Non-bam-analysis-related annotations not in database

[gregsoos]

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?

[gregsoos]

If we do plan to include the pulldown logfile pointer in the database, I would advocate for a system wherein we associate a single log file with the genetic analysis to which it corresponds. Then, the two columns in the anno file (original and repulldown log pointers) could be replaced with two slightly different ones:

• a column that shows the log pointer that corresponds to that genetic analysis
• a column which contains the log pointer for the earliest genetic analysis associated to the same data instance