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
- 1.3 lines changed: 3, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/makefile
- 1.268 lines changed: 1, context: html, text, full: html, text
Adding canFamPoodle1 to the build, Craig Venter's poodle "Shadow"
- src/hg/makeDb/trackDb/marmoset/trackDb.ra
- 1.2 lines changed: 2, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/medaka/trackDb.ra
- 1.14 lines changed: 4, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/mouse/mm4/rmsk.html
- 1.6 lines changed: 5, context: html, text, full: html, text
Clarified the Repeat Masker track description
- src/hg/makeDb/trackDb/opossum/monDom5/description.html
- 1.4 lines changed: 3, context: html, text, full: html, text
Added link to Broad.
- 1.3 lines changed: 40, context: html, text, full: html, text
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
- 1.4 lines changed: 1, context: html, text, full: html, text
new tree for new conservation track
- src/hg/makeDb/trackDb/orangutan/trackDb.ra
- 1.2 lines changed: 2, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/platypus/trackDb.ra
- 1.2 lines changed: 3, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/rhesus/trackDb.ra
- 1.10 lines changed: 3, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/rmsk.html
- 1.21 lines changed: 6, context: html, text, full: html, text
Clarified the Repeat Masker track description
- src/hg/makeDb/trackDb/sacCer/blastHg18KG.html
- 1.2 lines changed: 2, context: html, text, full: html, text
Scientific name needed italics.
- 1.1 lines changed: 27, context: html, text, full: html, text
Adding page to allow yeast specific italics.
- src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
- 1.17 lines changed: 3, context: html, text, full: html, text
italicizing scientific name.
- src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
- 1.6 lines changed: 4, context: html, text, full: html, text
italicizing scientific name.
- src/hg/makeDb/trackDb/sacCer/trackDb.ra
- 1.38 lines changed: 1, context: html, text, full: html, text
ATCC clone link now taken care of in hgc.c
- src/hg/makeDb/trackDb/squirt/rmsk.html
- 1.4 lines changed: 5, context: html, text, full: html, text
Clarified the Repeat Masker track description
- src/hg/makeDb/trackDb/stickleback/trackDb.ra
- 1.16 lines changed: 3, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/tetraodon/trackDb.ra
- 1.37 lines changed: 4, context: html, text, full: html, text
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
- 1.509 lines changed: 37, context: html, text, full: html, text
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
- 1.19 lines changed: 3, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
- 1.2 lines changed: 4, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/makeDb/trackDb/zebrafish/danRer5/rmsk.html
- 1.5 lines changed: 5, context: html, text, full: html, text
Clarified the Repeat Masker track description
- src/hg/makeDb/trackDb/zebrafish/trackDb.ra
- 1.51 lines changed: 4, context: html, text, full: html, text
Add humanChainNet override variables chainMinScore and chainLinearGap
- src/hg/utils/automation/HgAutomate.pm
- 1.27 lines changed: 15, context: html, text, full: html, text
Generalize the ssh command to avoid questions to the shell for new hosts
- src/hg/utils/automation/HgRemoteScript.pm
- 1.2 lines changed: 1, context: html, text, full: html, text
Generalize the ssh command to avoid questions to the shell for new hosts
- src/hg/utils/automation/doBlastzChainNet.pl
- 1.29 lines changed: 21, context: html, text, full: html, text
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
- 1.7 lines changed: 8, context: html, text, full: html, text
Generalize the ssh command to avoid questions to the shell for new hosts
- src/hg/utils/automation/doSimpleRepeat.pl
- 1.5 lines changed: 1, context: html, text, full: html, text
Generalize the ssh command to avoid questions to the shell for new hosts
- src/hg/utils/automation/makeDownloads.pl
- 1.22 lines changed: 1, context: html, text, full: html, text
Generalize the ssh command to avoid questions to the shell for new hosts
- src/hg/utils/automation/makeGenomeDb.pl
- 1.22 lines changed: 3, context: html, text, full: html, text
Generalize the ssh command to avoid questions to the shell for new hosts
- src/hg/utils/automation/makePushQSql.pl
- 1.25 lines changed: 6, context: html, text, full: html, text
hgofbeta is now hgsqlbeta, and generalize the ssh command
- src/inc/cgi_build_rules.mk
- 1.10 lines changed: 2, context: html, text, full: html, text
don't strip binaries to allow stack traces
- src/inc/cheapcgi.h
- 1.66 lines changed: 3, context: html, text, full: html, text
added option to generate stack dumps when browser errors occur
- src/inc/common.h
- 1.151 lines changed: 6, context: html, text, full: html, text
added option to generate stack dumps when browser errors occur
- src/inc/errabort.h
- 1.12 lines changed: 2, context: html, text, full: html, text
make stack dump on warn/abort stack under/overlow permanet
- 1.11 lines changed: 2, context: html, text, full: html, text
added tmp debugging code track down harmless but annoying warn/abort stack underflows
- src/lib/cheapcgi.c
- 1.122 lines changed: 7, context: html, text, full: html, text
added option to generate stack dumps when browser errors occur
- src/lib/errabort.c
- 1.15 lines changed: 18, context: html, text, full: html, text
make stack dump on warn/abort stack under/overlow permanet
- 1.14 lines changed: 10, context: html, text, full: html, text
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()
- 1.50 lines changed: 1, context: html, text, full: html, text
removed extra newline that added annoy line to log file
- src/lib/osunix.c
- 1.41 lines changed: 17, context: html, text, full: html, text
make sure dumpStack does end up being recusivel called due to an error
- 1.40 lines changed: 24, context: html, text, full: html, text
added option to generate stack dumps when browser errors occur
- src/product/ex.hg.conf
- 1.16 lines changed: 9, context: html, text, full: html, text
added option to generate stack dumps when browser errors occur
- src/utils/qa/compareTrackDbAll.csh
- src/utils/qa/compareTrackDbFast.csh
- 1.9 lines changed: 3, context: html, text, full: html, text
Added onintr to remove files when script has been killed.
- src/utils/qa/compareTrackDbs.csh
- 1.29 lines changed: 3, context: html, text, full: html, text
Added onintr to remove files when script has been killed.
- src/utils/qa/countPerChrom.csh
- 1.12 lines changed: 10, context: html, text, full: html, text
allowed use of "hgwbeta" as argument
- 1.11 lines changed: 1, context: html, text, full: html, text
Added a missing endif.
- src/utils/qa/countRows.csh
- 1.7 lines changed: 1, context: html, text, full: html, text
added missinf endquote
- src/utils/qa/doGenbankTests
- 1.15 lines changed: 1, context: html, text, full: html, text
added whitespace.
- 1.14 lines changed: 6, context: html, text, full: html, text
removed some slashes that were not doing anything and added some whitespace in usage output
- src/utils/qa/getRRtables.csh
- 1.5 lines changed: 1, context: html, text, full: html, text
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
- 1.6 lines changed: 2, context: html, text, full: html, text
two small tweaks based on code review with Bob
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 11646
- files changed: 161