic
of the highest quality read segments rather than a consensus, it provides
extensive assembly information to assist in trouble-shooting assembly
problems, and it handles large datasets.
This package also contains Swat and Cross_match.
Swat is a program for searching one or more DNA or protein query sequences
against a sequence database, using (an efficient implementation of) the
Smith-Waterman-Gotoh algorithm.
Cross_Match is a general-purpose utility based on Swat for comparing any
two sets of DNA sequences, and it can be used to:
* produce vector-masked versions of a set of reads
* compare a set of cDNA sequences to a set of cosmids
* compare contigs found by two altanative assembly procedures to each other
* compare phrap contigs to the final edited cosmid sequence.
sgf2tex is a system for typesetting Go games and diagrams using TeX. This
system may be used with either plain TeX or LaTeX. It includes the Metafont
sources for a new set of Go fonts, and a Perl script called Sgf2tex which
translates files in ``Smart Go Format'' (SGF) into TeX.
WebJob downloads a program or script from a remote WebJob server
over HTTP/HTTPS and executes it in one unified operation. Any output
produced by the program/script is packaged up and sent to a remote,
possibly different, WebJob server. WebJob is useful because it
provides a mechanism for running known good programs on damaged or
potentially compromised systems. This makes it ideal for remote
diagnostics, incident response, and evidence collection. WebJob
also provides a framework that is conducive to centralized management.
Therefore, it can support and help automate a large number of common
administrative tasks and host-based monitoring scenarios such as
periodic system checks, file updates, integrity monitoring,
patch/package management, and so on.
HTML::GenToc generates anchors and a table of contents for
HTML documents. Depending on the arguments, it will insert
the information it generates, or output to a string, a separate file
or STDOUT.
While it defaults to taking H1 and H2 elements as the significant
elements to put into the table of contents, any tag can be defined
as a significant element. Also, it doesn't matter if the input
HTML code is complete, pure HTML, one can input pseudo-html
or page-fragments, which makes it suitable for using on templates
and HTML meta-languages such as WML.
Also included in the distrubution is hypertoc, a script which uses the
module so that one can process files on the command-line in a
user-friendly manner.
Bcg729 is a software G729A encoder and decoder library written in C, developed
by Belledonne Communications, the company supporting the Linphone project.
It was written from scratch and is NOT a derivative work of ITU reference
source code in any kind.
It can be executed on many platforms, including both ARM and x86 with very
decent performances. libbcg729 supports concurrent channel encoding/decoding
for multi-call applications such as conferencing.
zssh (Zmodem SSH) is a program for interactively transferring files to a
remote machine while using the secure shell (ssh). It is intended to be a
convenient alternative to scp, allowing to transfer files without having to
open another session and re-authenticate oneself. zssh is an interactive
wrapper for ssh used to switch the ssh connection between the remote shell
and file transfers. Files are transferred through the zmodem protocol,
using the rz and sz commands.
Go-Json-Rest is a thin layer on top of net/http that helps building RESTful
JSON APIs easily. It provides fast URL routing using a Trie based
implementation, and helpers to deal with JSON requests and responses. It is
not a high-level REST framework that transparently maps HTTP requests
to procedure calls, on the opposite, you constantly have access to the
underlying net/http objects.
Data::Hexdumper provides a simple way to format and display arbitrary binary
data in a way similar to how some debuggers do for lesser languages. It
gives the programmer a considerable degree of flexibility in how the data is
formatted, with sensible defaults. It is envisaged that it will primarily be
of use for those wrestling alligators in the swamp of binary file formats,
which is why it was written in the first place.
Normally if a part of a pipe fails, depending on the location, it won't
be detected. This breaks down a command involving pipes and runs each
command separately.
It uses open3 to run each chunk of the pipe.
use IO::MultiPipe;
my $pipes = IO::MultiPipe->new();
#This sets the pipe that will be run.
$pipes->set('sed s/-// | sed s/123/abc/ | sed s/ABC/abc/');
if ($pipes->{error}){
print "Error!\n";
}
#'123-ABCxyz' through the command set above.
my $returned=$pipes->run('123-ABCxyz');
This module is a simple interface to extensible logging. It is
bundled with a really basic logger, Log::Contextual::SimpleLogger, but
in general you should use a real logger instead of that. For
something more serious but not overly complicated, try
Log::Dispatchouli (see "SYNOPSIS" for example.)
The reason for this module is to abstract your logging interface so
that logging is as painless as possible, while still allowing you to
switch from one logger to another.