CVS changes by file

review to branch (2009-06-02 to 2009-06-09) v208

• src/hg/archaeStuff/data/Genome-info-euk
  • 1.15 lines changed: 6, context: html, text, full: html, text
    update zebrafish to v8
• src/hg/archaeStuff/data/Genome-info-meta
  • 1.8 lines changed: 1, context: html, text, full: html, text
    fix multiz for cistSpri
  • 1.7 lines changed: 9, context: html, text, full: html, text
    add nanEqu1 to multiz
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.111 lines changed: 1, context: html, text, full: html, text
    Fixed STAT1 url
  • 1.110 lines changed: 8, context: html, text, full: html, text
    Added STAT2 for Yale
  • 1.109 lines changed: 21, context: html, text, full: html, text
    Added type treatment with 4 treatments for Yale
  • 1.108 lines changed: 2, context: html, text, full: html, text
    Did I happen to mention how much I hate updating cv.ra?
  • 1.107 lines changed: 31, context: html, text, full: html, text
    Missing orderUrl's
  • 1.106 lines changed: 1, context: html, text, full: html, text
    Missing type
  • 1.105 lines changed: 78, context: html, text, full: html, text
    Added a batch of cell lines
  • 1.104 lines changed: 53, context: html, text, full: html, text
    Added a bunch of new antibodies
  • 1.103 lines changed: 2, context: html, text, full: html, text
    url must be a url, move descriptoin to vendor name
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.182 lines changed: 1, context: html, text, full: html, text
    Adder controlde vocam term 'treatment'
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.86 lines changed: 1, context: html, text, full: html, text
    link to be allowed as requested by Tim D
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • 1.42 lines changed: 2, context: html, text, full: html, text
    Tim D wants validate link to be available
• src/hg/hgTables/custom.c
  • 1.42 lines changed: 1, context: html, text, full: html, text
    Restored a line of code inadvertently deleted in 1.38 (green beer ? ;)
• src/hg/hgTables/filterFields.c
  • 1.76 lines changed: 14, context: html, text, full: html, text
    cgiToDoubleFilter wasn't allocating quite enough space for its results, and callers of cgiToDoubleFilter weren't handling NULL results.
• src/hg/hgTracks/hgTracks.c
  • 1.1569 lines changed: 19, context: html, text, full: html, text
    Added logic for GISAID project.
• src/hg/hgTracks/simpleTracks.c
  • 1.83 lines changed: 1, context: html, text, full: html, text
    Added handler for h1n1_0602Seq.
• src/hg/hgc/hgc.c
  • 1.1551 lines changed: 4, context: html, text, full: html, text
    Added an errAboort.
  • 1.1550 lines changed: 1, context: html, text, full: html, text
    Proper ATCC URL link for Yeast clones
  • 1.1549 lines changed: 180, context: html, text, full: html, text
    Added showProtH1n1() to accomodate Kevin Karplus's new Modeller pipeline. This is work in progress.
  • 1.1548 lines changed: 124, context: html, text, full: html, text
    Added printSnp125CodingAnnotations, to display coding effects of SNPs from a table specified by a new trackDb setting (e.g. dbSNP's annotations).
• src/hg/inc/hCommon.h
  • 1.23 lines changed: 5, context: html, text, full: html, text
    Added gisaid selection file option variable names.
  • 1.22 lines changed: 4, context: html, text, full: html, text
    Added hIsGisaidServer().
• src/hg/inc/hgMaf.h
  • 1.23 lines changed: 3, context: html, text, full: html, text
    Added #defines for gisaidTable selection list files
• src/hg/inc/snp125CodingCoordless.h
  • 1.1 lines changed: 70, context: html, text, full: html, text
    Added snp125CodingCoordless: coding effects of SNPs identified only by ID (no disambiguating coords, tsk tsk dbSNP).
