All File Changes
v260_base to v261_preview (2011-12-06 to 2011-12-13) v261
- python/lib/ucscgenomics/mkChangeNotes.py
- lines changed 9, context: html, text, full: html, text
added some attributes needed externally
- lines changed 24, context: html, text, full: html, text
added verbose messagings to mkChange Notes
- python/lib/ucscgenomics/ordereddict.py
- lines changed 0, context: html, text, full: html, text
small bugfix to ra.py and changed tabs to spaces in ordereddict
- python/lib/ucscgenomics/ra.py
- lines changed 41, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- lines changed 27, context: html, text, full: html, text
small bugfix to ra.py and changed tabs to spaces in ordereddict
- python/lib/ucscgenomics/test/ra/input/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/GetItem.ra
- lines changed 5, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/IterItems.ra
- lines changed 8, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/IterValues.ra
- lines changed 19, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/input/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/ra/test_ra
- lines changed 188, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra
- lines changed 206, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_file/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/GetItem.ra
- lines changed 5, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/IterItems.ra
- lines changed 8, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/IterValues.ra
- lines changed 19, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/lib/ucscgenomics/test/test_ra_input/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
added optional key parameter as per redmine ticket #6227, and updated unit tests
- python/ucsc_virtualenv.py
- lines changed 2115, context: html, text, full: html, text
Added script and readme on how to create virtual environments for ucsc(ENCODE) developers and testers.
- python/virtual.txt
- lines changed 46, context: html, text, full: html, text
Added script and readme on how to create virtual environments for ucsc(ENCODE) developers and testers.
- src/hg/bedItemOverlapCount/bedItemOverlapCount.c
- lines changed 1, context: html, text, full: html, text
undid change to help message
- src/hg/encode/DAFs/2.0/uwChipSeq.daf
- src/hg/encode/DAFs/2.0/uwTfbs.daf
- src/hg/encode/DAFs/3.0/hg19/wgEncodeCaltechRnaSeq.daf
- lines changed 2, context: html, text, full: html, text
Removed sparse fastq validation inorder to validate the entire fastq file.
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGencode.daf
- lines changed 1, context: html, text, full: html, text
Making a dummy daf for Gencode
- src/hg/encode/DAFs/3.0/hg19/wgEncodeGencodeV7.daf
- lines changed 0, context: html, text, full: html, text
Making a dummy daf for Gencode
- src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibRnaSeq.daf
- lines changed 4, context: html, text, full: html, text
Adjusting the DAF to have less expVars
- src/hg/encode/DAFs/3.0/hg19/wgEncodeRikenCage.daf
- lines changed 23, context: html, text, full: html, text
Upgrading the DAF to have the elements in one daf and the required to be all no
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 2, context: html, text, full: html, text
added verbose messagings to mkChange Notes
- src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.py
- lines changed 33, context: html, text, full: html, text
added verbose messagings to mkChange Notes
- src/hg/encode/encodeMkFilesList/encodeMkFilesList
- lines changed 1, context: html, text, full: html, text
sorted the md5sum files array
- src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
- lines changed 73, context: html, text, full: html, text
first draft of tool to check if files exist in hgdownload
- lines changed 53, context: html, text, full: html, text
changed it to a recursive crawler so it can get all subdirectory contents
- src/hg/encode/encodeQaCheckHgdownloadFiles/makefile
- lines changed 27, context: html, text, full: html, text
first draft of tool to check if files exist in hgdownload
- src/hg/encode/encodeQaInit/encodeQaInit
- lines changed 8, context: html, text, full: html, text
first draft of tool to check if files exist in hgdownload
- lines changed 8, context: html, text, full: html, text
added ability to print out full files and tables list
- lines changed 2, context: html, text, full: html, text
corrected sample commands
- lines changed 2, context: html, text, full: html, text
added verbose mode to the local mkChangeNotes
- src/hg/encode/encodeValidate/config/fields.ra
- lines changed 6, context: html, text, full: html, text
Changing int to a string, I am not sure why this isn't in the cv
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 60, context: html, text, full: html, text
