All File Changes
v256_base to v257_preview (2011-08-29 to 2011-09-06) v257
- python/lib/ucscgenomics/compositetrack/CompositeTrack.py
- lines changed 90, context: html, text, full: html, text
added protocol checking functionality, partial support for deprecated, and revised the error messages to be more consistent
- python/lib/ucscgenomics/cvfile/CvFile.py
- lines changed 372, context: html, text, full: html, text
added protocol checking functionality, partial support for deprecated, and revised the error messages to be more consistent
- python/programs/DateCheck/dateCheck.py
- lines changed 117, context: html, text, full: html, text
first version of DateCheck.py, still doesn't output only mdbUpdate statements, but it's functional for now
- python/programs/cvValidate/cvValidate
- lines changed 10, context: html, text, full: html, text
added protocol checking functionality, partial support for deprecated, and revised the error messages to be more consistent
- python/programs/mkGeoPkg/mkGeoPkg
- lines changed 16, context: html, text, full: html, text
added protocol checking functionality, partial support for deprecated, and revised the error messages to be more consistent
- src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
- lines changed 1, context: html, text, full: html, text
Changing import to ucscgenomics
- src/hg/encode/cellTypeParser/cellTypeParser.py
- lines changed 1, context: html, text, full: html, text
Changing import to ucscgenomics
- src/hg/encode/inc/encodePatchTdb.h
- lines changed 67, context: html, text, full: html, text
oops. need to check-in the .h file
- src/hg/hgCustom/hgCustom.c
- lines changed 30, context: html, text, full: html, text
very initial experiment for progress meter, long way to go
- src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer3/otherOrgs.ra
- lines changed 17, context: html, text, full: html, text
turning on sgdGene details page for sacCer3
- src/hg/hgTables/mainPage.c
- lines changed 1, context: html, text, full: html, text
To Do #5164 change GREAT link in Table Browser
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
force dirty to false during a reload to avoid infinite loop that I have observed in chrome (similar to code in hgTracks.js)
- lines changed 2, context: html, text, full: html, text
give dirty input a name to make html validator happy
- lines changed 33, context: html, text, full: html, text
moving Session and PDF/PS links closer to center in the topbar so they are not offscreen. Ensembl and NCBI move to the right
- src/hg/hgTracks/simpleTracks.c
- lines changed 7, context: html, text, full: html, text
reverse complement was clipping map items in dragScroll. Turns out insideX is (at least in this case) unaware of reverse complement.
- lines changed 7, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/hgTracks/vcfTrack.c
- lines changed 9, context: html, text, full: html, text
Feature #2821 (VCF parser): Fun with flawed input. This file's rows have6 keywords in the format column, but most genotype columns have only 5
pieces of data:
ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/supporting/AFR.BI_withr2.20100804.genotypes.vcf.gz
This causes many vcfFileErr calls in vcfParseGenotypes. Turned out that
vcfFileErr was not stopping after the specified # of errors; and that the
warnings are so verbose that I don't think we really need to display them
in hgTracks and hgc. So they are now ignored, and we don't segv on missing
genotype info.
- lines changed 23, context: html, text, full: html, text
Feature #3711 (VCF haplotype-sorting display): Changing appearance ofcluster tree in the left label area. I was drawing trees as I had seen
in microarray & other clustering tools, but David wants something more
compatible with the species-tree view... I'll just quote David here:
It has to look like a legitmate species tree, exactly like the ones on
the details page of the vertebrate conservation track. The only
difference here is that some leaf objects are fatter than other, and it
is not clear where one leaf begins and the other ends.
You need to
1. always draw the branch all the way to the right side (leaf level) so
all the leaves are at the leaf level.
2. The vertical bar representing the "footprint" of each leaf (i.e. the
span of the rows of that cluster) needs to terminate at least 1 or 2
pixels before the edge of the cluster of rows for a given leaf, so there
is white space between clusters. (Or put a colored or bold or vertical
mark at the edge of a cluster of rows.)
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
Changed ordering URL for IKMC from komp to knowckoutmouse site.
- lines changed 6, context: html, text, full: html, text
Added logic to show only the first AA replacement string for omimAvSnp track if there are multiple.
- src/hg/hgc/rnaFoldClick.c
- lines changed 6, context: html, text, full: html, text
changed url to denmark per Jakob. changed ALT message if symlink to image not found
- lines changed 4, context: html, text, full: html, text
Bob and I figured out that if there is no cart set of for a user on the Denmark mirror, then the link to it needs c, l and r passed in the link.
