update job_upload.sh to add new arguments for cghubs create_... script, added normal uuid in sh file, and integrated pcap icgc metadata handling to create_... script
ok, this time its the update job_upload.sh to add new arguments for cghubs create_... script, added normal uuid in sh file, and integrated pcap icgc metadata handling to create_... script. last time was only to change the dir name for the cghub code
submission and upload working from sh program
adding realigned_bam_check.py for checking realigned bams against the original aligned bams
idxstats files are now written out as well as processed, job_upload.sh includes
all main pieces for upload are present
added additional check in the checking script to catch any chromosomes (not contigs) who have 0 mapped reads
Merge branch 'master' of ssh://github.com/kellrott/tcga_realign into chris
added exit code checking on the synapse calls, including checking for 1 instead of 0 on the getResultID synapse call
added job_upload.sh to job_all.sh, but its not tested
Merge remote-tracking branch 'origin/chris'
Merging Chris's changes and fixing how control UUIDs are determined