v126-final - 3 Feb. 2006

New things:

• Angie added support for new MGI/Jackson Lab tracks: jaxRepTranscript, jaxPhenotype, jaxAllele.
• Angie added bed12Source format.
• Mark added a function to return sequences in all lower-case without masking. (lib/twoBit.c and lib/nibTwo.c).
• Fan added -extra option to faSplit.
• Craig Lowe extended axtFilter to include options for the end of the axt.

Edits:

• Mark has edits to dystring.c and htmshell.c to use va_copy to handle reuse of va_list. The edits to htmshell.c are a refinement of edits from v125. Please see his comment in src/inc/common.h revision 1.105.
• Mark has improvements to pslCheck.
• Mark (as genbank user) has an edit to gbSanity.
• Jim is working on search and hgVisiGene.
• Galt is working on visiGene/jackson/get* scripts.
• Daryl has edits for the LD track.
• Heather tweaked snpLoadFasta and added hgc code for snp125 exceptions.

Bug fixes:

• Hiram has fixes to handle document root.

Data:

• Angie is cranking through an rn4 browser.
• Angie updated dm2 genes from FlyBase 4.1 to 4.2.
• Angie did mapping of flybase transcript ids to Uniprot IDs.
• Kate is working on 17-way Conservation for hg17.
• Fan is working on hg18 STS markers.
• Hiram is working on hg17 and monDom2.
• Rachel is working on danRer3: hg18 chains, multiz6way, KG.

Doc:

• Donna has extended the mm7 description to include a note about problems with chr5 and also include more details.