- src/hg/hgc/vcfClick.c
- lines changed 10, context: html, text, full: html, text
Feature #2821 (VCF parser): Fun with flawed input. This file's rows have6 keywords in the format column, but most genotype columns have only 5
pieces of data:
ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/supporting/AFR.BI_withr2.20100804.genotypes.vcf.gz
This causes many vcfFileErr calls in vcfParseGenotypes. Turned out that
vcfFileErr was not stopping after the specified # of errors; and that the
warnings are so verbose that I don't think we really need to display them
in hgTracks and hgc. So they are now ignored, and we don't segv on missing
genotype info.
- lines changed 15, context: html, text, full: html, text
Feature #2823 (VCF track handler): on details page, display allele andgenotype frequencies as percents. When genotypes are given, display
Hardy-Weinberg equilibrium genotype probabilities for comparison.
- src/hg/htdocs/ENCODE/dataStandards.html
- lines changed 67, context: html, text, full: html, text
intitial check in of new ENCODE data standards pages (a work in progress), redmine# 5135
- lines changed 2, context: html, text, full: html, text
added page links to data standards page (a work in progress), redmine# 5135
- lines changed 94, context: html, text, full: html, text
reverted changes to old page so it doesn't leak out yet, redmine# 5135
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 15, context: html, text, full: html, text
added SUNY RIP-seq and put Riken Cage in the proper section
- src/hg/htdocs/ENCODE/experiment_guidelines.html
- lines changed 47, context: html, text, full: html, text
intitial check in of new ENCODE data standards pages (a work in progress), redmine# 5135
- lines changed 6, context: html, text, full: html, text
fixed some html issues and added more styles (a work in progress), redmine# 5135
- src/hg/htdocs/ENCODE/platform_characterization.html
- lines changed 90, context: html, text, full: html, text
intitial check in of new ENCODE data standards pages (a work in progress), redmine# 5135
- lines changed 6, context: html, text, full: html, text
fixed some html issues and added more styles (a work in progress), redmine# 5135
- lines changed 4, context: html, text, full: html, text
added links out to pubmed, redmine# 5135
- src/hg/htdocs/ENCODE/template.html
- lines changed 19, context: html, text, full: html, text
Template for ENCODE portal pages using CSS file
- lines changed 3, context: html, text, full: html, text
updating template, redmine# 5135
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 37, context: html, text, full: html, text
adding Data Hub announcement
- src/hg/htdocs/inc/encodeProject.topbar.html
- lines changed 17, context: html, text, full: html, text
Style and topbar for ENCODE
- src/hg/htdocs/indexNews.html
- lines changed 70, context: html, text, full: html, text
adding Data Hub announcement
- src/hg/htdocs/js/jquery.easing.1.3.js
- lines changed 205, context: html, text, full: html, text
checking in this to test breadcrumbs out for encode pages
- lines changed 205, context: html, text, full: html, text
Removing breadcrumb files since Kate wasn't a fan, redmine# 5135
- src/hg/htdocs/js/jquery.jBreadCrumb.1.1.js
- lines changed 240, context: html, text, full: html, text
checking in this to test breadcrumbs out for encode pages
- lines changed 240, context: html, text, full: html, text
Removing breadcrumb files since Kate wasn't a fan, redmine# 5135
- src/hg/htdocs/style/encodeProject.css
- lines changed 14, context: html, text, full: html, text
intitial check in of new ENCODE data standards pages (a work in progress), redmine# 5135
- lines changed 13, context: html, text, full: html, text
fixed some html issues and added more styles (a work in progress), redmine# 5135
- src/hg/htdocs/style/images/Chevron.gif
- lines changed 0, context: html, text, full: html, text
checking in this to test breadcrumbs out for encode pages
- lines changed 0, context: html, text, full: html, text
Removing breadcrumb files since Kate wasn't a fan, redmine# 5135
- src/hg/htdocs/style/images/ChevronOverlay.png
- lines changed 0, context: html, text, full: html, text
checking in this to test breadcrumbs out for encode pages
- lines changed 0, context: html, text, full: html, text
Removing breadcrumb files since Kate wasn't a fan, redmine# 5135
- src/hg/htdocs/style/images/IconHome.gif
- lines changed 0, context: html, text, full: html, text
checking in this to test breadcrumbs out for encode pages
- lines changed 0, context: html, text, full: html, text
Removing breadcrumb files since Kate wasn't a fan, redmine# 5135
- src/hg/htdocs/style/makefile
- src/hg/inc/pbCommon.h
- lines changed 11, context: html, text, full: html, text
Added define of pbCommon
- src/hg/js/hgTracks.js
- lines changed 5, context: html, text, full: html, text
How embarassing... draScroll wasn't working correctly in reverseComp.
