v147-preview - 13 Nov. 2006

Code changes:

• Added denovo repeat-finder automation script doWindowMaker.pl. (Andy)
• Added options for computing log-ratios using hgRatioMicroarray, resulting in mods to the microarray library code. (Andy)
• Refactored control of base/codon/diff coloring: hgTracks and hgTrackUi now use a new set of trackDb variables (which have already been pushed) to specify coloring. hui has new lib routines for the new vars, simplifying hgTrackUi's code. Cleaned up cds.h interface. (Angie)
• Ongoing code cleanup for -Wall cleanliness. (Angie)
• Removed CGI code written for previous versions of Locus Variants track. (Belinda)
• Updated scripts used to convert from LDSB nomenclature to genome coords & track tables. (Belinda)
• Mod to hgBlat to support mirror sites with very few blat servers (genome-list now determines list from blatServers). (Galt)
• Fixed minor hgNear bug that caused extra tabs to appear just in the header line when the user presses the "text" button. (Galt)
• Ongoing work on customTrash DB. (Hiram)
• Fixed error in resolution calculation for intersection result from TB in wigDataStream.c. (Hiram)
• Added descriptions of "dataVersion" and "origAssembly" trackDb settings to trackDb/README. These settings were added for ENCODE, but can be used by any track to indicate data provenance (on the details page). (Kate)
• Replaced code in hgc.c and wigMafTrack.c for displaying protein sequence multiple alignments using DNA MAF data. (Fan)
• Fixed bugs in hgc.c ofr SNP alignments, added new function isAllDna() in src/lib/dnautil.c. (Heather)
• Added extra field to the ensXRefZfish table for a SWISS-PROT display ID and to the definition in the ensXRefZfish.as file, recreated .sql, .c, and .h files. Also updated the description of some fields for this structure. (Rachel)

Data changes:

• Updated all.joiner for QA of mm8 Jax tracks. (Angie)
• Added dm2 ORegAnno data. (Belinda)
• Ongoing work on felCat3. (Heather)
• Added AUGUSTUS Using Hints track to hg17. (Mario)
• Added encodeYaleChipRfbr to trackDb, created description page. (Rachel)
• Updated valid BAC end pair criteria in danRer3/4 descriptions. (Rachel)