CVS changes by file

branch to review (2009-03-31 to 2009-04-07) v203

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.65 lines changed: 1, context: html, text, full: html, text
    change seq_acc for vulcDist0
  • 1.64 lines changed: 2, context: html, text, full: html, text
    add seq size and gc for vulcDist0
  • 1.63 lines changed: 28, context: html, text, full: html, text
    add vulcDist0
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.12 lines changed: 71, context: html, text, full: html, text
    replace awk with file io
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.15 lines changed: 5, context: html, text, full: html, text
    copy gbRNAs fasta file from precomputed directory
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.10 lines changed: 23, context: html, text, full: html, text
    support host, user and password args
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.61 lines changed: 8, context: html, text, full: html, text
    try and avoid mysql timeout errors for stuff that takes 14,000 seconds or more
  • 1.60 lines changed: 1, context: html, text, full: html, text
    use pushq B (i.e. to force human review before QA sees the entry)
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.176 lines changed: 7, context: html, text, full: html, text
    Subtracks are no longer by default set to be configurable, due to performance issues. Change at wrangler's discretion
  • 1.175 lines changed: 8, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • 1.174 lines changed: 20, context: html, text, full: html, text
    Cosmetics (whitespace in trackDb)
  • 1.173 lines changed: 46, context: html, text, full: html, text
    validate csfasta and csqual files with validateFiles prog
  • 1.172 lines changed: 7, context: html, text, full: html, text
    add quick option to validateFiles
  • 1.171 lines changed: 26, context: html, text, full: html, text
    fix warning on comparison with undefined; add fasta file validation by validateFiles program
• src/hg/encode/encodeValidate/makefile
  • 1.16 lines changed: 0, context: html, text, full: html, text
    Changed 8-spaces to tab to avoid make error.
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Install cv.ra as part of 'make alpha'
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Subtracks are no longer by default set to be configurable, due to performance issues. Change at wrangler's discretion
• src/hg/encode/encodeValidate/test/expected/methylseq/README.txt
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • 1.2 lines changed: 3, context: html, text, full: html, text
    table name changed
• src/hg/encode/encodeValidate/test/expected/methylseq/load.ra
  • 1.4 lines changed: 16, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • 1.3 lines changed: 2, context: html, text, full: html, text
    table name changed
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Adjust name of HCT cell line to match cv.ra
• src/hg/encode/encodeValidate/test/expected/methylseq/trackDb.ra
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Subtracks are no longer by default set to be configurable, due to performance issues. Change at wrangler's discretion
  • 1.4 lines changed: 12, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
  • 1.3 lines changed: 20, context: html, text, full: html, text
    table name changed
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Adjust name of HCT cell line to match cv.ra
• src/hg/encode/encodeValidate/test/input/methylseq/GM12878.txt.BED
  • 1.1 lines changed: 100, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
• src/hg/encode/encodeValidate/test/input/methylseq/GM12878.txt.peaks
  • 1.1 lines changed: 4999, context: html, text, full: html, text
    Set subtrack defaults based on cell type (only Tier1 default on). Change at wrangler's discretion
• src/hg/encode/encodeValidate/test/input/methylseq/HudsonAlphaMethylSeq.DDF
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Adjust name of HCT cell line to match cv.ra
• src/hg/encode/validateFiles/validateFiles.c
  • 1.16 lines changed: 26, context: html, text, full: html, text
    option for quick checking of files (1000 lines of each)
  • 1.15 lines changed: 43, context: html, text, full: html, text
    validation of fasta files (single-line of sequence, no quality)
  • 1.14 lines changed: 7, context: html, text, full: html, text
    making code easier to read
• src/hg/hgGenome/hgGenome.c
  • 1.64 lines changed: 22, context: html, text, full: html, text
    add function checkAndClear so that do commands are not stuck in cart after an errAbort
• src/hg/hgGenome/import.c
  • 1.14 lines changed: 20, context: html, text, full: html, text
    use genoLayDbChromsExt for chromList
• src/hg/hgGenome/mainPage.c
  • 1.26 lines changed: 64, context: html, text, full: html, text
    deal with javascript and cases where only cga (clade,genome,assembly) will appear since there are no usable chroms
• src/hg/hgTables/schema.c
  • 1.58 lines changed: 6, context: html, text, full: html, text
    curTrack is NULL when group is All Tables -- in that case, call hAllocConn instead of hAllocConnTrack in showSchemaDb.
  • 1.57 lines changed: 1, context: html, text, full: html, text
    In showSchemaDb's call to hAllocConnTrack, use passed-in db instead of database (genome db) in case db is hgFixed etc. Should still be reachable by selected track's profile.