- src/hg/js/lowetooltip.js
- lines changed 4, context: html, text, full: html, text
comment out code for auto-set width button; it is replaced by the resize buttom from genome browser
- src/hg/js/makefile
- lines changed 1, context: html, text, full: html, text
remove extra line which contains duplicate file names (presumably from last merge); this caused a make error (see redmine 5140)
- src/hg/lib/hubConnect.c
- lines changed 1, context: html, text, full: html, text
use safef instead of strcpy. What was I thinking?
- lines changed 1, context: html, text, full: html, text
Use safecpy instead of safef when there is no formatting to do, so we avoidstrict compiler warnings about variable used as format string.
- src/hg/lib/mdb.c
- lines changed 2, context: html, text, full: html, text
Be sure to print mdb validation errors to std out, but return non-zero value when invalids
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
- lines changed 424, context: html, text, full: html, text
dealt with fastqs and wrong error messages
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhRnaSeq.release1.notes
- lines changed 6, context: html, text, full: html, text
Reran the make change notes as there were so many difficulites
- src/hg/makeDb/doc/hg18.txt
- lines changed 68, context: html, text, full: html, text
adding HapMap recombination maps to deCODE track
- lines changed 16, context: html, text, full: html, text
Track #1656 (GWAS Catalog): monthly update on hgwdev.
- src/hg/makeDb/doc/hg19.txt
- lines changed 378, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- lines changed 16, context: html, text, full: html, text
Track #1656 (GWAS Catalog): monthly update on hgwdev.
- src/hg/makeDb/doc/myoLuc2.txt
- src/hg/makeDb/doc/proteins/101005.txt
- lines changed 631, context: html, text, full: html, text
Added a build script for the proteins101005 database. It looks like the database and some files were created, and the initial steps of the build happened, but only the initial steps
- src/hg/makeDb/doc/sacCer1.txt
- lines changed 12, context: html, text, full: html, text
liftOver to sacCer3 completed
- src/hg/makeDb/doc/sacCer2.txt
- lines changed 13, context: html, text, full: html, text
liftOver to sacCer3 completed
- src/hg/makeDb/doc/sacCer3.txt
- lines changed 140, context: html, text, full: html, text
genbank run done, well into the sgdGene construction
- lines changed 18, context: html, text, full: html, text
adding clone location track
- lines changed 102, context: html, text, full: html, text
adding Regulatory Code, Oreganno track and Regulatory Module
- lines changed 149, context: html, text, full: html, text
starting the multiple alignment
- lines changed 106, context: html, text, full: html, text
pairwise maf alignments are done for the 32 query sequences
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
Added sacCer3 - S. cerevisiae
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
Added sacCer3 - S. cerevisiae
- src/hg/makeDb/mdbUpdate/mdbPrint.c
- lines changed 9, context: html, text, full: html, text
Be sure to print mdb validation errors to std out, but return non-zero value when invalids
- src/hg/makeDb/mdbUpdate/mdbUpdate.c
- lines changed 8, context: html, text, full: html, text
Be sure to print mdb validation errors to std out, but return non-zero value when invalids
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
added evofoldV2 to tablesIgnored
- lines changed 1, context: html, text, full: html, text
adding sacCer3 to the ensGeneDb list
- src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
- lines changed 4, context: html, text, full: html, text
Closing some open html tags found by hgTables robot.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 21, context: html, text, full: html, text
Removed duplicate registration of E2F6 antibody from Santa Cruz Biotech. Consolidated documents into one line. Updated antibody and target descriptions. Redmine #4995.
- lines changed 21, context: html, text, full: html, text
Removed duplicate registration of E2F6 antibody from Santa Cruz Biotech. Consolidated documents into one line. Updated antibody and target descriptions. Redmine #4995.
- lines changed 7, context: html, text, full: html, text
Updated description based on Jeff's recommendations. Redmine #5025.
- lines changed 5, context: html, text, full: html, text
Updated tags to be shorter and unique based on vendor ID. This will allow for submissions to pass validation.
