v182-preview - 6 May 2008    (Pairings)

Code changes:

• Moved most of webIncludeFile in web.c out to hFileContentsOrWarning in hui.c so the error-checking can be shared with code that stores the content (e.g. in tdb->html) instead of immediately printing it. Also changed the return type of webInclude{,Help}File to void because all callers ignore it and it simplified the code move. Incorporated new webIncludeHelpFile in several places. (Angie)
• Added UI setting to PCR Results track: non-genomic target results can be drawn either with the matching part tall and the non-matching parts short, or just trimmed to the matching part. Added support for non-genomic PCR target items with accession plus display name encoded into the targetDb 2bit names. Target PSL qNames are just the accessions. Works the same for targets with just accessions. (Angie)
• Updated hgc.c:doPscreen's obsolete external links and added support for FBgn IDs in pscreen.geneIds. (Angie)
• Mod to lib/hgSeq.c - just show strand instead of the confusing pair of revComp (whether we rc'd genomic sequence) plus strand (item strand), or '?' when there is no item. strand is now like the old meaning of revComp, but reflects the item strand when there is an item because we don't offer the revComp checkbox in that case. (Angie)
• Two changes to lib/jksql.c to help InnoDB performance, where count(*) causes a very slow full table scan: 1. In sqlTableExists, use describe instead of select count(*). 2. In sqlTableOk, try the select query first and count rows only if it fails. (Angie)
• Mods to doRepeatMasker.pl automation script - changed the load step to install and moved up a few earlier operations that could overwrite top-level files into the install step. Thanks Robert H. for pointing out that -stop mask test runs had side-effects. (Angie)
• Fixed bug in hgGene/sequence.c - when a user clicked on the mRNA or protein link on the hgGene details page before the page finished drawing, the cart was not yet updated and therefore the user saw information for the the previously viewed gene instead of the current gene. (Galt)
• Added increment int function to lib/hash.c. (Galt)
• Turned off killTime by default in parasol. (Galt)
• Ongoing work on new UCSC Genes. (Jim)
• Added bedBlockSizeInRange and related functions to lib/bed.c. (Jim)
• Mods to jsHelper.c - change jsIncludeFile to locate files in cgi-bin/js; add jsCheckAllOnClickHandler and cgiMakeCheckAllSubmitButton, change errAbort to fprintf(stderr,...) (will revert once apache configuration is in place for all developers). (Larry)
• Added hCgiRoot() to lib/hui.c. (Larry)
• In hgTables/filterFields.c, moved javascript-specific code into cgiMakeCheckAllSubmitButton, js mods backed out until post-v181 release. (Larry)
• Added option to utils/faSize/faSize.c to output stats in parseable format. (Mark)
• Mod to makeDb/hgLoadBed/hgLoadBed.c - comment lines beginning with '#' and empty lines are now ignored. (Tim)

Data changes:

• Added Gene Disruption Project Insertions track to dm3. (Angie)
• Ongoing work on braFlo1 and petMar1. (Hiram)
• Ongoing work on equCab2 multiple alignments. (Larry)
• Updated CCDS on human, mouse assemblies. (Mark)
• Added N-SCAN predictions for equCab2. (Mark)