• src/hg/inc/versionInfo.h
  • 1.148 lines changed: 1, context: html, text, full: html, text
    "New version number v208"
• src/hg/inc/web.h
  • 1.43 lines changed: 7, context: html, text, full: html, text
    don't dumps stacks on find errors; doing stack dump in abort handler rather than warn handler simplifies
  • 1.42 lines changed: 10, context: html, text, full: html, text
    added option to generate stack dumps when browser errors occur
• src/hg/instinct/bioInt2/grabData.c
  • 1.7 lines changed: 21, context: html, text, full: html, text
    Fixed issue where clinical data was querying wrong field, also starting to add pathway stuff
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.66 lines changed: 5, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgAnnotations.c
  • 1.10 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgChromGraph.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgCircleMaps.c
  • 1.11 lines changed: 6, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgGenesets.c
  • 1.10 lines changed: 6, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.76 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgHeatmap2.h
  • 1.48 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb.ra
  • 1.5 lines changed: 157, context: html, text, full: html, text
    update ispy clinical data
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    replaced TCGAopen.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgSessions.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgToolTip.c
  • 1.8 lines changed: 6, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/hgUsers.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/hgHeatmap2/trashDirMD5.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/cluster.h
  • 1.2 lines changed: 92, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/featuresLib.h
  • 1.15 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/filterFeatures.h
  • 1.5 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/heatmapUtility.h
  • 1.4 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/hgHeatmapCustomDb.h
  • 1.2 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/hgHeatmapLib.h
  • 1.37 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/hgStats.h
  • 1.6 lines changed: 67, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/hgStatsLib.h
  • 1.6 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/ispyTableDefs.h
  • 1.3 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/json.h
  • 1.2 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/sortFeatures.h
  • 1.3 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/inc/tcgaTableDefs.h
  • 1.2 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/cluster.c
  • 1.3 lines changed: 4262, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/featuresLib.c
  • 1.30 lines changed: 5, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/filterFeatures.c
  • 1.9 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/heatmapUtility.c
  • 1.6 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/hgHeatmapCustomDb.c
  • 1.2 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.60 lines changed: 1, context: html, text, full: html, text
    removed hgStats.h ref
  • 1.59 lines changed: 214, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/hgStats.c
  • 1.5 lines changed: 1206, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/hgStatsLib.c
  • 1.14 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/ispyTableDefs.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/json.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/makefile
  • 1.15 lines changed: 2, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/sortFeatures.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/instinct/lib/tcgaTableDefs.c
  • 1.2 lines changed: 4, context: html, text, full: html, text
    added copyright notices, removed cluster library
• src/hg/js/hui.js
  • 1.29 lines changed: 33, context: html, text, full: html, text
    Rearranged a little and added subtrackCBsSetAll() for 'allButtonPair' tdb setting
• src/hg/lib/cart.c
  • 1.109 lines changed: 4, context: html, text, full: html, text
    don't dumps stacks on find errors; doing stack dump in abort handler rather than warn handler simplifies
  • 1.108 lines changed: 3, context: html, text, full: html, text
    added option to generate stack dumps when browser errors occur
• src/hg/lib/gisaidXref.sql
  • 1.1 lines changed: 10, context: html, text, full: html, text
    Created gisaidXref.sql.
• src/hg/lib/hCommon.c
  • 1.37 lines changed: 15, context: html, text, full: html, text
    Added hIsGisaidServer().
• src/hg/lib/hVarSubst.c
  • 1.4 lines changed: 47, context: html, text, full: html, text
    Properly look for ClosestToHome variables during substitution and add chain linearGap matrix variable recognition
• src/hg/lib/hgFind.c
  • 1.219 lines changed: 24, context: html, text, full: html, text
    don't dumps stacks on find errors; doing stack dump in abort handler rather than warn handler simplifies
• src/hg/lib/hui.c
  • 1.208 lines changed: 23, context: html, text, full: html, text
    Added support for 'allButtonPair' UI
• src/hg/lib/makefile
  • 1.389 lines changed: 1, context: html, text, full: html, text
    Added snp125CodingCoordless: coding effects of SNPs identified only by ID (no disambiguating coords, tsk tsk dbSNP).
• src/hg/lib/snp125CodingCoordless.as
  • 1.1 lines changed: 12, context: html, text, full: html, text
    Added snp125CodingCoordless: coding effects of SNPs identified only by ID (no disambiguating coords, tsk tsk dbSNP).
