v155-preview1 - 20 Mar. 2007    (Pairings)

Code changes:

• Added formMethod cart var to hgCustom.c for debugging. (Angie)
• Added a new view-ali-in-window link to the GenBank details page. (Angie)
• Added customFactoryParseAnyDb, a variant of customFactoryParse that doesn't die if the tracks are for a database other than hGetDb. (Angie)
• Added cartCopyCustomTracks to cartLoadUserSession and cartLoadSettings, so that a user who loads a session that contains custom tracks cannot modify the original session's custom tracks. (Angie)
• Added formMethod cart var to hgNear/advFilter.c for debugging and errAbort in a situation caused by out-of-sync gene and canonical tables that would lead to a later segv. (Angie)
• Added -type=.bed8 to the bed8 tests and updated expected/bed8.bed so that the last 2 columns are lifted. (Angie)
• Since strict and allowStartEqualEnd are now the default behavior for hgLoadBed, removed -strict and -allowStartEqualEnd and updated usage. Added -noStrict option for test loads of tables with coord problems, to test checkTableCoords. (Angie)
• Updated GeneSorter acc and FlyBaseId links to latest FlyBase gene query format. (Angie)
• Added ffShAliPartPart to fuzzyFind, which extends ffShAliPart by accepting two lists, partial and whole, and displaying the whole needle but with the partial portion in bold, plus the partial haystack and blocks. (Angie)
• Ongoing work to GSID. (Fan, Galt)
• Updated GeneSorter and hgGene GO and Amigo URLs. (Fan)
• Added sqlRandomSampleWithSeed function in jksql.h to allow specifying seed for reproducible random numbers during debugging. (Galt)
• Fixed threshold type in chromGraph. (Galt)
• Fixed err in chromGraphFactory.c caused by previewing lines: later reuse had no access to the original linefile object, so segfault when it tried to use it in some input error reporting errAborts. (Galt)
• Added support for reporting multiple missing values as a warning instead of just errAbort in GeneSorter advFilter.c. (Galt)
• Ongoing HapMap SNPs work. (Heather)
• Added better error-reporting on bad bed chrom coordinate input, better management of environment variables while pipeline loaders are being run in customFactory.c. (Hiram)
• Added mods to hgLoadBed.c: ignore empty lines in input, add new options to usage message, don't error out on loader warnings for the customTrackLoader, properly handle bedGraph column--it can be anywhere--and check for chromEnd of 0, check input as it is being read rather than after the fact. (Hiram)
• More KGIII-related work. (Jim)
• Fixed bug with not reversing the query range when orientation is changed. (Mark)
• Added support for obtaining GenBank orientation info files. (Mark)
• Added option to pslPartition to drop alignments completely contained in the exon of another alignment. (Mark)
• Added code to ratStuff/mafOrtholog to look up orthologs in other gene sets using maf. (Robert)
• Added new field hmmScore to snoRNAs. (Todd)

Data changes:

• Added first draft of ACEScan track to hg18. (Andy)
• Added gasAcu1 chainSelf. (Angie)
• Added ctgPos2 definition for caeRem2 contigs track. (Hiram)
• Changed AUGUSTUS track to a compound track w/2 subtracks. (Mario)
• Added automated Ensembl build. (Robert)