angie: changes by commit

branch to review (2009-03-31 to 2009-04-07) v203

• Calls to hDnaFromSeq are rather expensive for 2bit, so cache genomic sequence from a single hDnaFromSeq call covering all of a track's items (even the ones that are only partly in the window). Replaced several strncpy/snprintf calls with memcpy because strncpy/snprintf can include strlen(source) which can be large (cached seq), bad news when called in codon inner loop. Also fixed off-by-one error that caused blue insert line to be drawn 1 base to the left of the end of + strand items (thx Brooke).
  • src/hg/hgTracks/cds.c 1.91 - lines changed: 338, context: html, text, full: html, text
  • src/hg/hgTracks/cds.h 1.21 - lines changed: 12, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.74 - lines changed: 5, context: html, text, full: html, text
• Must not pass null tdb to hAllocConnTrack, so if selected table does not have its own tdb, use current track's tdb.
  • src/hg/hgTables/schema.c 1.56 - lines changed: 1, context: html, text, full: html, text
• Added missing <TR> to wigFilterStatRow.
  • src/hg/hgTables/sumStats.c 1.26 - lines changed: 1, context: html, text, full: html, text
• Changed 8-spaces to tab to avoid make error.
  • src/hg/encode/encodeValidate/makefile 1.16 - lines changed: 0, context: html, text, full: html, text
• In lfFromEncodePeak, pass scoreMin and scoreMax to grayInRange too, not just to adjustBedScoreGrayLevel.
  • src/hg/hgTracks/encode.c 1.21 - lines changed: 1, context: html, text, full: html, text
• In showSchemaDb's call to hAllocConnTrack, use passed-in db instead of database (genome db) in case db is hgFixed etc. Should still be reachable by selected track's profile.
  • src/hg/hgTables/schema.c 1.57 - lines changed: 1, context: html, text, full: html, text
• Added minLimit and maxLimit settings to HGDP bedGraph tracks.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.444 - lines changed: 8, context: html, text, full: html, text
• curTrack is NULL when group is All Tables -- in that case, call hAllocConn instead of hAllocConnTrack in showSchemaDb.
  • src/hg/hgTables/schema.c 1.58 - lines changed: 6, context: html, text, full: html, text
• Shortened HGDP analysis track labels to fit in 80 chars for longLabel, 16 for shortLabel.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.445 - lines changed: 32, context: html, text, full: html, text
• Fix for printf format in cgiMakeDoubleVarInRange so value doesn't get truncated to int.
  • src/lib/cheapcgi.c 1.116 - lines changed: 1, context: html, text, full: html, text
• Added comment that 12fly dpse_caf1 is the same assembly as FlyBase dpse_r2.1_FB2008_02.
  • src/hg/makeDb/doc/dp4.txt 1.5 - lines changed: 1, context: html, text, full: html, text
• HGDP Heterozygosity label and description tweaks after more info from Joe.
  • src/hg/makeDb/trackDb/human/hgdpHzy.html 1.8 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.446 - lines changed: 10, context: html, text, full: html, text
• Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
  • src/hg/makeDb/doc/droAna3.txt 1.3 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/droEre2.txt 1.2 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/droGri2.txt 1.3 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/droMoj3.txt 1.4 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/droVir3.txt 1.3 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/droWil1.txt 1.3 - lines changed: 12, context: html, text, full: html, text
• Don't call drawCdsDiffCodonsOnly if lf->codons is NULL. (not sure how this was prevented before my recent mods to pslTrack.c, simpleTracks.c and cds.c)
  • src/hg/hgTracks/cds.c 1.92 - lines changed: 1, context: html, text, full: html, text
• Added "Smoothed" to hgdpFst labels.
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.447 - lines changed: 2, context: html, text, full: html, text