• src/hg/lib/snp125CodingCoordless.c
  • 1.1 lines changed: 256, context: html, text, full: html, text
    Added snp125CodingCoordless: coding effects of SNPs identified only by ID (no disambiguating coords, tsk tsk dbSNP).
• src/hg/lib/snp125CodingCoordless.sql
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Added snp125CodingCoordless: coding effects of SNPs identified only by ID (no disambiguating coords, tsk tsk dbSNP).
• src/hg/lib/web.c
  • 1.166 lines changed: 1, context: html, text, full: html, text
    Bumped up a buf size -- caught by Mark, checking the error_log for his new pstack dumps.
  • 1.165 lines changed: 1, context: html, text, full: html, text
    make stack dump on warn/abort stack under/overlow permanet
  • 1.164 lines changed: 4, context: html, text, full: html, text
    don't webEnd if didn't webStart
  • 1.163 lines changed: 4, context: html, text, full: html, text
    added tmp debugging code track down harmless but annoying warn/abort stack underflows
  • 1.162 lines changed: 27, context: html, text, full: html, text
    don't dumps stacks on find errors; doing stack dump in abort handler rather than warn handler simplifies
  • 1.161 lines changed: 43, context: html, text, full: html, text
    added option to generate stack dumps when browser errors occur
• src/hg/makeDb/doc/aplCal1.txt
  • 1.8 lines changed: 9, context: html, text, full: html, text
    making pushQ entry
  • 1.7 lines changed: 14, context: html, text, full: html, text
    making pushQ entry
  • 1.6 lines changed: 164, context: html, text, full: html, text
    human proteins
• src/hg/makeDb/doc/hg18.txt
  • 1.364 lines changed: 22, context: html, text, full: html, text
    update nucleosome occupance track due to corrupted data on chr3
• src/hg/makeDb/doc/hg19.txt
  • 1.24 lines changed: 244, context: html, text, full: html, text
    Andy's blastzs to hg19.
  • 1.23 lines changed: 69, context: html, text, full: html, text
    the swap lastz are done for those genomes that are public on the RR
  • 1.22 lines changed: 282, context: html, text, full: html, text
    Begin running the swaps
• src/hg/makeDb/doc/monDom5.txt
  • 1.9 lines changed: 6, context: html, text, full: html, text
    one tiny bit about the goldenPath/monDom5/database dir + README.
  • 1.8 lines changed: 51, context: html, text, full: html, text
    big zips/downloads
• src/hg/makeDb/doc/taeGut1.txt
  • 1.17 lines changed: 5, context: html, text, full: html, text
    rebuild incorrect data that was submitted
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.338 lines changed: 2, context: html, text, full: html, text
    per-chrom = no, and got a lift file for monDom5.
• src/hg/makeDb/genbank/etc/hgofbeta-dbload
  • 1.2 lines changed: 24, context: html, text, full: html, text
    removed unused hgofbeta stuff
• src/hg/makeDb/genbank/etc/hgofbeta.crontab
  • 1.2 lines changed: 16, context: html, text, full: html, text
    removed unused hgofbeta stuff
• src/hg/makeDb/genbank/etc/hgofbeta.dbs
  • 1.2 lines changed: 76, context: html, text, full: html, text
    removed unused hgofbeta stuff
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.52 lines changed: 30, context: html, text, full: html, text
    Fix error for -strict operation, and properly clean up subTracks that had parents disappear
  • 1.51 lines changed: 11, context: html, text, full: html, text
    Properly mark composite parents and children so that ClosestToHome settings will function OK
• src/hg/makeDb/schema/all.joiner
  • 1.719 lines changed: 3, context: html, text, full: html, text
    adding aplCal1 sea hare
  • 1.718 lines changed: 4, context: html, text, full: html, text
    Added nucleosome occupancy tables.
  • 1.717 lines changed: 69, context: html, text, full: html, text
    Added snp130CodingDbSnp to identifier snpName130. Consolidated identifiers for snp*.name.