reworked the validateBed subroutine
- lines changed 11, context: html, text, full: html, text
changed the bed validation rules a bit
- lines changed 17, context: html, text, full: html, text
added in chrom Size check and streamlined another check
- lines changed 5, context: html, text, full: html, text
added in more info for error message
- lines changed 18, context: html, text, full: html, text
streamlined the validateBed routine
- src/hg/encode/qaTableCheck/makefile
- lines changed 27, context: html, text, full: html, text
added in first draft of program to check a list of tables against the ones on the RR
- src/hg/encode/qaTableCheck/qaTableCheck
- lines changed 54, context: html, text, full: html, text
added in first draft of program to check a list of tables against the ones on the RR
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 1, context: html, text, full: html, text
fix comment. Thanks Angie! (#6212)
- lines changed 4, context: html, text, full: html, text
fix a problem with disconnecting a hub, followed by using the blue bar to navigate away (#6273)
- 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/hgTracks.c
- lines changed 13, context: html, text, full: html, text
report accurate errors when errors are encountered when navigating in hgTracks (redmine #6229)
- src/hg/hgTracks/renderMain.c
- lines changed 4, context: html, text, full: html, text
add hgt.internal code to support internal use of hgRenderTracks
- src/hg/hgTracks/rmskTrack.c
- lines changed 1, context: html, text, full: html, text
fix repeatMasker display bug (redmin #6275)
- src/hg/hgTracks/simpleTracks.c
- lines changed 19, context: html, text, full: html, text
patches to t2g to make it work even if no article/sequence table exist
- 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/hgc/t2g.c
- lines changed 16, context: html, text, full: html, text
patches to t2g to make it work even if no article/sequence table exist
- lines changed 1, context: html, text, full: html, text
t2g hgc bugfix to show sequences that dont match
- lines changed 1, context: html, text, full: html, text
added target=blank to outlinks in t2g
- src/hg/htdocs/ENCODE/pubs.html
- lines changed 32, context: html, text, full: html, text
Adding some pubs according to ticket 6090
- src/hg/htdocs/FAQ/FAQdownloads.html
- lines changed 5, context: html, text, full: html, text
Changed hard links to relative
- lines changed 1, context: html, text, full: html, text
Changed hard links to relative
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 1, context: html, text, full: html, text
Changed hard links to relative
- src/hg/htdocs/FAQ/FAQlicense.html
- lines changed 2, context: html, text, full: html, text
Changed hard links to relative
- src/hg/htdocs/FAQ/FAQlink.html
- lines changed 3, context: html, text, full: html, text
Changed hard link to relative
- src/hg/htdocs/FAQ/FAQtracks.html
- lines changed 5, context: html, text, full: html, text
Changed hard links to relative
- src/hg/htdocs/Neandertal/index.html
- lines changed 2, context: html, text, full: html, text
Changed hard links to relative
- src/hg/htdocs/admin/mirror.html
- lines changed 1, context: html, text, full: html, text
Changed hard links to relative
- src/hg/htdocs/contacts.html
- lines changed 1, context: html, text, full: html, text
Changed hard links to relative
- lines changed 1, context: html, text, full: html, text
Changed hard links to relative
- 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/htdocs/goldenPath/help/trackDescriptions.html
- lines changed 154, context: html, text, full: html, text
Changed hard links to relative
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 3, context: html, text, full: html, text
Fixed weird typo found by Greg...how did it get there?
- lines changed 1, context: html, text, full: html, text
Changed hard link to relative
- src/hg/htdocs/indexInfo.html
- lines changed 3, context: html, text, full: html, text
Changed hard link to relative
- src/hg/htdocs/indexIntro.html
- lines changed 7, context: html, text, full: html, text
Changed hard links to relative
- 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/js/ajax.js
- lines changed 3, context: html, text, full: html, text
use scrollTop in showWarning so users see warnings
- src/hg/js/hgTracks.js
- lines changed 24, context: html, text, full: html, text
report accurate errors when errors are encountered when navigating in hgTracks (redmine #6229)
- 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/rgdGene2ToKeggEntrez.as
- lines changed 7, context: html, text, full: html, text
Created rgdGene2ToKeggEntrez.as
- src/hg/lib/rgdGene2ToSymbol.as
- lines changed 7, context: html, text, full: html, text
Created rgdGene2ToSymbol.as.
