Beta_v0.2.12

• gdc_report now gracefully tolerates absence of a sample filter list
• CPTAC3 config file updated
• gdc_loadfile now enforces that any single loadfile contains data for only 1 GDC program

Beta_v0.2.11

update CPTAC3 handling to re-enable WXS-based segfile processing

Beta_v0.2.10

. Initial support for CPTAC3 data, including EPIC methylation data, TSV-based clinical, CN and expression
. Diminished, but not entirely removed, defaults that still reflect TCGA heritage
. Updated regression test baselines to reflect latest GDC data
. The --help output for gdc_list now gives several usage examples

Beta_v0.2.9

Support new V2 seg files; update regression tests to latest data GDC data release, and ensure they are downloaded outside of repo directory tree so as to not slow down builds/installs

Beta_v0.2.8

• Install .cfg files to bin dir
• Avoid mirroring pathology slides for now, as they are extremely large; issue
• Created issue #73 so that this avoidance can happen via config files, instead

Beta_v0.2.7

Ensure that reference and config files are installed; update baseline regression test data to reflect latest GDC data release

Beta_v0.2.6

Version 0.2.6:
. More polish on the regression tests
. Better segregation of FFPE samples by gdc_loadfile when generating sample sets
Version 0.2.5:
. gdc_miror now longer exposes --date CLI arg; it was never relevant because
the mirror creates datestamps
. rest of tools more intelligently infer correct datestamp to use
. gdc_loadfile now exposes --format arg, to choose between FireCloud/Firehose

Beta_v0.2.4

GDCtools v0.2.4 Beta: corrected file paths in files generated by gdc_loadfile (v0.3.3)

Beta_v0.2.1

New release to reflect that in Data Release v7 (and API v1.9.0) GDC appears to have changed paging in the API to be zero-based. Until this our code had been working from the assumption that first page to be returned was page=1, but now it uses page=0. All regression tests pass, for both Python 2 and 3, with baseline regression data also updated to reflect V7 of the data release.

Beta_v0.2.0

Re-establish that both Python 2 and Python 3 are supported, thanks in part to Pranjal Aswani.