initial pipeline for cram
run pipeline for cram import
validate number of reads
fix reference name
filter everything but cram files
find the irods full path of file
use vrlane
space after mem param
split array
wip
filter secondary and supplementary
no db reference
list of fastq files
print cram header
output cram rather than sam
cram file without path
dont cleanup md5
create md5s for fastq files
Merge pull request #305 from andrewjpage/cram_import

Cram import