- src/hg/lib/rgdGene2Xref.as
- src/hg/lib/rgdGenePathway.as
- lines changed 6, context: html, text, full: html, text
Created rgdGenePathway.as.
- src/hg/lib/rgdPathway.as
- 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/encodeDccHg19/gencodeV9.txt
- lines changed 27, context: html, text, full: html, text
Adding some notes about what i am doing
- lines changed 26, context: html, text, full: html, text
Adding a GencodeV10 structure, cleaning up v9 notes and submission date
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV9.release1.notes
- lines changed 0, context: html, text, full: html, text
The encodeMkChangeNotes fails on Gencode
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromChip.release2.notes
- lines changed 708, context: html, text, full: html, text
added release2 notes for open chrom tracks
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromFaire.release2.notes
- lines changed 487, context: html, text, full: html, text
added release2 notes for open chrom tracks
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
- lines changed 7, context: html, text, full: html, text
Adding the V2 data for the broken TssHmm files
- src/hg/makeDb/doc/gorGor3.txt
- lines changed 816, context: html, text, full: html, text
annotation done, phastCons and phyloP done for 11-way multiz
- lines changed 80, context: html, text, full: html, text
download data for 11-way business is done
- lines changed 60, context: html, text, full: html, text
hgPal downloads constructed for 11-way
- src/hg/makeDb/doc/hetGla1.txt
- lines changed 18, context: html, text, full: html, text
Finished maheGenomeDb for hetGla1
- lines changed 135, context: html, text, full: html, text
Finished masking for hetGla1
- 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.
- lines changed 14, context: html, text, full: html, text
When parsing the Rfam data, skip over comment lines
- lines changed 13, context: html, text, full: html, text
When parsing the Rfam data, skip over comment lines
- src/hg/makeDb/doc/macEug2.txt
- lines changed 45, context: html, text, full: html, text
Finished windowMasker run for wallby
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 37, context: html, text, full: html, text
Making two refinements on how we use the Rfam alignments. First, remove any duplicate hits. In some cases, Rfam has duplicate hits from closely-related models (e.g. one model being a subtype of another), and in these cases we only want one of them. Second, before combining Rfam (and trnas) with the txWalk output, weed out any alignment that overlaps a txWalk alignment. In most cases, these will be duplicates
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 2, context: html, text, full: html, text
set the upstreamGeneTbl and upstreamMaf for gorGor3
- lines changed 1, context: html, text, full: html, text
use new coverage rule for native mRNA on finished assemblys that takes into account the length of the query sequence using a linear function that requires more coverage the shorter the mRNA is. Related to #20.
- src/hg/makeDb/genbank/src/align/gbBlat
- lines changed 2, context: html, text, full: html, text
another tweak, stepSize=5 only on native mrna (#20)
- src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
- lines changed 6, context: html, text, full: html, text
increase SQL wait_timeout to 24 hours. Default of 8 hours wasn't long enough to load all of genbank on hg19. Related to #20
- src/hg/makeDb/schema/all.joiner
- lines changed 38, context: html, text, full: html, text
Updated rgdGene2 related entries to accomodate recent deletion of some rgdGene2 entries due to problems in RGD's raw data file.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 1, context: html, text, full: html, text
Fixes made from recommendation in Redmine #4577
1. Changed View label and long labels from "Wavelet Smoothed Signal" -> "Wavelet-smoothed Signal"
2. Added Year for Genome Res. article
3. Update Long labels to have -Phase for "Percentage-normalized Signal"
- lines changed 22, context: html, text, full: html, text
Reviewed PROVISIONAL entries
- lines changed 5, context: html, text, full: html, text
Fixing merge conflict- removed PROVISIONAL
- lines changed 43, context: html, text, full: html, text
removing rnaTreatment and run
- lines changed 28, context: html, text, full: html, text
Removing tags with jeff according to code review
- lines changed 1, context: html, text, full: html, text
Changing TM to R for trademark
- lines changed 52, context: html, text, full: html, text
Registering a new cell line
- lines changed 35, context: html, text, full: html, text
Registering 2 new cell lines
- lines changed 10, context: html, text, full: html, text
Updated track defaults to be 2 view only: Percentage-normalized Signl and Wavelet-smoothed Signal. Updated description of phases in cv.ra and Wavelet-smoothed signal in cv.ra and track description. Based on Lab and Kate's recommendations. Redmine #4577.
