angie: changes by file

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

• src/hg/encode/encodeValidate/makefile
  • 1.16 lines changed: 0, context: html, text, full: html, text
    Changed 8-spaces to tab to avoid make error.
• src/hg/hgTables/schema.c
  • 1.58 lines changed: 6, context: html, text, full: html, text
    curTrack is NULL when group is All Tables -- in that case, call hAllocConn instead of hAllocConnTrack in showSchemaDb.
  • 1.57 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.
  • 1.56 lines changed: 1, 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/sumStats.c
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Added missing <TR> to wigFilterStatRow.
• src/hg/hgTracks/cds.c
  • 1.92 lines changed: 1, 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)
  • 1.91 lines changed: 338, context: html, text, full: html, text
    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.h
  • 1.21 lines changed: 12, context: html, text, full: html, text
    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/encode.c
  • 1.21 lines changed: 1, context: html, text, full: html, text
    In lfFromEncodePeak, pass scoreMin and scoreMax to grayInRange too, not just to adjustBedScoreGrayLevel.
• src/hg/hgTracks/simpleTracks.c
  • 1.74 lines changed: 5, context: html, text, full: html, text
    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/makeDb/doc/dp4.txt
  • 1.5 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/droAna3.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droEre2.txt
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droGri2.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droMoj3.txt
  • 1.4 lines changed: 11, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droVir3.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droWil1.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/trackDb/human/hgdpHzy.html
  • 1.8 lines changed: 7, context: html, text, full: html, text
    HGDP Heterozygosity label and description tweaks after more info from Joe.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.447 lines changed: 2, context: html, text, full: html, text
    Added "Smoothed" to hgdpFst labels.
  • 1.446 lines changed: 10, context: html, text, full: html, text
    HGDP Heterozygosity label and description tweaks after more info from Joe.
  • 1.445 lines changed: 32, context: html, text, full: html, text
    Shortened HGDP analysis track labels to fit in 80 chars for longLabel, 16 for shortLabel.
  • 1.444 lines changed: 8, context: html, text, full: html, text
    Added minLimit and maxLimit settings to HGDP bedGraph tracks.
• src/lib/cheapcgi.c
  • 1.116 lines changed: 1, context: html, text, full: html, text
    Fix for printf format in cgiMakeDoubleVarInRange so value doesn't get truncated to int.