Commits

Author Commit Message Labels Comments Date
Faheem Mitha
Bug fixes to 'add_illumina_calls_to_glist', courtesy of Robert V. Baron.
Faheem Mitha
Fix command for Illumina annotation file (Thanks to Robert V. Baron).
Faheem Mitha
Add function get_datasets. Add exception for simaffy6 and simillum - output files are not calculated for these.
Faheem Mitha
Changes to output.py and make_output.py.
Faheem Mitha
Typo fix in "Output filter" section. 'sex' should be 'sex_id', 'race' should be 'race_id'.
Faheem Mitha
Add note about PostgreSQL identifiers, and correct make_output.py command line examples.
Faheem Mitha
Correct Affymetrix Hapmap pheno file.
Faheem Mitha
Mention that downloading and processing of HapMap data is current as of 1st July 2012.
Faheem Mitha
Typo fix in Single_Illumina and Shard_Illumina.
Faheem Mitha
Minor fixes to docs/MANUAL. Update Illumina annotation file download information.
Faheem Mitha
Update Illumina HapMap genofile names.
Faheem Mitha
Update Affymetrix HapMap pheno file. Add R script pheno.R to automate update. Rename pheno file from hapmappheno_909.csv to hapmappheno.csv. Add README.
Faheem Mitha
Rename data/Hapmap6.0/Pheno/hapmappheno_909.csv to data/Hapmap6.0/Pheno/hapmappheno.csv in MANUAL.
Faheem Mitha
Rewrite "Downloading and Processing HapMap data" section.
Faheem Mitha
Rewrite and expand "Relationship between datasets and schemas" section.
Faheem Mitha
Update dependencies section.
Faheem Mitha
Change cite from Duke Biostat tech report to PLoS ONE article.
Faheem Mitha
Handle case where phenofiles contain expids which are not contained in the genotype calls file.
Faheem Mitha
Remove trailing slash for BASEDIR.
Faheem Mitha
Add CXX flags to environments.
Faheem Mitha
Remove pragma diagnostics which gcc 4.4 can't handle.
Faheem Mitha
Change BASEDIR.
Faheem Mitha
Change pg_url, text_autocommit and create_engine_wrapper to work with SQLAlchemy 0.7.x.
Faheem Mitha
Add Boost Python unicode string converter for use with geno.cpp.
Faheem Mitha
Corrections to default_conf.
Faheem Mitha
Fix up error_rsid error messages in write_geno_tables_illumina_to_file and write_geno_table_illumina_to_file.
Faheem Mitha
Work around exception pickling python bug http://bugs.python.org/issue1692335.
Faheem Mitha
Factor out common code in write_geno_tables_illumina_to_file and write_geno_table_illumina_to_file into add_illumina_calls_to_glist.
Faheem Mitha
Rework test_simdata.py to use illumina_username and affy6_username. Modify init_db.py to not call exit at the end of the init_db function.
Faheem Mitha
Add --seed option to test_simdata.py and document it.
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