- lines changed 3, context: html, text, full: html, text
added cd20 protocol to the donor children
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 137, context: html, text, full: html, text
Moving alpha cv to beta
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 82, context: html, text, full: html, text
Removed stanza's with PROVISIONAL tags. Also update registered trademakr symbol to be (R).
- lines changed 14, context: html, text, full: html, text
Added back a missing typeOfTerm (bioRep).
- lines changed 74, context: html, text, full: html, text
Moved over approved changes from beta/cv.ra. Redmine #6202.
- src/hg/makeDb/trackDb/dog/canFam2/trackDb.merckPolyA.all.ra
- lines changed 113, context: html, text, full: html, text
Created trackDb.merckPolyA.all.ra
- src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Added include trackDb.merckPolyA.all.ra.
- src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
- lines changed 406, context: html, text, full: html, text
initial text derived from xenTro3
- lines changed 21, context: html, text, full: html, text
Changed the order of species in the table in the description section. Updated some outdated links.
- src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Changed phyloP subtrack to default to on
- src/hg/makeDb/trackDb/human/est.html
- lines changed 7, context: html, text, full: html, text
Updated outdated journal links
- src/hg/makeDb/trackDb/human/gwasCatalog.html
- lines changed 6, context: html, text, full: html, text
Made some minor content and URL corrections
- src/hg/makeDb/trackDb/human/hg18/trackDb.merckPolyA.all.ra
- lines changed 306, context: html, text, full: html, text
Created trackDb.merckPolyA.all.ra.
- src/hg/makeDb/trackDb/human/hg19/lincRNAs.html
- lines changed 10, context: html, text, full: html, text
Fixed some grammar for correctness and/or readability. Added missing citation. Corrected in text citation formats.
- lines changed 1, context: html, text, full: html, text
Fixed a dash at the very end that was a non-standard character and appearing as gibberish in the html.
- src/hg/makeDb/trackDb/human/hg19/lincRNAs.ra
- lines changed 2, context: html, text, full: html, text
Remove extraFields for rawScore and log2RawScore.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Adding a GencodeV10 structure, cleaning up v9 notes and submission date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 217, context: html, text, full: html, text
replaced the bad fastqs
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 124, context: html, text, full: html, text
updated cshllong to releaseN structure, also added submission 5120
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV10.ra
- lines changed 278, context: html, text, full: html, text
Adding a GencodeV10 structure, cleaning up v9 notes and submission date
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV9.ra
- lines changed 42, context: html, text, full: html, text
Adding a new object and the correct md5sums
- lines changed 17, context: html, text, full: html, text
Adding a GencodeV10 structure, cleaning up v9 notes and submission date
- lines changed 18, context: html, text, full: html, text
removing duplicate metaDb entry
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
- lines changed 23, context: html, text, full: html, text
added data from submission 5128
- lines changed 2, context: html, text, full: html, text
corrected space and added md5sum
- lines changed 2, context: html, text, full: html, text
revoking a bad table, and a replaced table
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 3, context: html, text, full: html, text
restored some lines so the revoked table would get properly displayed in mkChangeNotes
- lines changed 271, context: html, text, full: html, text
added None treatment valeus to objects missing them
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 145, context: html, text, full: html, text
Adding the V2 data for the broken TssHmm files
- lines changed 19, context: html, text, full: html, text
Adding the accession and md5sums
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 3334, context: html, text, full: html, text
batch added a lot of new tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 1, context: html, text, full: html, text
Revert "added in bai in fileName"
This reverts commit 3445aea17002c3c53f9ac99eccccb17710df7b65.