• src/hg/makeDb/trackDb/README
  • 1.76 lines changed: 89, context: html, text, full: html, text
    Added allButtonPair and hopefully clarified some details
• src/hg/makeDb/trackDb/anopheles/rmsk.html
  • 1.4 lines changed: 5, context: html, text, full: html, text
    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/apis/rmsk.html
  • 1.4 lines changed: 5, context: html, text, full: html, text
    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/chicken/galGal2/description.html
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Updated link to wustl.
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Updated link to wustl.
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.19 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/dog/canFam1/description.html
  • 1.23 lines changed: 2, context: html, text, full: html, text
    Add Tasha's name to the photo caption
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Add Tasha's name to the photo caption
• src/hg/makeDb/trackDb/drosophila/rmsk.html
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.57 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/human/hg16/cnp.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to nature paper.
• src/hg/makeDb/trackDb/human/hg17/cnp.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Removed session ID from link to nature paper.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipPval.html
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid froom nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipPvalOld.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid froom nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipPvalue.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid froom nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipRfbr.html
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Link to american statistical association paper stopped working. Updated link.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSig.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid froom nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSignal.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid froom nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSites.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid froom nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg18/divMKAR.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Removed jsessionid from nature paper link.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipPval.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid from nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSig.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid from nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSites.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Removed jsessionid from nature paper and linked to abstract instead of full article.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.395 lines changed: 6, context: html, text, full: html, text
    a temporary and quick fix for the fact that the phyloP and phastCons tracks have been accidentally dropped from beta and the RR
  • 1.394 lines changed: 2, context: html, text, full: html, text
    Added new setting codingAnnotations to snp130 (for hgc).
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.340 lines changed: 2159, context: html, text, full: html, text
    Added tracks for Yale amd cleaned up a lot of obsolete settings
  • 1.339 lines changed: 6, context: html, text, full: html, text
    Minor typos
  • 1.338 lines changed: 40, context: html, text, full: html, text
    Added Bryal Lajoie's uniqueness track
  • 1.337 lines changed: 40, context: html, text, full: html, text
    these are the 40 subtracks that are going to be released initially
  • 1.336 lines changed: 2, context: html, text, full: html, text
    corrected date (per Tim)
  • 1.335 lines changed: 5, context: html, text, full: html, text
    Adjust defaults for HudsonAlpha TFBS
  • 1.334 lines changed: 1, context: html, text, full: html, text
    Overkill with the drip drip drip of changes
  • 1.333 lines changed: 1, context: html, text, full: html, text
    And alignability should be selected by default
  • 1.332 lines changed: 1, context: html, text, full: html, text
    Tarjei requested windowFunction=mean on his alignability track
  • 1.331 lines changed: 36, context: html, text, full: html, text
    Added Broad's alignability track to the Mapability composite
  • 1.330 lines changed: 1, context: html, text, full: html, text
    Fix label for Open Chromatin subtrack
  • 1.329 lines changed: 1, context: html, text, full: html, text
    Adjust default views for Open CHromatin
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.9 lines changed: 9, context: html, text, full: html, text
    Angie's review found <DD>s where there should be </DD>s. I bet this is in other description pages as well. But it is really not a worry.
  • 1.8 lines changed: 39, context: html, text, full: html, text
    Adhere to Details pages -- conventions
  • 1.7 lines changed: 16, context: html, text, full: html, text
    Edit for spelling and formatting
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.17 lines changed: 9, context: html, text, full: html, text
    Edited for redundancy.
  • 1.16 lines changed: 9, context: html, text, full: html, text
    added Data Release Policy
  • 1.15 lines changed: 11, context: html, text, full: html, text
    initial tweaks
  • 1.14 lines changed: 58, context: html, text, full: html, text
    Complete for release, as per wiki instructions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.5 lines changed: 22, context: html, text, full: html, text
    Added Bryan Lajoie's uniqueness track
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Tarjei requested a credit change
  • 1.3 lines changed: 21, context: html, text, full: html, text
    Added Broad's alignability track
• src/hg/makeDb/trackDb/human/snpRecombHotspot.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Removed session ID from links to nature papers.
• src/hg/makeDb/trackDb/human/snpRecombRate.html
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Removed session ID from links to nature papers.