- lines changed 19, context: html, text, full: html, text
Capitalizing all tissue, fixing spaces
- lines changed 1, context: html, text, full: html, text
recommented first line in cv.ra that was uncommented.
- lines changed 18, context: html, text, full: html, text
Finished standardizing tissue term
- lines changed 9, context: html, text, full: html, text
Adding descriptions and deprecated status
- lines changed 19, context: html, text, full: html, text
Registering UCH-1 cell line
- lines changed 2, context: html, text, full: html, text
Adding karyotype and lineage
- lines changed 68, context: html, text, full: html, text
Adding CD20 cell lines and fixes
- lines changed 1, context: html, text, full: html, text
Adding commented out deprecated term for Astrocy
- lines changed 22, context: html, text, full: html, text
Adding lots, fixes and antibodies
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 872, context: html, text, full: html, text
The weeks changes to the cv
- src/hg/makeDb/trackDb/human/decode.rmap.ra
- lines changed 39, context: html, text, full: html, text
adding HapMap recomb rate data to decode tracks
- src/hg/makeDb/trackDb/human/decodeRmap.html
- lines changed 14, context: html, text, full: html, text
adding comments from Thorgeir
- lines changed 5, context: html, text, full: html, text
adding HapMap recomb rate data to decode tracks
- src/hg/makeDb/trackDb/human/evofold.html
- lines changed 2, context: html, text, full: html, text
changed some links offsite to open new window
- src/hg/makeDb/trackDb/human/hg18/evofoldV2.html
- lines changed 4, context: html, text, full: html, text
changed some links offsite to open new window
- src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra
- lines changed 1, context: html, text, full: html, text
Removing the UCSC accession column for an hg18 track
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 9, context: html, text, full: html, text
Removing V2 that were not really V2, there never was a V1
- lines changed 5, context: html, text, full: html, text
One more file that says V2 when there was never a V1
- lines changed 1195, context: html, text, full: html, text
Added back the 50 bigwigs that were replaced and are on the RR
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 397, context: html, text, full: html, text
Adding new data and pulling old data
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- lines changed 287, context: html, text, full: html, text
Adding 13 new cell lines to this composite
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 139, context: html, text, full: html, text
Changing astrocy to NH-A
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 2, context: html, text, full: html, text
updated md5sum file for one entry
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
Staging SYDY RNA-seq on beta, redmine #383
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhRnaSeq.ra
- lines changed 270, context: html, text, full: html, text
Staging SYDY RNA-seq on beta, redmine #383
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Releasing SUNY RIP-seq, redmine# 1709
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyRipSeq.ra
- lines changed 1158, context: html, text, full: html, text
Releasing SUNY RIP-seq, redmine# 1709
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 45, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Staging SYDY RNA-seq on beta, redmine #383
- lines changed 1, context: html, text, full: html, text
Releasing SUNY RIP-seq, redmine# 1709
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
- lines changed 21, context: html, text, full: html, text
Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html
- lines changed 105, context: html, text, full: html, text
Basic track description outline for new Single Cell RNA Seq track
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- lines changed 118, context: html, text, full: html, text
Adding new data and pulling old data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
- lines changed 7, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 94, context: html, text, full: html, text
Changing labels to have clone-fee clone-based
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
- lines changed 13, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 123, context: html, text, full: html, text
Adding 13 new cell lines to this composite
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
- lines changed 3, context: html, text, full: html, text
Standardizing the cell line labels so that they play well with encodePatchTdb
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
- lines changed 3, context: html, text, full: html, text
Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
- lines changed 3, context: html, text, full: html, text
These were checked in prematurely before with the tags changed, they are fixed now.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
- lines changed 60, context: html, text, full: html, text
Standardizing the cell line labels so that they play well with encodePatchTdb
- lines changed 11, context: html, text, full: html, text
Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
- lines changed 22, context: html, text, full: html, text
Standardizing the cell line labels so that they play well with encodePatchTdb
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
- lines changed 31, context: html, text, full: html, text
Standardizing the cell line labels so that they play well with encodePatchTdb
- lines changed 1, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html
- lines changed 11, context: html, text, full: html, text
Addressing Jacobs concerns #2020
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 2, context: html, text, full: html, text
Addressing Jacobs concerns #2020
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