- lines changed 533, context: html, text, full: html, text
batch added tfbs tracks
- src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
- src/hg/makeDb/trackDb/human/hg19/trackDb.merckPolyA.all.ra
- lines changed 1, context: html, text, full: html, text
take out release alpha on parent for merck track (for Fan)
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 10, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
added alpha .ra for mapability
- lines changed 2, context: html, text, full: html, text
made changes to revoke in a patch.ra for qa to review over
- lines changed 1, context: html, text, full: html, text
updated cshllong to releaseN structure, also added submission 5120
- lines changed 1, context: html, text, full: html, text
Changing the release structure for Haib RNA Seq
- lines changed 1, context: html, text, full: html, text
added in include statement for new haib genotype trackDb
- lines changed 2, context: html, text, full: html, text
checking patch for uwhistone
- lines changed 3, context: html, text, full: html, text
changed trackDb to include the release2 and 3 histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
- lines changed 4, context: html, text, full: html, text
changed headers to h4 for sub-categories
- src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
- lines changed 99, context: html, text, full: html, text
New chromatin interactions supertrack description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.new.html
- lines changed 77, context: html, text, full: html, text
Adding a new chromatin interaction supertrack description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
- lines changed 1, context: html, text, full: html, text
Changing the html to not say pooled, dropping the extraFields
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.html
- lines changed 4, context: html, text, full: html, text
Changing the html to not say pooled, dropping the extraFields
- lines changed 175, context: html, text, full: html, text
updated cshllong to releaseN structure, also added submission 5120
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.ra
- lines changed 6, context: html, text, full: html, text
Changing the html to not say pooled, dropping the extraFields
- lines changed 4629, context: html, text, full: html, text
updated cshllong to releaseN structure, also added submission 5120
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
- lines changed 175, context: html, text, full: html, text
updated cshllong to releaseN structure, also added submission 5120
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
- lines changed 4653, context: html, text, full: html, text
updated cshllong to releaseN structure, also added submission 5120
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- lines changed 7, context: html, text, full: html, text
uncommented out a track that works now
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.html
- lines changed 82, context: html, text, full: html, text
renamed files to new release convention
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.ra
- lines changed 8, context: html, text, full: html, text
added data from submission 5128
- lines changed 743, context: html, text, full: html, text
renamed files to new release convention
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
- lines changed 82, context: html, text, full: html, text
renamed files to new release convention
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.ra
- lines changed 743, context: html, text, full: html, text
renamed files to new release convention
- lines changed 6, context: html, text, full: html, text
commenting out version 1 data
- lines changed 8, context: html, text, full: html, text
revoking a bad table, and a replaced table
- lines changed 9, context: html, text, full: html, text
changed html and added stanza back in
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
- lines changed 1, context: html, text, full: html, text
changing the date back to 2011 which Katrina pointed out was wrong in my code review, redmine #6219
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
- lines changed 123, context: html, text, full: html, text
Changing the release structure for Haib RNA Seq
- lines changed 25, context: html, text, full: html, text
Changing details as requested in ticket 1710
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.new.html
- lines changed 94, context: html, text, full: html, text
Changing the release structure for Haib RNA Seq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.new.ra
- lines changed 1212, context: html, text, full: html, text
Changing the release structure for Haib RNA Seq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
- lines changed 10, context: html, text, full: html, text
Changing the release structure for Haib RNA Seq
- lines changed 188, context: html, text, full: html, text
Changing details as requested in ticket 1710
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.release2.html
- lines changed 94, context: html, text, full: html, text
Changing the release structure for Haib RNA Seq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.release2.ra
- lines changed 1212, context: html, text, full: html, text
Changing the release structure for Haib RNA Seq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.html
- lines changed 166, context: html, text, full: html, text
copying over html to new.html
- lines changed 166, context: html, text, full: html, text
renaming to new release convention
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.patch.ra
- lines changed 6839, context: html, text, full: html, text
made changes to revoke in a patch.ra for qa to review over
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 28, context: html, text, full: html, text
Revert "the K562/BCL3 objects need to be revoke also"
This reverts commit bf663af7e2a654939d6c8395a50661e48658f0a5.
- lines changed 64, context: html, text, full: html, text
Revert "revokeing HEY1 tracks in trackDb, this will leak out at the the of the week."
