From 930082314a186c75941cdc05ac38ab24e8446643 Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 15 Jan 2010 21:48:30 +0000 Subject: [PATCH] Put a major.minor version into the GATK Javadoc for reading. Also, update some straggler packages to the new package-info.java format introduced in 1.5. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2604 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/package-info.java | 4 ++-- .../sting/utils/cmdLine/package-info.java | 4 ++++ .../broadinstitute/sting/utils/cmdLine/package.html | 11 ----------- .../sting/utils/fasta/package-info.java | 4 ++++ .../org/broadinstitute/sting/utils/fasta/package.html | 11 ----------- .../org/broadinstitute/sting/utils/package-info.java | 4 ++++ java/src/org/broadinstitute/sting/utils/package.html | 11 ----------- .../broadinstitute/sting/utils/sam/package-info.java | 4 ++++ .../org/broadinstitute/sting/utils/sam/package.html | 11 ----------- .../sting/utils/threading/package-info.java | 4 ++++ .../broadinstitute/sting/utils/threading/package.html | 10 ---------- 11 files changed, 22 insertions(+), 56 deletions(-) create mode 100644 java/src/org/broadinstitute/sting/utils/cmdLine/package-info.java delete mode 100644 java/src/org/broadinstitute/sting/utils/cmdLine/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/fasta/package-info.java delete mode 100644 java/src/org/broadinstitute/sting/utils/fasta/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/package-info.java delete mode 100644 java/src/org/broadinstitute/sting/utils/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/sam/package-info.java delete mode 100644 java/src/org/broadinstitute/sting/utils/sam/package.html create mode 100644 java/src/org/broadinstitute/sting/utils/threading/package-info.java delete mode 100644 java/src/org/broadinstitute/sting/utils/threading/package.html diff --git a/java/src/org/broadinstitute/sting/gatk/package-info.java b/java/src/org/broadinstitute/sting/gatk/package-info.java index 4110d8c80..83480c1ba 100644 --- a/java/src/org/broadinstitute/sting/gatk/package-info.java +++ b/java/src/org/broadinstitute/sting/gatk/package-info.java @@ -1,5 +1,5 @@ /** - * Provides map/reduce application framework highly optimized for - * analysis of sequencing data. + * Provides map/reduce application framework highly optimized for analysis of sequencing data. + * @version 1.0 */ package org.broadinstitute.sting.gatk; \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/package-info.java b/java/src/org/broadinstitute/sting/utils/cmdLine/package-info.java new file mode 100644 index 000000000..5afdbb1bb --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/cmdLine/package-info.java @@ -0,0 +1,4 @@ +/** + * Parses a wide variety of command-line arguments in single-pass and multipass strategies. + */ +package org.broadinstitute.sting.utils.cmdLine; \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/package.html b/java/src/org/broadinstitute/sting/utils/cmdLine/package.html deleted file mode 100644 index 614fc2002..000000000 --- a/java/src/org/broadinstitute/sting/utils/cmdLine/package.html +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - -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-info.java b/java/src/org/broadinstitute/sting/utils/fasta/package-info.java new file mode 100644 index 000000000..6f0148abd --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/fasta/package-info.java @@ -0,0 +1,4 @@ +/** + * Provides services and utilities for fast random access to reference sequence files. + */ +package org.broadinstitute.sting.utils.fasta; \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/fasta/package.html b/java/src/org/broadinstitute/sting/utils/fasta/package.html deleted file mode 100644 index 28b4e499b..000000000 --- a/java/src/org/broadinstitute/sting/utils/fasta/package.html +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - -Provides services and utilities for fast random access to reference -sequence files. - - - diff --git a/java/src/org/broadinstitute/sting/utils/package-info.java b/java/src/org/broadinstitute/sting/utils/package-info.java new file mode 100644 index 000000000..b0256f7c0 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/package-info.java @@ -0,0 +1,4 @@ +/** + * Provides tools that have use across a wide range of Sting and GenomeAnalysisTK applications and tools. + */ +package org.broadinstitute.sting.utils; \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/package.html b/java/src/org/broadinstitute/sting/utils/package.html deleted file mode 100644 index f9591fa99..000000000 --- a/java/src/org/broadinstitute/sting/utils/package.html +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - -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-info.java b/java/src/org/broadinstitute/sting/utils/sam/package-info.java new file mode 100644 index 000000000..701a43d3d --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/sam/package-info.java @@ -0,0 +1,4 @@ +/** + * Generates mock reads, headers, and other read-oriented data, largely for consumption by the unit testing framework. + */ +package org.broadinstitute.sting.utils.sam; \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/utils/sam/package.html b/java/src/org/broadinstitute/sting/utils/sam/package.html deleted file mode 100644 index 9aaac573a..000000000 --- a/java/src/org/broadinstitute/sting/utils/sam/package.html +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - -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-info.java b/java/src/org/broadinstitute/sting/utils/threading/package-info.java new file mode 100644 index 000000000..dc350920e --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/threading/package-info.java @@ -0,0 +1,4 @@ +/** + * Provides tools for managing threads, thread pools, and parallelization in general. + */ +package org.broadinstitute.sting.utils.threading; diff --git a/java/src/org/broadinstitute/sting/utils/threading/package.html b/java/src/org/broadinstitute/sting/utils/threading/package.html deleted file mode 100644 index 3548d4054..000000000 --- a/java/src/org/broadinstitute/sting/utils/threading/package.html +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - -Provides tools for managing threads, thread pools, and parallelization -in general. - -