Commits for angie
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v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260
- 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.
- src/hg/htdocs/goldenPath/help/bam.html - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/README - lines changed 4, context: html, text, full: html, text
- One more place to mention showNames in bam.html.
- src/hg/htdocs/goldenPath/help/bam.html - lines changed 2, 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.
- hgBam.h should include samAlignment.h regardless of USE_BAM, in order toavoid compilation error when USE_BAM is not defined.
- 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.
- src/hg/hgTracks/vcfTrack.c - lines changed 23, context: html, text, full: html, text
- Feature #3711 (VCF haplotype-sorting display): suggestion from David:draw boundaries of leaf clusters in purple.
- src/hg/hgTracks/vcfTrack.c - lines changed 5, 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/hgTracks/vcfTrack.c - lines changed 181, context: html, text, full: html, text
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