<commit_before>#############################
Release History
#############################

0.6.2 (in development)
=======================================
1. Moved --tped and --json options into the more generic --format option.
2. Fixed bug in handling missing phenotypes in the sample table.
3. Fixed --tped output formatting error.

0.6.1 (2013-Sep-09)
=======================================
1. Corrected bug in de_novo tool that was undetected in 0.6.0.  Unit tests have been added to head this off in the future. Thanks to **<NAME>**
2. Added the `-d` option (minimum sequence depth allowed for a genotype) to the `autosmal_recessive` and `autosmal_dominant` tools.
3. New `--tped` option in the `query` tool for reporting variants in TPED format. Thanks to **<NAME>**.
4. New `--tfam` option in the `dump` tool for reporting sample infor in TFAM format. Thanks to **<NAME>**.



0.6.0 (2013-Sep-02)
=======================================
1. Add the ``--min-kindreds`` option to the ``autosomal_recessive`` and ``autosomal_dominant`` tools to restrict candidate variants/genes to those affecting at least ``--min-kindreds``. Thanks to **<NAME>**
2. Addition of a new ``burden`` tool for gene or region based burden tests.  First release supports the C-alpha test.  Thanks to **<NAME>**.
3. Use of Continuum Analytics Anaconda python package for the automated installer. Thanks to **<NAME>**.
4. Enhancements to the ``annotate`` tool allowing one to create new database columns from values in custom BED+ annotation files.  Thanks to **<NAME>** and **<NAME>**.
5. Addition of the ``--column``, ``--filter``, and ``--json`` options to the ``region`` tool.
6. Improvements to unit tests.
7. Allow alternate sample deleimiters in the ``query`` tool via the ``--sample-delim`` option.  Thanks to **<NAME>**.
8. Provide a REST-like interface to the gemini browser.  In support of future visualization tools.<commit_msg>Added --phenotype and --exclude-phenotype flags.<commit_after>#############################
Release History
#############################

0.6.2 (in development)
=======================================
1. Moved --tped and --json options into the more generic --format option.
2. Fixed bug in handling missing phenotypes in the sample table.
3. Fixed --tped output formatting error.
4. API change: GeminiQuery.run takes an optional list of predicates that a row
   must pass to be returned
5. --phenotype option added to gemini query which restricts variants returned to only
   variants in which all the individuals with the variant have the given phenotype.
6. --exclude-phenotype option added to gemini query which restricts variants returned
   to only variants in which none of the individuals with the variant have the
   given phenotype.

0.6.1 (2013-Sep-09)
=======================================
1. Corrected bug in de_novo tool that was undetected in 0.6.0.  Unit tests have been added to head this off in the future. Thanks to **<NAME>**
2. Added the `-d` option (minimum sequence depth allowed for a genotype) to the `autosmal_recessive` and `autosmal_dominant` tools.
3. New `--tped` option in the `query` tool for reporting variants in TPED format. Thanks to **<NAME>**.
4. New `--tfam` option in the `dump` tool for reporting sample infor in TFAM format. Thanks to **<NAME>**.



0.6.0 (2013-Sep-02)
=======================================
1. Add the ``--min-kindreds`` option to the ``autosomal_recessive`` and ``autosomal_dominant`` tools to restrict candidate variants/genes to those affecting at least ``--min-kindreds``. Thanks to **<NAME>**
2. Addition of a new ``burden`` tool for gene or region based burden tests.  First release supports the C-alpha test.  Thanks to **<NAME>**.
3. Use of Continuum Analytics Anaconda python package for the automated installer. Thanks to **<NAME>**.
4. Enhancements to the ``annotate`` tool allowing one to create new database columns from values in custom BED+ annotation files.  Thanks to **<NAME>** and **<NAME>**.
5. Addition of the ``--column``, ``--filter``, and ``--json`` options to the ``region`` tool.
6. Improvements to unit tests.
7. Allow alternate sample delimiters in the ``query`` tool via the ``--sample-delim`` option.  Thanks to **<NAME>**.
8. Provide a REST-like interface to the gemini browser.  In support of future visualization tools.
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