File Changes for angie

v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260

• src/hg/hgTracks/vcfTrack.c
  • lines changed 23, context: html, text, full: html, text
    Feature #3711 (VCF haplotype-sorting display): Reverting to the originalstyle of drawing the hap-cluster tree (clustering-tool style instead of phylogenetic-ish style). This reverts commit 5770f49f480bbfe5d920ece22f96961954e43116.
  • lines changed 5, context: html, text, full: html, text
    Feature #3711 (VCF haplotype-sorting display): suggestion from David:draw boundaries of leaf clusters in purple.
  • lines changed 181, context: html, text, full: html, text
    Feature #3711 (VCF haplotype-sorting display): Added mouseover titles forclusters in left label area. Thanks Tim for adding the capability to make a mouseover title with no link! Also fixed mapBox for center variant: it needs to be created *before* the other variants are drawn and mapped; this is the opposite of drawing (center variant is drawn last so it appears on top). Also added variant name (if not "." placeholder) to variant mouseover.
• src/hg/hgc/t2g.c
  • lines changed 4, context: html, text, full: html, text
    Fixes for stricter -Wall warnings: use puts instead of printf if there's noformat argument, and use TRUE & FALSE instead of true & false.
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 2, context: html, text, full: html, text
    Doc #5964 (document some trackDb variables): added BAM-specificsettings showNames and noColorTag to trackDb/README. noColorTag is internal-use-only, and I'm considering dropping it and just not offering the bamColorTag UI option if the bamColorTag setting is not present. So I added only showNames to goldenPath/help/bam.html.
  • lines changed 2, context: html, text, full: html, text
    One more place to mention showNames in bam.html.
• src/hg/inc/hgBam.h
  • lines changed 4, context: html, text, full: html, text
    hgBam.h should include samAlignment.h regardless of USE_BAM, in order toavoid compilation error when USE_BAM is not defined.
• src/hg/makeDb/trackDb/README
  • lines changed 4, context: html, text, full: html, text
    Doc #5964 (document some trackDb variables): added BAM-specificsettings showNames and noColorTag to trackDb/README. noColorTag is internal-use-only, and I'm considering dropping it and just not offering the bamColorTag UI option if the bamColorTag setting is not present. So I added only showNames to goldenPath/help/bam.html.