The source tree

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"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