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Commits on May 15, 2014

• Modified generate_annotated_vcfs to take file with a list of files to annotate. More in-line with lab norm and makes easier to use.

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Commits on May 13, 2014

• Removed duplicate functions from vcf function (merge artifact?). Made header parsing case-insensitive.

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• Merge branch 'vcf_parser'

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• Updated documentation.

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• Bug fix. File name not object incorrectly passed to function.

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• Added more advanced VCF parsing.

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• Minor code cleanup.

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Commits on May 12, 2014

• Cleaned up VCF parsing code -- consolidating functions.

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• Added VEP support for detecting Mac or Linux system to alter which compression is used.

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Commits on May 11, 2014

• Made LeidenDatabase and GeneData super classes public (no _ in front of name) to make documentation generation work.

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• Updated scripts and unit tests to use new leiden_database interface style.

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• Added safety check that requested gene ID is available on database. Maintains efficiency by storing list of available genes at start-up.

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• Updated documentation and shortened function names. Updated documentation with terms of use for LOVD.

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• Bug fix. Genes with 1 entry returned variant count of zero because of insufficient regex.

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• New interface for LeidenDatabase objects. Now request gene data returns an object with its own functions. Makes it as efficient as possible while also keeping clean interface.

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• Changed from urllib to requests for HTML requests.

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• Refactored leiden_database functions to eliminate need to set gene before calling other functions. LeidenDatabase objects are now fully initialized after contruction. Unit tests updated with Mock o…

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Commits on May 9, 2014

• Updated to correct intra-package import statements to resolve importing errors.

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• Updated README.

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• Removed VEP refseq flag as is no longer needed. Updated VEP documentation.

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• Updated documentation.

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• Updated unit tests

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• Made VCF parsing of tags with lists -- like VEP -- more general. Now handles any tag name, not just LOVD.

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• Major update merged from other project. Now uses standard VEP annotation for annotation and validation purposes. No Broad-specific dependencies.

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Commits on May 6, 2014

• Bug-fix added alternative table class used for some LOVD websites. First tries the typical value and then tries the backup if needed.

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Commits on May 5, 2014

• Added HGVS notaiton correction. Does not handle mismatched parentheses.

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• Added extra code to ensure all excess whitespace and weird characters are removed from table headers and table data.

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Commits on May 4, 2014

• Added files for READTHEDOCS and package distribution.

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Commits on Apr 30, 2014

• Added README. Moved annotate_vcf module to broad_cluster module.

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• Renamed imports to look for leiden module to avoid module name conflicts. Fixed bug where run_all.py saved some files to script directory rather than output directory.

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• Bug fix for DBSNP annotation. Appears to be working now.

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Commits on Apr 28, 2014

• Added external modules into this project. Eventually, some may become PyPI packages to promote reuse, but they will remain in this project for now.

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Commits on Apr 23, 2014

• Updated with changes from Software Carpentry session. Large commit due to iterations through this process.

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Commits on Apr 8, 2014

• Improved plotting.

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Commits on Mar 28, 2014

• Updated unit tests and minor fixes for robustness.

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