v144-preview - 4 Oct. 2006

Code changes:

• Support for mutiple sequences in AGP and FA and support for compressed FASTA input in -simpleMulti(Mixed) mode for agpToFa.c (Angie)
• Make use of agpToFa's new ability to handle multiple sequence (makeGenomeDb.pl) (Angie)
• Bug fix in cds.c (Angie)
• Added checkTableStatus.csh script to check to see on what date the table dumps last happened for each machine (Ann)
• Fixes to variation.c and UI button added to control inclusion of ortho alleles in SNP name in hgTracks image (hgTrackUi.c and snp125Ui.c) and ortho allele restricted to panTro2 (Daryl)
• Support for color and filter UI options to loadSnp125Extended and sort SNP list so drawn in increasing order independent of the snp125ExtendedNames variable for including/excluding the orthologous states in variation.c (Daryl)
• Created acemblPep.sql for AceView Genes track (Fan)
• Script to find stale CVS locks (Galt)
• Removed hgCustom suppression from buildCgi32.csh script for 32-bit build (Rachel)
• Refactoring of printSnpAligment to read file defined in snpSeq table changes for SNP processing in hgc.c (Heather)
• Addition of fields for autosql file and sql file and illuminaLookup.c for snpArrayIllumina300 table for SNP arrays (Heather)
• Bug fixes and mods for snpReadSeq.c (Heather)
• Generic utility: trimHeader.c for bosTau3 (Heather)
• hgc.c change to print description text for bed 3 type custom tracks (Hiram)
• Fix for composite tracks in hui.c (Kate)
• Added GenBank link for TransMap details page (Mark)
• Support added for bed8 files (Mark)
• Automation of database and tables creation by ccdsImport.c (Mark)
• GenBank: parse misc_difference fields into .ra file (Mark)
• Options added to stringify.c to create C variable definitions (Mark)

Data changes:

• Assembly-masking for dp4, droGri2, droWil1 for alignments (Angie)
• Added 15-way Conservation and Most Conserved tracks for dm2 (Angie)
• Work on chain/net 7 new fly assemblies and triCas2 (Angie)
• Added new ancestor (homIni14) and tracks to trackDb (Brian)
• Added Acembly track for hg18, lifted from hg17 (Fan)
• Added NIA Gene track for mm8 (Fan)
• Adding Vega Gene track for danRer4 (Rachel)
• Updated Affy Zebrafish track with stricter alignment filtering on danRer3 and danRer4 (Rachel)
• Work on bosTau3 (Heather)
• Merged ENCODE Crawford DNaseI data into a single track (Kate)