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Commits on Sep 22, 2014

• add index for sv_event_id

  

  arq5x

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• added support for structural variants in VCF format. Integration with speedseq.

  

  arq5x

  committed
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Commits on Sep 18, 2014

• Support for fitCons: indicator of potential for interesting function in genomic variants

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  chapmanb

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Commits on Apr 29, 2014

• add column for SO impacts

  

  udp3f

  committed
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Commits on Apr 26, 2014

• add new columns for gene tables

  

  udp3f

  committed
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Commits on Apr 6, 2014

• add CADD scores to variant table; add new indices, remove duplicates

  

  udp3f

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Commits on Feb 8, 2014

• add new indices

  

  arq5x

  committed
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Commits on Jan 21, 2014

• add index

  

  udp3f

  committed
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Commits on Jan 20, 2014

• [ENH] add in_cosmic_census flag to gene_summary table.

  

  arq5x

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Commits on Jan 17, 2014

• new additions:summary gene table & detailed gene table

  

  udp3f

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Commits on Jan 10, 2014

• Reverted to storing Info as pickled OrdredDict object

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  dgaston

  committed
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Commits on Jan 9, 2014

• Storing of full INFO in variants table

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  dgaston

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Commits on Jan 5, 2014

• [ENH] added COSMIC mutation info with cosmic_ids column. Cheers to @chapmanb.

  

  arq5x

  committed
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Commits on Dec 14, 2013

• [ENH] add VISTA enahncers as new annotation.

  

  arq5x

  committed
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Commits on Oct 30, 2013

• Added a database_transaction context.

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  roryk

  committed
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Commits on Oct 1, 2013

• Extended PED format added.

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  roryk

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Commits on Sep 24, 2013

• [ENH] add ID field from VCF to database as vcf_id

  

  arq5x

  committed
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Commits on Aug 23, 2013

• add index on gene column

  

  arq5x

  committed
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Commits on Aug 13, 2013

• store sample names and ids as text

  

  arq5x

  committed
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Commits on Jun 12, 2013

• [ENH] support for genotype quals, ref_depths, and alt_depths.

  

  arq5x

  committed
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Commits on May 1, 2013

• make room for gerp and cse

  

  arq5x

  committed
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• resolve merge conflicts with GERP branch

  

  arq5x

  committed
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• support for GERP elements and (opt.) support for bp GERP scores.

  

  arq5x

  committed
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Commits on Apr 25, 2013

• support for GERP BigWig annotations. SLOW.

  

  arq5x

  committed
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Commits on Apr 18, 2013

• Provide a variant annotation to identify context specific sequencing errors (CSEs): useful to identify potential false negative calls.

  chapmanb

  committed
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• Merge with master.

  roryk

  committed
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• Code to spit out problem variants added.

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  roryk

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Commits on Apr 17, 2013

• added a new track for Pfam domains

  

  Uma Paila

  committed
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Commits on Mar 25, 2013

• use a version table to track which version of gemini was used to create a DB.

  

  arq5x

  committed
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Commits on Mar 24, 2013

• pep8

  

  arq5x

  committed
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Commits on Mar 14, 2013

• enforce precision of frequency columns

  

  arq5x

  committed
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Commits on Feb 24, 2013

• Add table of annotation resources used to build a database. Provides filenames with version to allow traceability of annotations

  chapmanb

  committed
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Commits on Feb 14, 2013

• [ENH] add ENCODE TFBS and DnaseI clusters; cull to consensus ChromHMM and Segway calls

  

  arq5x

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Commits on Feb 12, 2013

• [ENH] add Clinvar annotations

  

  arq5x

  committed
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Commits on Dec 28, 2012

• omitted from previous commit

  

  arq5x

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