This reverts commit bda0bda2243900af9728abec0406bf9b3d8e3614.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html
- lines changed 166, context: html, text, full: html, text
renaming to new release convention
- lines changed 19, context: html, text, full: html, text
added in html about shRNA verfication data
- lines changed 8, context: html, text, full: html, text
corrected paragraph for validation
- lines changed 7, context: html, text, full: html, text
Bringing some of Flo's words back into this html description of shRNA
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
- lines changed 1, context: html, text, full: html, text
added in html about shRNA verfication data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
- lines changed 92, context: html, text, full: html, text
moved html over to release2
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
- lines changed 92, context: html, text, full: html, text
renamed histone html to release3
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- lines changed 5242, context: html, text, full: html, text
renamed new.ra to patch.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
- lines changed 5242, context: html, text, full: html, text
renamed new.ra to patch.ra
- lines changed 1, context: html, text, full: html, text
checking patch for uwhistone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
- lines changed 5241, context: html, text, full: html, text
renamed histone to release2.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.html
- lines changed 92, context: html, text, full: html, text
moved html over to release2
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.ra
- lines changed 5241, context: html, text, full: html, text
renamed histone to release2.ra
- lines changed 1, context: html, text, full: html, text
moved histone over to release2
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html
- lines changed 92, context: html, text, full: html, text
renamed histone html to release3
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
- lines changed 5242, context: html, text, full: html, text
added in release3 ra for histone
- lines changed 805, context: html, text, full: html, text
batch added a lot of new tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
- lines changed 3, context: html, text, full: html, text
Fixes made from recommendation in Redmine #4577
1. Changed View label and long labels from "Wavelet Smoothed Signal" -> "Wavelet-smoothed Signal"
2. Added Year for Genome Res. article
3. Update Long labels to have -Phase for "Percentage-normalized Signal"
- lines changed 2, context: html, text, full: html, text
Updated track defaults to be 2 view only: Percentage-normalized Signl and Wavelet-smoothed Signal. Updated description of phases in cv.ra and Wavelet-smoothed signal in cv.ra and track description. Based on Lab and Kate's recommendations. Redmine #4577.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
- lines changed 118, context: html, text, full: html, text
Fixes made from recommendation in Redmine #4577
1. Changed View label and long labels from "Wavelet Smoothed Signal" -> "Wavelet-smoothed Signal"
2. Added Year for Genome Res. article
3. Update Long labels to have -Phase for "Percentage-normalized Signal"
- lines changed 18, context: html, text, full: html, text
Updated track defaults to be 2 view only: Percentage-normalized Signl and Wavelet-smoothed Signal. Updated description of phases in cv.ra and Wavelet-smoothed signal in cv.ra and track description. Based on Lab and Kate's recommendations. Redmine #4577.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
- lines changed 91, context: html, text, full: html, text
renamed to have release number
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
- lines changed 3502, context: html, text, full: html, text
renamed to have release number
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html
- lines changed 91, context: html, text, full: html, text
renamed to have release number
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.ra
- lines changed 3502, context: html, text, full: html, text
renamed to have release number
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.ra
- lines changed 3502, context: html, text, full: html, text
created release3 trackDb
- 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/hg/makeDb/trackDb/intronEst.html
- lines changed 6, context: html, text, full: html, text
Updated outdated journal links
- src/hg/makeDb/trackDb/knownGene.html
- lines changed 7, context: html, text, full: html, text
Based on discussion with Brooke, unmade some changes regarding UniProt/SWISS-PROT
- src/hg/makeDb/trackDb/makefile
- src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
- lines changed 139, context: html, text, full: html, text
Initial descriptions for hetGla1.
- src/hg/makeDb/trackDb/moleRat/hetGla1/gap.html
- lines changed 64, context: html, text, full: html, text
Initial descriptions for hetGla1.
- src/hg/makeDb/trackDb/moleRat/hetGla1/gold.html
- lines changed 22, context: html, text, full: html, text
Initial descriptions for hetGla1.
- src/hg/makeDb/trackDb/moleRat/hetGla1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
Initial descriptions for hetGla1.
- src/hg/makeDb/trackDb/mouse/mm7/knownGene.html
- lines changed 3, context: html, text, full: html, text
Based on discussion with Brooke, unmade some changes regarding UniProt/SWISS-PROT
- src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 728, context: html, text, full: html, text
Did some metaDb cleanup and added 6 inputs. Redmine #110.
