File Changes for angie

v260_base to v261_preview (2011-12-06 to 2011-12-13) v261

• src/hg/hgTables/bam.c
  • lines changed 13, context: html, text, full: html, text
    Thanks Brian for catching the "need to warn here" loose end in code review --now there is an actual warning. I also updated bam.c to have the same maxOut improvements as vcf.c. Unfortunately, we still have the problem that several layers of code will have to be modified in order to have genome-wide maxOut instead of per-region, for non-wiggle data types.
• src/hg/hgTables/filterFields.c
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix in hgTables): the filter page was not showingthe "Limit data output to [100,000]" option for BAM and VCF custom tracks.
• src/hg/hgTables/vcf.c
  • lines changed 7, context: html, text, full: html, text
    Thanks Brian for catching the "need to warn here" loose end in code review --now there is an actual warning. I also updated bam.c to have the same maxOut improvements as vcf.c. Unfortunately, we still have the problem that several layers of code will have to be modified in order to have genome-wide maxOut instead of per-region, for non-wiggle data types.
  • lines changed 16, context: html, text, full: html, text
    Feature #3707 (VCF in hgTables): Brooke pointed out that the headerline that shows the selected fields should appear just before the data rows (note 25). I had put it up top to invalidate the VCF header, but that was silly. Instead, put an informational comment up top explaining that the output is not valid VCF, and put the selected-columns header line where it belongs.
• src/hg/hgTracks/gvfTrack.c
  • lines changed 28, context: html, text, full: html, text
    Feature #6172 (ISCA track tweaks): per ISCA's request, appendabbreviated variant origin to display names.
  • lines changed 1, context: html, text, full: html, text
    Feature #6172 (ISCA track tweaks): refinements suggested by b0b;also spotted the opportunity to link to the Human Phenotype Ontology browser, helpful when the Phenotype is something like "Craniosynostosis".
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    More informative error message for debugging.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 10, context: html, text, full: html, text
    Feature #3711 (VCF haplo-sorting display): David requested that non-leafbranches always appear as rectangles. Now the triangular vs. rectangular option applies only to leaf clusters.
  • lines changed 6, context: html, text, full: html, text
    Feature #3711 (VCF haplo-sorting display): minor tweaks to horizontalendpoints of clustering tree lines, so that they join up in PS/PDF instead of leaving a little gap.
  • lines changed 38, context: html, text, full: html, text
    Feature #2823 (VCF+tabix track handler): found & fixed more non-reentrant code that can lead to race conditions when multiple VCF tracks are loaded in parallel. More than 1000 tries have been successful compared to 5 or 6 failures per 1000 tries before.
  • lines changed 4, context: html, text, full: html, text
    Feature #5019 (VCF support in track hubs): Pauline found that next/previtem arrows were appearing for VCF tracks in hubs, but they don't work. Brian pointed out that the hgTracks handler can disable the inherited settings that enable the arrows. Done. Not sure why the arrows appeared only for hub VCF tracks, not VCF custom tracks.
• src/hg/hgc/gvfClick.c
  • lines changed 4, context: html, text, full: html, text
    Feature #6172 (ISCA track tweaks): per ISCA's requests, change"Structural variant cluster" to "Variant region", add link to dbVar's variant page, and add link to dbVar's page for the ISCA study (nstd37).
  • lines changed 14, context: html, text, full: html, text
    Feature #6172 (ISCA track tweaks): refinements suggested by b0b;also spotted the opportunity to link to the Human Phenotype Ontology browser, helpful when the Phenotype is something like "Craniosynostosis".
• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
  • lines changed 53, context: html, text, full: html, text
    Doc #5529 (VCF+tabix doc): updated for recent enhancements (see #3711).Also reworked some parts to be more clear & accurate.
• src/hg/inc/gwasCatalog.h
  • lines changed 0, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update. The initSample columnneeds to be a longblob not varchar because there are a couple very long descriptions -- no change to the C code fortunately because it's just a char * either way.
• src/hg/lib/gwasCatalog.as
  • lines changed 1, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update. The initSample columnneeds to be a longblob not varchar because there are a couple very long descriptions -- no change to the C code fortunately because it's just a char * either way.
• src/hg/lib/gwasCatalog.sql
  • lines changed 1, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update. The initSample columnneeds to be a longblob not varchar because there are a couple very long descriptions -- no change to the C code fortunately because it's just a char * either way.
• src/hg/lib/pgSnp.c
  • lines changed 6, context: html, text, full: html, text
    Fixing some dumb non-reentrant code that caused a race condition whenmultiple VCF tracks are translating VCF to pgSnp in different threads. This led to a sporadic error reported by Greg and caught in a session by Brooke in #2823 (VCF track handler, notes 12 & 14).
  • lines changed 7, context: html, text, full: html, text
    Feature #2823 (VCF+tabix track handler): found & fixed more non-reentrant code that can lead to race conditions when multiple VCF tracks are loaded in parallel. More than 1000 tries have been successful compared to 5 or 6 failures per 1000 tries before.
• src/hg/lib/vcfUi.c
  • lines changed 3, context: html, text, full: html, text
    Feature #3711 (VCF haplo-sorting display): David requested that non-leafbranches always appear as rectangles. Now the triangular vs. rectangular option applies only to leaf clusters.
  • lines changed 2, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI): describe QUAL using the same words as in hgc, as Katrina suggests.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 11, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update. The initSample columnneeds to be a longblob not varchar because there are a couple very long descriptions -- no change to the C code fortunately because it's just a char * either way.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 7, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update. The initSample columnneeds to be a longblob not varchar because there are a couple very long descriptions -- no change to the C code fortunately because it's just a char * either way.
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 3, context: html, text, full: html, text
    Feature #6172 (ISCA track tweaks): per ISCA's requests, change"Structural variant cluster" to "Variant region", add link to dbVar's variant page, and add link to dbVar's page for the ISCA study (nstd37).
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    Updating local default version of tabix to 0.2.5.