removing unnecssary file.
added #!/bin/bash at the top of script
added a few more places to look for MAF files
assumes/checks that environment variables are set like the other scripts already do
added a few lines to create a new directory for the specified tumor type
if this is the first time a feature matrix is being built for that tumor
modified to creat the "all" matrix which combines both array- and sequencing-based gene expression data
modified to creat the "all" matrix which combines both array- and sequencing-based gene expression data
modified to creat the "all" matrix which combines both array- and sequencing-based gene expression data
added a tag on the end of the platform feature names so that we can have both array- and sequencing-based gene expression data in the same feature matrix
also added the tumor type "acc" to the list of tumor types
added the tumor type "acc" to the list of tumor types
added the tumor type "acc" to the list of tumor types
added the tumor type "acc" to the list of tumor types
added the tumor type "acc" to the list of tumor types
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
replacing wget with curl.
grouping code logicially.
cleaner use of sed.
Store original timestamps for NCBI's Gene for archival purposes.
NCBI's Gene database is potentially updated daily; see
http://www.ncbi.nlm.nih.gov/books/NBK3841/#EntrezGene.How_Data_Are_Maintained
save NCBI Gene files with original timestamp in name for archiving.
added checkFollowupInfo() which resets vital_status to LIVING if the days_to_death is NA,
and also sets the days_to_last_followup to 0 if it is NA