EX-212: convert md to rst; bump version

umich-brcf-bioinf · Apr 8, 2015 · 6d72b78 · 6d72b78
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diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -0,0 +1,41 @@
+Changelog
+=========
+
+0.4 (4/8/2015)
+--------------
+ - Adjusted code to support Python >=2.7 or 3.x
+ - Fixed bug in summarize that caused error if variant was called by subset of callers 
+ - Improved checks for consistent VCF file sets
+
+0.3.1 (3/17/2015)
+-----------------
+ - Downgraded VCF format from 4.2 to 4.1
+ - Fixed a bug that omitted CALLERS_REPORTED_LIST summary tag
+ - Simplified summary tags; removed dependency on numpy
+ - Adjusted VarScan translation to accept a file pattern to identify high-confidence files 
+
+
+0.3 (3/9/2015)
+--------------
+ - Replaced [normalize], [tag] commands with [translate]; relaxed constraints on incoming data.
+ - Renamed [consensus] to [summarize]
+ - More consistent behavior in [expand]
+ - Significantly improved [merge] performance 
+ - Added new summary tags:
+   - CALLERS_REPORTED_COUNT
+   - CALLERS_REPORTED_LIST
+   - SAMPLES_REPORTED_COUNT
+   - CALLERS_PASSED_COUNT
+   - CALLERS_PASSED_LIST
+   - SAMPLES_PASSED_COUNT
+ - Fixed bug in how Strelka calculated AF on indels
+ - Improved command validation and error handling
+ - Added project/code documentation 
+ - Removed dependencies on pandas
+
+
+0.21 (10/2014)
+--------------
+ - Initial public release
+
+
diff --git a/INSTALL.md → INSTALL.rst b/INSTALL.md → INSTALL.rst
@@ -1,15 +1,16 @@
-##Installing Jaquard
-__________________
+Installing Jaquard
+==================
+Jacquard has been tested python 2.7 and 3.4 on Windows7, OSX, and *nix.
 
-###Prerequisites
-
-* Jacquard has been tested python 2.7 on Windows7, OSX, and Unix.
-* natsort (3.5.2) and  
+Prerequisites
+-------------
+* natsort (3.5.2)  
 * nosetests, testfixtures (3.0.2), and numpy (>=1.7.1) are required are 
       required for running automated tests
 * Note that pip installs all required libraries; see [Installing] below.
 
-###Installing
+Installing
+----------
 The easiest way to install Jacquard is through PyPI system. Get pip if it's 
 not available in your system:
 

diff --git a/README.md → README.rst b/README.md → README.rst
@@ -1,25 +1,27 @@
 
-#Jacquard
-________
+Jacquard
+========
 Suite of command-line tools to expedite analysis of exome variant data from multiple patients and multiple variant callers.
 
 [![Build Status](https://travis-ci.org/umich-brcf-bioinf/Jacquard.svg?branch=develop)](https://travis-ci.org/umich-brcf-bioinf/Jacquard) 
 [![Coverage Status](https://coveralls.io/repos/umich-brcf-bioinf/Jacquard/badge.png?branch=develop)](https://coveralls.io/r/umich-brcf-bioinf/Jacquard?branch=develop)
 
-### Directory List
+Files
+-----
 * jacquard-runner.py : Convenience wrapper for running Jacquard directly from source tree.
 * jacquard : Python libraries
 * spikes : Unsupported prototypes and other experiements
 * test : Automated unit tests
 
-### Usage
-
-jacquard <subcommand> [options] [arguments]
+Usage
+-----
+`$jacquard <subcommand> [options] [arguments]`
 
 For help on a specific subcommand:
 jacquard-runner.py <subcommand> --help 
 
-#### Subcommands
+*Subcommands*
+
     translate           Accepts a directory of VCF results (including VarScan high
                         confidence files). Creates a new directory of VCFs,
                         adding Jacquard-specific FORMAT tags for each VCF
@@ -37,7 +39,7 @@ jacquard-runner.py <subcommand> --help
                         expanding INFO fields and FORMAT tags into distinct
                         columns.
 
-================
+---
 
 Email bfx-jacquard@umich.edu for support and questions.
 

diff --git a/TODO.md b/TODO.md
diff --git a/TODO.rst b/TODO.rst
@@ -0,0 +1,15 @@
+TODO
+====
+- Improved workflow documentation with example data
+- Extend [translate] to support more tags (e.g. GT)
+- Extend [merge] to filter and disambiguate tag collisions
+- Add [weave] command to combine [translate, filter, merge, summarize]
+- Extend [expand] generate glossary
+- Extend [expand] to parse SnpEff/Annovar annotated results
+- Extend [expand] to generate formatted results
+- Improve command validation (check source tags, check "shape" of inputs)
+- Enable 4.2 VCF support
+- Add support for new somatic callers
+- Add support for Germline workflows
+- Add support for Galaxy integration
+- Add gene-level rollup for annotated data
diff --git a/jacquard/__init__.py b/jacquard/__init__.py
@@ -1 +1 @@
-__version__ = 0.31
+__version__ = "0.4"
diff --git a/test/jacquard_test.py b/test/jacquard_test.py
@@ -55,7 +55,7 @@ def test_error_raisesTransformedMessage(self):
 
 class JacquardTestCase(test_case.JacquardBaseTestCase):
     def test_version(self):
-        self.assertEquals(0.31, jacquard.__version__)
+        self.assertEquals("0.4", jacquard.__version__)
 
     def test_get_execution_context(self):
         command = "foo input_dir output_dir"