From 43a28750e0da0109cc266c705d4d8889e7d45208 Mon Sep 17 00:00:00 2001 From: hanna Date: Wed, 17 Jun 2009 16:27:48 +0000 Subject: [PATCH] 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 --- .../sting/gatk/datasources/package.html | 11 +++++++++++ .../sting/gatk/datasources/providers/package.html | 12 ++++++++++++ .../sting/gatk/datasources/shards/package.html | 12 ++++++++++++ .../gatk/datasources/simpleDataSources/package.html | 12 ++++++++++++ .../sting/gatk/traversals/package.html | 11 +++++++++++ .../broadinstitute/sting/utils/cmdLine/package.html | 11 +++++++++++ .../broadinstitute/sting/utils/fasta/package.html | 11 +++++++++++ .../org/broadinstitute/sting/utils/io/package.html | 11 +++++++++++ java/src/org/broadinstitute/sting/utils/package.html | 11 +++++++++++ .../org/broadinstitute/sting/utils/sam/package.html | 11 +++++++++++ .../sting/utils/threading/package.html | 10 ++++++++++ 11 files changed, 123 insertions(+) create mode 100644 java/src/org/broadinstitute/sting/gatk/datasources/package.html create mode 100644 java/src/org/broadinstitute/sting/gatk/datasources/providers/package.html create mode 100644 java/src/org/broadinstitute/sting/gatk/datasources/shards/package.html create mode 100644 java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/package.html create mode 100644 java/src/org/broadinstitute/sting/gatk/traversals/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/cmdLine/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/fasta/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/io/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/sam/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/threading/package.html diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/package.html b/java/src/org/broadinstitute/sting/gatk/datasources/package.html new file mode 100644 index 000000000..c60831f50 --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/datasources/package.html @@ -0,0 +1,11 @@ + + + + + + +Provides efficient access to GATK primary data sources +such as SAM files, fasta files, and reference-ordered data. + + + diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/package.html b/java/src/org/broadinstitute/sting/gatk/datasources/providers/package.html new file mode 100644 index 000000000..eddb660b2 --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/package.html @@ -0,0 +1,12 @@ + + + + + + +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. + + + diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/package.html b/java/src/org/broadinstitute/sting/gatk/datasources/shards/package.html new file mode 100644 index 000000000..e13aba69a --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/package.html @@ -0,0 +1,12 @@ + + + + + + +Divides core input data into manageable blocks, each representing +a subsection of data that is small enough to be processed by a single +worker. + + + diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/package.html b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/package.html new file mode 100644 index 000000000..21587f902 --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/package.html @@ -0,0 +1,12 @@ + + + + + + +Retrieves core GATK data, given a shard which represents a contiguous +subsequence of core GATK data (reads, reference, or reference-ordered +data). + + + diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/package.html b/java/src/org/broadinstitute/sting/gatk/traversals/package.html new file mode 100644 index 000000000..82ff0a1f9 --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/traversals/package.html @@ -0,0 +1,11 @@ + + + + + + +Traverses over a shard of data, performing a mini-map/reduce on that +dataset. + + + diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/package.html b/java/src/org/broadinstitute/sting/utils/cmdLine/package.html new file mode 100644 index 000000000..614fc2002 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/cmdLine/package.html @@ -0,0 +1,11 @@ + + + + + + +Parses a wide variety of command-line arguments in single-pass and +multipass strategies. + + + diff --git a/java/src/org/broadinstitute/sting/utils/fasta/package.html b/java/src/org/broadinstitute/sting/utils/fasta/package.html new file mode 100644 index 000000000..28b4e499b --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/fasta/package.html @@ -0,0 +1,11 @@ + + + + + + +Provides services and utilities for fast random access to reference +sequence files. + + + diff --git a/java/src/org/broadinstitute/sting/utils/io/package.html b/java/src/org/broadinstitute/sting/utils/io/package.html new file mode 100644 index 000000000..aec310579 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/io/package.html @@ -0,0 +1,11 @@ + + + + + + +Provides general-purpose tools for handling freeform access to files +on disk. + + + diff --git a/java/src/org/broadinstitute/sting/utils/package.html b/java/src/org/broadinstitute/sting/utils/package.html new file mode 100644 index 000000000..f9591fa99 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/package.html @@ -0,0 +1,11 @@ + + + + + + +Provides tools that have use across a wide range of Sting and +GenomeAnalysisTK applications and tools. + + + diff --git a/java/src/org/broadinstitute/sting/utils/sam/package.html b/java/src/org/broadinstitute/sting/utils/sam/package.html new file mode 100644 index 000000000..9aaac573a --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/sam/package.html @@ -0,0 +1,11 @@ + + + + + + +Generates mock reads, headers, and other read-oriented data, largely +for consumption by the unit testing framework. + + + diff --git a/java/src/org/broadinstitute/sting/utils/threading/package.html b/java/src/org/broadinstitute/sting/utils/threading/package.html new file mode 100644 index 000000000..3548d4054 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/threading/package.html @@ -0,0 +1,10 @@ + + + + + + +Provides tools for managing threads, thread pools, and parallelization +in general. + +