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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.