The source tree

"If you can conceive of a bioinformatics job that could be done, it probably already has been done in the kent source tree." (Hiram)

• Tools to explore the source tree:
  • you can use ctags to index the source tree
  • and use cscope to search in the source tree (any better ideas for searching?)
  • midnight commander and a rainy day to explore the source tree...
  • Hiram has a nice list created from the help infos

src/java

You better hate Java if you're dealing with UCSC. Repeat: "We love pointers!".

src/product

Very important info on how to install the gbdb on your own computer

src/utils

Various small tools, not especially related to a particular genome

src/hg

Almost all tools related to any kind of genome

src/hg/mousestuff

everything related to chaining, netting and whole-genome alignments

src/hg/makeDb

Tools and scripts (!) that were used to load data into the databases. Most of them in subdirs here in the format hgLoadx with x for maf/bed/wiggle/axt/net/chain/out/etc. If you understand these, you can build your own genome browser. :-)

src/parasol

Jim's parasol cluster system with documentation

• UCSC terms:
  • axt: some aligner, maybe called faAlign? Also the name of a file format for local alignments.
  • psl file: A format for local alignment hits used by blat. (axt and psl are convertible with axtToPsl)
  • chaining: post-treating local alignments to see if two aligned regions that were located close on the query are located close to each other on the subject.
  • chain file: positions of identical nucleotides
  • netting: post-treating chains to group together many chains into one long alignment.
  • net file: positions of alignable regions
  • Xa file: ? pslToXa ?

Cool Files:

• /kent/src/oneShot/testScripters: cool collection of scripts to test the speed of various languages, result as expected: C with Jim's libs is much faster than anything else