added some more checks to make sure that the TCGA barcodes in the
MutSig output files are as expected (or can be fixed)
modified code to be able to work from the code_potential features
as well, and also turned off the pathway-level features
changed the pairwise call to use the new code
new script for processing output of perl binarization step -- keeps
only the code_potential features and those with at least one '1'
have now also turned off the "combineGnabCnvr" step
modified so that only the "important" parts of feature names are required
to match to call them the "same" feature (eg for GEXP features, the
genomic coordinates don't matter -- only the gene symbol and the gene id,
if available)
there was a bug in the part of the code that picked the most recent
Firehose analysis outputs to use -- it was not properly giving
precedence to earlier AWG-specific analysis runs
the uuid-to-barcode mapping file is now set based on the specified
snapshot name
added a line to set up a symbolic link from the metadata.current.txt within
the dcc-snapshot to the current metadata file in $TCGAFMP_DCC_REPOSITORIES/uuids/
added a call to wget_metadata.sh
this script grabs the current uuid-to-barcode metadata file
added new functionality to handle having the uuid-to-barcode mapping
file in the dcc-snapshot rather than in a single fixed place