- lines changed 19, context: html, text, full: html, text
Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
- lines changed 9, context: html, text, full: html, text
These were checked in prematurely before with the tags changed, they are fixed now.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 25, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- lines changed 5, context: html, text, full: html, text
These were checked in prematurely before with the tags changed, they are fixed now.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
- lines changed 39, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
- lines changed 3, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html
- lines changed 6, context: html, text, full: html, text
Added the SAM explaination and fixed Farhnam reference
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra
- lines changed 2, context: html, text, full: html, text
The view limits are set to 10
- lines changed 9, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
- lines changed 13, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
- lines changed 80, context: html, text, full: html, text
(1) in the UNC/BSU ProtGeno details page, replaced a [to appear] reference with a pointer to a URL. (2) Added the peptideMapping format to the format FAQ, now that I'm aware that there is a format FAQ
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
- lines changed 8, context: html, text, full: html, text
Standardizing the cell line labels so that they play well with encodePatchTdb
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
- lines changed 8, context: html, text, full: html, text
Standardizing the cell line labels so that they play well with encodePatchTdb
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
- lines changed 10, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
- lines changed 9, context: html, text, full: html, text
Trying out the new labeling
- lines changed 136, context: html, text, full: html, text
Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding sacCer3 to the build
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
- lines changed 2, context: html, text, full: html, text
Added 31 submission for Caltech TFBS track. First pass at display settings and html
- lines changed 2, context: html, text, full: html, text
Added 12 submission for Caltech Histone track. First pass at display settings and html. Redmine #4155
- lines changed 1, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
- lines changed 1369, context: html, text, full: html, text
Added 12 submission for Caltech Histone track. First pass at display settings and html. Redmine #4155
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
- lines changed 3303, context: html, text, full: html, text
Added 31 submission for Caltech TFBS track. First pass at display settings and html
- lines changed 19, context: html, text, full: html, text
Replaced submission 4715 with 4448. 4715 is actually replicate 2 and will need an updated DDF.
- lines changed 144, context: html, text, full: html, text
Updated submission 4717 with new metadata and loaded submissions 4715, 4450.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 100, context: html, text, full: html, text
Replaced submission 3052 with submission 4800.
- lines changed 296, context: html, text, full: html, text
Added 2 more submissions that replaced previous submissions.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
- lines changed 751, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 751, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
- lines changed 724, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHistone.ra
- lines changed 724, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
- lines changed 724, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHistone.ra
- lines changed 724, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
Added 12 submission for Caltech Histone track. First pass at display settings and html. Redmine #4155
- lines changed 1, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
- lines changed 152, context: html, text, full: html, text
Added 12 submission for Caltech Histone track. First pass at display settings and html. Redmine #4155
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
- lines changed 272, context: html, text, full: html, text
Added 12 submission for Caltech Histone track. First pass at display settings and html. Redmine #4155
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
- lines changed 152, context: html, text, full: html, text
Added 31 submission for Caltech TFBS track. First pass at display settings and html
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
- lines changed 479, context: html, text, full: html, text
Added 31 submission for Caltech TFBS track. First pass at display settings and html
- lines changed 18, context: html, text, full: html, text
Replaced submission 4715 with 4448. 4715 is actually replicate 2 and will need an updated DDF.
- lines changed 47, context: html, text, full: html, text
Updated submission 4717 with new metadata and loaded submissions 4715, 4450.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
- lines changed 36, context: html, text, full: html, text
Replaced submission 3052 with submission 4800.
- lines changed 78, context: html, text, full: html, text
Added 2 more submissions that replaced previous submissions.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.ra
- lines changed 163, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
- lines changed 163, context: html, text, full: html, text
Updated naming schema of trackDb and metaDb to reflect name of composite as wgEncodeSydhHist instead of wgEncodeSydhHistone. This provides consistency for GEO tools to correctly submit the data. Redmine #4754.
