broadinstitute / cms / 30

Builds Branch Commit Type Ran Committer Via Coverage
30 ct-cms fixed type comparison problem in genotype coding function push tomkinsc travis-ci pending completion   set done
29 ct-cms ./norm binary is now copied from build directory push tomkinsc travis-ci pending completion   set done
28 ct-cms intermediate commit SQLite data ingestion, updated but perhaps not correct coding function for VCF->TPED conversion (may need changes to properly handle multi-allelic sites). greater test coverage is needed push tomkinsc travis-ci pending completion   set done
27 ct-cms speed improvements to file conversion, some refactoring/fixes regexes and operator.itemgetter() are now used to parse and access the genotypes for the selected samples. from profiling this has been found to be faster than numpy index vectors, and... push tomkinsc travis-ci pending completion   set done
26 ct-cms removed old-style print statement for py3 push tomkinsc travis-ci pending completion   set done
25 ct-cms intermediate checkin commit fixed: SNP identification where VT k=v pair is absent from INFO column; progress on aggregation of metadata across the calculation process, and ingestion of data into an abstracted SQLite database. incremented selscan ... push tomkinsc travis-ci pending completion   set done
24 ct-cms selscan binary is now compiled as part of the install process Due to an incompatibility between pre-built selscan and the Broad’s LSF cluster (lack of GLIBC_2.14), we now build selscan as part of the install process, overwriting the pre-build ver... push tomkinsc travis-ci pending completion   set done
23 ct-cms docs req change push tomkinsc travis-ci pending completion   set done
22 ct-cms mocked out dependency from docs requirements push tomkinsc travis-ci pending completion   set done
21 ct-cms fixed sphinx-argparse relative directory push tomkinsc travis-ci pending completion   set done
20 ct-cms added sphinxarg.ext to document extensions push tomkinsc travis-ci pending completion   set done
19 ct-cms added to docs push tomkinsc travis-ci pending completion   set done
18 ct-cms fixed urllib import for py3 push tomkinsc travis-ci pending completion   set done
17 ct-cms fixed izip import for py 3 compatibility push tomkinsc travis-ci pending completion   set done
16 ct-cms integration of selscan into common command line interface integration of selscan into common command line interface. selscan_file_conversion command also added to take a compressed 1000G Phase3 VCF and generate a compressed tped file of the sort ... push tomkinsc travis-ci pending completion   set done