v125-final
New features:
- Brian has committed extensive changes to wigMafTrack.c.
- Hiram editted featureBits to use chrom name and gap hashes to speed up
measurements on scaffold based assemblies.
- Hiram added support for .wab files to liftUp.
- Mark added a mapInfo option to pslMap.
- Andy added new features to rtdbServer (startServer, doUpdate).
- Heather has started on snp125 exception annotating.
New utils:
- Hiram has a new util hg/near/hgWormLinks/mkSangerLinks.pl.
- Mark wrote build/kentBuild. Here is his comment:
"Designed for running under a cron job, this saves the stdout/err in *.log
files in kentDir. It then parses the output file to find errors reported
by make an copies the regions of the output log containing the errors to
stderr. This way, both the error message and the context can be seen
without needing to read through the entire log. If there are no errors, there is
no output."
- Heather wrote a quick-and-dirty util qa/gbSeqCheck.
Edits:
- Daryl has enhancements to the LD track.
- Jim has visiGene edits.
- Heather (with guidance from Mark) added an fprintf to htmshell.c that will
log user errors to the Apache error log.
- Heather has cleanup/corrections to the snp125 code
Bug fixes:
- Mark has a fix to genePred.c regarding the bin column.
- Angie has fixes to doHgNearBlastp.pl.
Speed tweaks:
- Jim has a speed tweak in hdb.c: change call to hFindSplitTable to hTableForTrack.
Data:
- Angie added *BlastTab tables to dm2.
- Angie has 500 lines changed in makeGalGal2.doc.
- Fan added hg18/bosTau2 blastz pairwise.
- Hiram started working on hg18 clone coverage.
- Hiram added several sections to makeCe3.doc.
- Kate continues to work on hg17 Conservation.