- src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
- lines changed 120, context: html, text, full: html, text
initial file contents ready to go
- src/hg/makeDb/trackDb/sacCer/sacCer3/gap.html
- lines changed 11, context: html, text, full: html, text
initial file contents ready to go
- src/hg/makeDb/trackDb/sacCer/sacCer3/gold.html
- lines changed 21, context: html, text, full: html, text
initial file contents ready to go
- src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
- lines changed 223, context: html, text, full: html, text
turning on the 7-way conservation track
- src/hg/makeDb/trackDb/sacCer/sacCer3/sgdGene.html
- lines changed 14, context: html, text, full: html, text
turning on the 7-way conservation track
- src/hg/makeDb/trackDb/sacCer/sacCer3/sgdOther.html
- lines changed 14, context: html, text, full: html, text
turning on the 7-way conservation track
- src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra
- lines changed 18, context: html, text, full: html, text
initial file contents ready to go
- lines changed 34, context: html, text, full: html, text
turning on the 7-way conservation track
- src/hg/makeDb/trackDb/snp134.html
- lines changed 36, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/makeDb/trackDb/snp134.shared.html
- lines changed 360, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/makeDb/trackDb/snp134Common.html
- lines changed 28, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/makeDb/trackDb/snp134Flagged.html
- lines changed 29, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/makeDb/trackDb/snp134Mult.html
- lines changed 25, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
Fixing the snpDb error for Angie
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 55, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/oneShot/doOmimGene2/doOmimGene2.c
- lines changed 4, context: html, text, full: html, text
added mrnaAcc as the 2nd ordering condition
- src/hg/protein/pbCalDist/pbCalDist.c
- lines changed 1, context: html, text, full: html, text
Reinstated some global variables that I'd mistakenly removed, thus breaking the build. Reordered the #defined amino acids, on the guess that the order might be important. Renamed the #define for the number of standard amino acids, for clarity
- src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
- lines changed 1, context: html, text, full: html, text
Reinstated some global variables that I'd mistakenly removed, thus breaking the build. Reordered the #defined amino acids, on the guess that the order might be important. Renamed the #define for the number of standard amino acids, for clarity
- src/hg/protein/pbCalResStd/pbCalResStd.c
- src/hg/protein/pbTracks/pbTracks.c
- lines changed 0, context: html, text, full: html, text
Making sure that some changes are checked in so that the build can be un-broken
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 21, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/snp/snpMask/snpMaskSingle.c
- lines changed 17, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/txGene/txGeneValidation/compareTableSizesFromDbSnoop.py
- lines changed 1, context: html, text, full: html, text
Fixed a bug that led to the column labels being reversed
- src/hg/txGene/txGeneValidation/makefile
- lines changed 2, context: html, text, full: html, text
Added one more script to the makefile, so it will be copied to the appropriate places
- src/hg/utils/automation/doDbSnp.pl
- lines changed 39, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/utils/automation/snpAddTGPAlleleFreq.pl
- lines changed 221, context: html, text, full: html, text
Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/lib/vcf.c
- lines changed 6, context: html, text, full: html, text
Feature #2821 (VCF parser): Fun with flawed input. This file's rows have6 keywords in the format column, but most genotype columns have only 5
pieces of data:
ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/supporting/AFR.BI_withr2.20100804.genotypes.vcf.gz
This causes many vcfFileErr calls in vcfParseGenotypes. Turned out that
vcfFileErr was not stopping after the specified # of errors; and that the
warnings are so verbose that I don't think we really need to display them
in hgTracks and hgc. So they are now ignored, and we don't segv on missing
genotype info.
- src/product/README.local.git.source
- lines changed 1, context: html, text, full: html, text
Changed the note that says we update every two weeks to say we update every three weeks.
- src/utils/bigWigMerge/bigWigMerge.c
- lines changed 20, context: html, text, full: html, text
fix bug in bigWigMerge #4561. Add test that would have found it.
- src/utils/bigWigMerge/makefile
- lines changed 13, context: html, text, full: html, text
fix bug in bigWigMerge #4561. Add test that would have found it.
- lines changed 16, context: html, text, full: html, text
make tests a little more stand-alone and easier to clean (include chrom.sizes in test dir)
- src/utils/bigWigMerge/test/expected/12merge.bedGraph
- lines changed 4, context: html, text, full: html, text
fix bug in bigWigMerge #4561. Add test that would have found it.
- src/utils/bigWigMerge/test/expected/21merge.bedGraph
- lines changed 3, context: html, text, full: html, text
fix bug in bigWigMerge #4561. Add test that would have found it.
- src/utils/bigWigMerge/test/in/hg19.chrom.sizes
- lines changed 93, context: html, text, full: html, text
make tests a little more stand-alone and easier to clean (include chrom.sizes in test dir)
- src/utils/bigWigMerge/test/in/t1.bed
- lines changed 2, context: html, text, full: html, text
fix bug in bigWigMerge #4561. Add test that would have found it.
- src/utils/bigWigMerge/test/in/t2.bed
- lines changed 1, context: html, text, full: html, text
fix bug in bigWigMerge #4561. Add test that would have found it.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 23736
- files changed: 229
