Implementation Notes

This page is intended to serve as a resource for QAers and/or developers who are asking questions that probe the murky inner workings of our system. The contents may also come in handy for mirror sites with local development, but it would be nice to keep this page focused on the core system, and address mirror-specific issues on a mirror page.

• autoSql: generate .c, .h and .sql files from .as file

• Blastz

• Chains and Nets

• Cookie_Session: Our hguid cookie, hgsid CGI variable, and central databases's userDb and sessionDb

• CpG Islands: the difference between cpgIslandExt and cpgIslandGgfAndy{,Masked}

• genscanSubopt: putative exons that don't make the final cut in GenScan. We don't push this track, but we keep it around on hgwdev so that researches can use it in featureBits when they want to be very conservative in screening out anything that might be coding.

• tableDescriptions: .as descriptions of database tables (buildTableDescriptions.pl vs. makeTableDescriptions)

• Conservation Track: Slides from Kate's talk to Q/A (April 2006)

• ThreeStateTrackDb: A proposal for a three-state trackDb system.