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. + +