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Package level documentation -- helps new users get acclimated to the codebase more quickly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1029 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2009-06-17 16:27:48 +00:00
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java/src/org/broadinstitute/sting/gatk/datasources/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Provides efficient access to GATK primary data sources
such as SAM files, fasta files, and reference-ordered data.
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java/src/org/broadinstitute/sting/gatk/datasources/providers/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Provides a bridge from the block-at-a-time data access provided by
the datasource system to the locus / read-at-a-time data access
required by the traversal engine.
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java/src/org/broadinstitute/sting/gatk/datasources/shards/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Divides core input data into manageable blocks, each representing
a subsection of data that is small enough to be processed by a single
worker.
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java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Retrieves core GATK data, given a shard which represents a contiguous
subsequence of core GATK data (reads, reference, or reference-ordered
data).
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java/src/org/broadinstitute/sting/gatk/traversals/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Traverses over a shard of data, performing a mini-map/reduce on that
dataset.
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java/src/org/broadinstitute/sting/utils/cmdLine/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Parses a wide variety of command-line arguments in single-pass and
multipass strategies.
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java/src/org/broadinstitute/sting/utils/fasta/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Provides services and utilities for fast random access to reference
sequence files.
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java/src/org/broadinstitute/sting/utils/io/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Provides general-purpose tools for handling freeform access to files
on disk.
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java/src/org/broadinstitute/sting/utils/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Provides tools that have use across a wide range of Sting and
GenomeAnalysisTK applications and tools.
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java/src/org/broadinstitute/sting/utils/sam/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Generates mock reads, headers, and other read-oriented data, largely
for consumption by the unit testing framework.
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java/src/org/broadinstitute/sting/utils/threading/package.html 100644
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
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Provides tools for managing threads, thread pools, and parallelization
in general.
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