Non-bam-analysis-related annotations not in database

There are a handful of columns in the anno file that are not metrics and currently do not have representation in the database and/or are not generated by anno_file_generate. These are:

• Index
• Pulldown Strategy
• Suffices (indicating data types used for sources which can be a subset of that in bam)
• Data type
• No. Libraries
• Data original pulldown logfile location
• Data repulldown logfile location
• Library type (minus=no.damage.correction, half=damage.retained.at.last.position, plus=damage.fully.corrected, ds=double.stranded.library.preparation, ss=single.stranded.library.preparation)

There are also a couple of columns which do pertain to metrics but cannot be calculated just by running bam analysis blindly on the nuclear/MT bams. These are:

• Mean length of shotgun sequences (merged data)
• endogenous by library (computed on shotgun data)

Do we plan to represent any and/or all of these in the database? Would some be better dropped or combined?

No files or tests are named. Start by locating anno_file_generate and the database representation for annotation columns, then determine which listed fields are supported or computable; done requires an agreed scope for retaining, combining, or dropping them and a corresponding implementation plan.