• src/hg/makeDb/trackDb/humanChainNet.html
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Now showing chain minScore and linearGap options
  • 1.1 lines changed: 151, context: html, text, full: html, text
    Adding hg19 chain and net composite track
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/lizard/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/makefile
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    Adding canFamPoodle1 to the build, Craig Venter's poodle "Shadow"
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/medaka/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/mouse/mm4/rmsk.html
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    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/opossum/monDom5/description.html
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    Added link to Broad.
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    Some stats filled in.
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.5 lines changed: 32, context: html, text, full: html, text
    Added unsplit mRNA and EST trackDbs
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    new tree for new conservation track
• src/hg/makeDb/trackDb/orangutan/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/platypus/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/rmsk.html
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    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/sacCer/blastHg18KG.html
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    Scientific name needed italics.
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    Adding page to allow yeast specific italics.
• src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
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    italicizing scientific name.
• src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
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    italicizing scientific name.
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
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    ATCC clone link now taken care of in hgc.c
• src/hg/makeDb/trackDb/squirt/rmsk.html
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    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.510 lines changed: 7, context: html, text, full: html, text
    Now showing chain minScore and linearGap options
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    Adding hg19 chain and net composite track
• src/hg/makeDb/trackDb/worm/rmsk.html
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/zebrafish/danRer5/rmsk.html
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    Clarified the Repeat Masker track description
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
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    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/utils/automation/HgAutomate.pm
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    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/HgRemoteScript.pm
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    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/doBlastzChainNet.pl
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    Find db name from /scratch/data/ directory name, and generalize the ssh command to avoid questions to the shell for new hosts, and properly verify all DEF variables before they start
• src/hg/utils/automation/doHgNearBlastp.pl
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    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/doSimpleRepeat.pl
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    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/makeDownloads.pl
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    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/makeGenomeDb.pl
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    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/makePushQSql.pl
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    hgofbeta is now hgsqlbeta, and generalize the ssh command
• src/inc/cgi_build_rules.mk
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    don't strip binaries to allow stack traces
• src/inc/cheapcgi.h
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    added option to generate stack dumps when browser errors occur
• src/inc/common.h
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    added option to generate stack dumps when browser errors occur
• src/inc/errabort.h
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    make stack dump on warn/abort stack under/overlow permanet
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    added tmp debugging code track down harmless but annoying warn/abort stack underflows
• src/lib/cheapcgi.c
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    added option to generate stack dumps when browser errors occur
• src/lib/errabort.c
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    make stack dump on warn/abort stack under/overlow permanet
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    added tmp debugging code track down harmless but annoying warn/abort stack underflows
• src/lib/htmshell.c
  • 1.51 lines changed: 1, context: html, text, full: html, text
    Mark caught my sloppy code. vsprintf replaced with vsnprintf()
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    removed extra newline that added annoy line to log file
• src/lib/osunix.c
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    make sure dumpStack does end up being recusivel called due to an error
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    added option to generate stack dumps when browser errors occur
• src/product/ex.hg.conf
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    added option to generate stack dumps when browser errors occur
• src/utils/qa/compareTrackDbAll.csh
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    grammar tweak
• src/utils/qa/compareTrackDbFast.csh
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    Added onintr to remove files when script has been killed.
• src/utils/qa/compareTrackDbs.csh
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    Added onintr to remove files when script has been killed.
• src/utils/qa/countPerChrom.csh
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    allowed use of "hgwbeta" as argument
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    Added a missing endif.
• src/utils/qa/countRows.csh
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    added missinf endquote
• src/utils/qa/doGenbankTests
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    added whitespace.
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    removed some slashes that were not doing anything and added some whitespace in usage output
• src/utils/qa/getRRtables.csh
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    droppped a comma from the usage statement
• src/utils/qa/makeUniProtFile.csh
  • 1.7 lines changed: 2, context: html, text, full: html, text
    grammar tweak
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    two small tweaks based on code review with Bob
• src/utils/qa/weeklybld/buildEnv.csh
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    v208 final build

• lines changed: 11646
• files changed: 161