- lines changed 211, context: html, text, full: html, text
Updated Filenames to be standard format. Redmine #110.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.merckPolyA.all.ra
- lines changed 178, context: html, text, full: html, text
Created trackDb.merckPolyA.all.ra.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Added trackDb.merckPolyA.all.ra.
- lines changed 2, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/mouse/mm9/transcriptome.html
- lines changed 3, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
- lines changed 55, context: html, text, full: html, text
Did some metaDb cleanup and added 6 inputs. Redmine #110.
- src/hg/makeDb/trackDb/mrna.html
- lines changed 5, context: html, text, full: html, text
Updated outdated journal links
- src/hg/makeDb/trackDb/rat/rn4/trackDb.merckPolyA.all.ra
- lines changed 82, context: html, text, full: html, text
Created trackDb.merckPolyA.all.ra.
- src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
- lines changed 1, context: html, text, full: html, text
added include trackDb.merckPolyA.all.ra
- src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.merckPolyA.all.ra
- lines changed 177, context: html, text, full: html, text
Created trackDb.merckPolyA.all.ra
- src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
- lines changed 2, context: html, text, full: html, text
Added trackDb.merckPolyA.all.ra.
- src/hg/makeDb/trackDb/rhesus/trackDb.ra
- lines changed 4, context: html, text, full: html, text
fixed name of table in refSeqAnno search spec. thanks, steve.
- src/hg/makeDb/trackDb/sibGene.html
- lines changed 1, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/sibTxGraph.html
- lines changed 1, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 2, context: html, text, full: html, text
added prevItem/nextItemText to t2g track
- lines changed 2, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/worm/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Replace 'www.isrec.isb-sib.ch' with 'ccg.vital-it.ch'
- src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
- lines changed 58, context: html, text, full: html, text
Corrected order of species in description section. Italicized all instances of X. tropicalis. Updated outdated links.
- src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
- lines changed 1, context: html, text, full: html, text
rearranged species order in checkboxes to match tree image. thanks, steve
- lines changed 1, context: html, text, full: html, text
Changed phyloP subtrack to default to on
- src/hg/makeDb/trackDb/xenoEst.html
- lines changed 8, context: html, text, full: html, text
Updated outdated journal links
- src/hg/makeDb/trackDb/xenoMrna.html
- lines changed 5, context: html, text, full: html, text
Updated outdated journal links
- src/hg/pslCDnaFilter/algo.txt
- lines changed 4, context: html, text, full: html, text
added decay model option to calculate minimum coverage based on query size (#20)
- src/hg/pslCDnaFilter/pslCDnaFilter.c
- lines changed 37, context: html, text, full: html, text
added decay model option to calculate minimum coverage based on query size (#20)
- src/hg/pslCDnaFilter/usage.txt
- lines changed 5, context: html, text, full: html, text
added decay model option to calculate minimum coverage based on query size (#20)
- src/hg/txCds/txCdsRedoUniprotPicks/txCdsRedoUniprotPicks.c
- lines changed 7, context: html, text, full: html, text
Fixing Redmine Bug #3497, in which the wrong UniProt protein is mapped to a specific gene. The code read through the PSL alignments of UniProt sequences to the gene to pick the best one. In picking the best one, it computed a heuristic score with credits for the matching positions and penalties for the various types of alignment errors. But while computing the score, which was a double, unsigned ints were effectively multiplied by negative numbers without type conversion, resulting in a quantity close to MAX_INT. The net effect of this was that poor-quality alignments were receiving massive scores, and were being chosen as the 'best' alignments
- src/hg/utils/phyloTrees/57way.nh
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rearrange the fish a bit, and coelacanth, alligator, crocodile
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now with new distances for the primates from the 11-way gorGor3 calculations
- src/hg/utils/phyloTrees/speciesList.sh
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initial contents seem to work
- src/hg/zoo/zooLib/args.c
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oops, missed a few edits. Thanks Angie (#6212)
- src/hg/zoo/zooLib/util.c
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oops, missed a few edits. Thanks Angie (#6212)
- src/inc/common.mk
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Updating local default version of tabix to 0.2.5.
- src/product/scripts/updateHtml.sh
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allow Encode html hierarchy to be pulled
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 75840
- files changed: 328