SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. This library provides classes to manipulate SAM and BAM files. A command line wrapper for this library is provided in the picard-tools package.

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This package is a helper function for the other Starjava packages. It contains a number of helper and utility classes that don’t fit elsewhere. Classes include some basic functionality like lists for Java primitives, input/output classes, gui classes, DTD and xsd etc.

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Eclipse Platform defines the set of frameworks and common services that collectively make up infrastructure required to support the use of Eclipse as a component model, as a Rich Client Platform (RCP) and as a comprehensive tool integration platform. The core component provides basic platform infrastructure that does …

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Bi-directional URI dispatch. Like compojure, but when you want to go both ways. If you are serving REST resources, you should be providing links to other resources, and without full support for forming URIs from handlers your code will become coupled with your routing. In short, hard-coded URIs will eventually break. …

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Cheshire is a fast JSON encoding library for Clojure, based off of clj-json and clojure-json, with additional features like Date/UUID/Set/Symbol encoding and SMILE support. It offers the speed of clj-json and the features of clojure-json.

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Executing external processes from Java is a well-known problem area. It is inherently platform dependent and requires the developer to know and test for platform specific behaviors, for example using cmd.exe on Windows or limited buffer sizes causing deadlocks. The JRE support for this is very limited, albeit better …

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HdrHistogram is designed for recording histograms of value measurements in latency and performance sensitive applications. It supports the recording and analyzing of sampled data value counts across a configurable integer value range with configurable value precision within the range. Value precision is expressed as …

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