This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across...

• Bio::DB::Sam::Constants - Constants for use with SAM/BAM
• lib/Bio/DB/Sam/SamToGBrowse.pm
• lib/Bio/DB/Sam/Segment.pm
• 8 more results from Bio-SamTools »

This object implements methods to read a sam file line by line....

• GenOO::RegionCollection::Factory::SAM - Factory for creating GenOO::RegionCollection object from a SAM file
• GenOO::Data::File::SAM::MDZ - Role - The MD:Z tag in a SAM file
• GenOO::Data::File::SAM::Cigar - Role that corresponds to the SAM file CIGAR string
• 3 more results from GenOO »

• App::Sandy::Command::Transcriptome - simulate command class. Simulate transcriptome sequencing

• Parse::SAMGov::Mo
• Parse::SAMGov::Entity - Object to denote each Entity in SAM
• Parse::SAMGov::Exclusion - defines the SAM Exclusions object
• 3 more results from Parse-SAMGov »

Filesys::SamFS makes the SamFS API available to Perl. SamFS is a HSM (Hierarchical Storage Management) Filesystem; it manages files in two storage levels - a cache on disks and an archive on removable media like magneto-optical disks or tapes. SamFS ...

Download, build, and install the SamTools C headers and libraries into a well-known location, "File::ShareDir::dist_dir('Alien-SamTools')", from whence other packages can make use of them. It currently installs samtools-0.1.19.tar.bz2 <http://colocro...

Reader for SAM format, including CRAC special fields....

• CracTools::SAMReader::SAMline - The object for manipulation a SAM line.
• CracTools - A set of tools designed to extract data from CRAC's SAM files and to provide annotations.
• CracTools::Utils - A set of useful functions
• 3 more results from CracTools »

This class implements directly so-called *materialized* topic maps, i.e. those maps which completely reside in memory. Non-materialized and non-materializable maps can be implemented by deriving from this class by overloading one or all of the sub-in...

• TM::DM - Topic Maps, read-only TMDM layer

Catalyst is a modern framework for making web applications without the pain usually associated with this process. This document is a reference to the main Catalyst application. If you are a new user, we suggest you start with Catalyst::Manual::Tutori...

DateTime is a class for the representation of date/time combinations, and is part of the Perl DateTime project. For details on this project please see <http://datetime.perl.org/>. The DateTime site has a FAQ which may help answer many "how do I do X?...

Many Perl release announcements included an *epigraph*, a short excerpt from a literary or other creative work, chosen by the pumpking or release manager. This file assembles the known list of epigraph for posterity, and also links to the release ann...

• perlepigraphs - list of Perl release epigraphs
• perl5160delta - what is new for perl v5.16.0
• perl5160delta - what is new for perl v5.16.0
• 6 more results from perl »

Jail - Just an_other Image Library This extension is running _only_ on SGI IRIX systems. You need the Image Vision Library, Video Library and STL. You need a X11 Display _only_ if you want to display an image. The newest version you can get under htt...

Oryx is an object persistence framework which supports both object-relational mapping as well as DMB style databases and as such is not coupled with any particular storage back-end. In other words, you should be able to swap out an RDMBS with a DBM s...

• Oryx::Class - abstract base class for Oryx classes

Moose is an extension of the Perl 5 object system. The main goal of Moose is to make Perl 5 Object Oriented programming easier, more consistent, and less tedious. With Moose you can think more about what you want to do and less about the mechanics of...

• Moose::Manual::Resources - Links to various tutorials, videos, blogs, presentations, interviews, etc...

Background Perl "one-liners" have a great many uses for quick data processing tasks, often replacing the UNIX tools "grep", "sed", and "awk". For example, a simple "grep" function can be written as: perl -lne '/pattern/ and print' file.txt which impr...

A reverse-chronological ordered list of changes...

The Spreadsheet::WriteExcel Perl module can be used to create a cross-platform Excel binary file. Multiple worksheets can be added to a workbook and formatting can be applied to cells. Text, numbers, formulas, hyperlinks, images and charts can be wri...

The "Class::Generate" package exports functions that take as arguments a class specification and create from these specifications a Perl 5 class. The specification language allows many object-oriented constructs: typed members, inheritance, private m...