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

0.7.1 (in progress)
=======================================


0.7.0
=======================================
1. Added support for CADD scores via new `cadd_raw` and `cadd_scaled` columns.
2. Added support for genotype wildcards in query select statements. E.g., "select chrom, start, end (gts).(phenotype==2)". See http://gemini.readthedocs.org/en/latest/content/querying.html#selecting-sample-genotypes-based-on-wildcards.
3. Added support for genotype wildcards in the --gt-filter. E.g., "--gt-filter "(gt_types).(phenotype==2).(==HET)"". See http://gemini.readthedocs.org/en/latest/content/querying.html#gt-filter-wildcard-filtering-on-genotype-columns.
4. Added support for the VCF INFO field both in the API and as a column that can be SELECT'ed.
5. Upgraded to the latest version of ClinVar.
6. Standardized impacts to use Sequence Ontology (SO) terms.
7. Automatically add indexes to custom, user-supplied annotation columns.
8. Improvements to the installation script.
9. Fixed bugs in the handling of ClinVar UTF8 encoded strings.
10. Upgraded the `gene_summary` and `gene_detailed` tables to version 75 of Ensembl.
11. Added support for the MPI Mouse Phenotype database via the `mam_phenotype_id` column in the `gene_summary` table.
12. Enhanced security.
13. Corrected the ESP allele frequencies to be based report _alternate_ allele frequency instead of _minor_ allele frequency.
14. VEP version support updated (73-75) Support for aa length and bio type in VEP. 
15. The `lof_sieve` tool support has been extended to VEP annotations.


0.6.6
=======================================
1. Added COSMIC mutation information via new cosmic_ids column.


0.6.4 (2014-Jan-03)
=======================================

1. New annotation: experimentally validated human enhancers from VISTA.
2. Installation improvements to enable isolated installations inside of virtual
   machines and containers without data. Allow data-only upgrades as part of
   ``update`` process.
3. Fix for gemini query error when ``--header`` specified (#241).

0.6.3.2 (2013-Dec-10)
=======================================
1. Fixed a bug that caused ``--gt-filter`` to no be enforced from ``query`` tool unless a GT* column was selected.
2. Support for ref and alt allele depths provided by FreeBayes.

0.6.3.1 (2013-Nov-19)
=======================================
1. Fixed undetected bug preventing the ``comp_hets`` tool from functioning.
2. Added unit tests for the ``comp_hets`` tool.

0.6.3 (2013-Nov-7)
=======================================
1. Addition permutation testing to the c-alpha test via the ``--permutations``
   option.
2. Addition of the ``--passonly`` option during loading to filter out all<commit_msg>[DOC] more detail on 0.7.0 release.<commit_after>#############################
Release History
#############################

0.7.1 (in progress)
=======================================


0.7.0
=======================================
1. Added support for CADD scores via new ``cadd_raw`` and ``cadd_scaled`` columns.
2. Added support for genotype wildcards in query select statements. E.g., ``SELECT chrom, start, end (gts).(phenotype==2) FROM variants``. See http://gemini.readthedocs.org/en/latest/content/querying.html#selecting-sample-genotypes-based-on-wildcards.
3. Added support for genotype wildcards in the --gt-filter. E.g., ``--gt-filter "(gt_types).(phenotype==2).(==HET)``. See http://gemini.readthedocs.org/en/latest/content/querying.html#gt-filter-wildcard-filtering-on-genotype-columns.
4. Added support for the VCF INFO field both in the API and as a column that can be SELECT'ed.
5. Upgraded to the latest version of ClinVar.
6. Standardized impacts to use Sequence Ontology (SO) terms.
7. Automatically add indexes to custom, user-supplied annotation columns.
8. Improvements to the installation script.
9. Fixed bugs in the handling of ClinVar UTF8 encoded strings.
10. Upgraded the ``gene_summary`` and ``gene_detailed`` tables to version 75 of Ensembl.
11. Added support for the MPI Mouse Phenotype database via the ``mam_phenotype_id`` column in the ``gene_summary`` table.
12. Enhanced security.
13. Corrected the ESP allele frequencies to be based report _alternate_ allele frequency instead of _minor_ allele frequency.
14. VEP version support updated (73-75) Support for aa length and bio type in VEP. 
15. The `lof_sieve` tool support has been extended to VEP annotations.
16. Added the ``ccds_id`` and ``entrez_id`` columns to the ``gene_detailed`` table.


0.6.6
=======================================
1. Added COSMIC mutation information via new cosmic_ids column.


0.6.4 (2014-Jan-03)
=======================================

1. New annotation: experimentally validated human enhancers from VISTA.
2. Installation improvements to enable isolated installations inside of virtual
   machines and containers without data. Allow data-only upgrades as part of
   ``update`` process.
3. Fix for gemini query error when ``--header`` specified (#241).

0.6.3.2 (2013-Dec-10)
=======================================
1. Fixed a bug that caused ``--gt-filter`` to no be enforced from ``query`` tool unless a GT* column was selected.
2. Support for ref and alt allele depths provided by FreeBayes.

0.6.3.1 (2013-Nov-19)
=======================================
1. Fixed undetected bug preventing the ``comp_hets`` tool from functioning.
2. Added unit tests for the ``comp_hets`` tool.

0.6.3 (2013-Nov-7)
=======================================
1. Addition permutation testing to the c-alpha test via the ``--permutations``
   option.
2. Addition of the ``--passonly`` option during loading to filter out all
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