  • 1.56 lines changed: 1, context: html, text, full: html, text
    Must not pass null tdb to hAllocConnTrack, so if selected table does not have its own tdb, use current track's tdb.
• src/hg/hgTables/sumStats.c
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Added missing <TR> to wigFilterStatRow.
• src/hg/hgTracks/cds.c
  • 1.92 lines changed: 1, context: html, text, full: html, text
    Don't call drawCdsDiffCodonsOnly if lf->codons is NULL. (not sure how this was prevented before my recent mods to pslTrack.c, simpleTracks.c and cds.c)
  • 1.91 lines changed: 338, context: html, text, full: html, text
    Calls to hDnaFromSeq are rather expensive for 2bit, so cache genomic sequence from a single hDnaFromSeq call covering all of a track's items (even the ones that are only partly in the window). Replaced several strncpy/snprintf calls with memcpy because strncpy/snprintf can include strlen(source) which can be large (cached seq), bad news when called in codon inner loop. Also fixed off-by-one error that caused blue insert line to be drawn 1 base to the left of the end of + strand items (thx Brooke).
• src/hg/hgTracks/cds.h
  • 1.21 lines changed: 12, context: html, text, full: html, text
    Calls to hDnaFromSeq are rather expensive for 2bit, so cache genomic sequence from a single hDnaFromSeq call covering all of a track's items (even the ones that are only partly in the window). Replaced several strncpy/snprintf calls with memcpy because strncpy/snprintf can include strlen(source) which can be large (cached seq), bad news when called in codon inner loop. Also fixed off-by-one error that caused blue insert line to be drawn 1 base to the left of the end of + strand items (thx Brooke).
• src/hg/hgTracks/config.c
  • 1.77 lines changed: 21, context: html, text, full: html, text
    Made hgTracks expand/colapse groups work identiacally between config and image version
• src/hg/hgTracks/encode.c
  • 1.21 lines changed: 1, context: html, text, full: html, text
    In lfFromEncodePeak, pass scoreMin and scoreMax to grayInRange too, not just to adjustBedScoreGrayLevel.
• src/hg/hgTracks/simpleTracks.c
  • 1.74 lines changed: 5, context: html, text, full: html, text
    Calls to hDnaFromSeq are rather expensive for 2bit, so cache genomic sequence from a single hDnaFromSeq call covering all of a track's items (even the ones that are only partly in the window). Replaced several strncpy/snprintf calls with memcpy because strncpy/snprintf can include strlen(source) which can be large (cached seq), bad news when called in codon inner loop. Also fixed off-by-one error that caused blue insert line to be drawn 1 base to the left of the end of + strand items (thx Brooke).
• src/hg/inc/genoLay.h
  • 1.5 lines changed: 4, context: html, text, full: html, text
    add genoLayDbChromsExt to handle case of not abort on error
• src/hg/instinct/bioInt2/bioGeneLevel.c
  • 1.4 lines changed: 19, context: html, text, full: html, text
    added cohorts api
• src/hg/instinct/bioInt2/bioIntDb.c
  • 1.6 lines changed: 27, context: html, text, full: html, text
    fixed db code
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntStyle.css
  • 1.14 lines changed: 6, context: html, text, full: html, text
    Total rework of storage and layout
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Fixed issue where adding wasn't appending the needed extra cells when samples got added
  • 1.12 lines changed: 23, context: html, text, full: html, text
    Added start of toolbar
  • 1.11 lines changed: 5, context: html, text, full: html, text
    Added suggest on feature input
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Committing current changes
  • 1.9 lines changed: 36, context: html, text, full: html, text
    Committing current changes
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.25 lines changed: 1, context: html, text, full: html, text
    fixed bug with mouseovers
  • 1.24 lines changed: 20, context: html, text, full: html, text
    Changed middle col to ... and added sample names to mouseovers
  • 1.23 lines changed: 116, context: html, text, full: html, text
    Added new wizard at the beginning
  • 1.22 lines changed: 437, context: html, text, full: html, text
    Total rework of storage and layout
  • 1.21 lines changed: 1, context: html, text, full: html, text
    removed debug statement
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Fixed issue where adding wasn't appending the needed extra cells when samples got added
  • 1.19 lines changed: 8, context: html, text, full: html, text
    fixed issue with safari and onkeypress
  • 1.18 lines changed: 44, context: html, text, full: html, text
    Added start of toolbar
  • 1.17 lines changed: 2, context: html, text, full: html, text
    A few minor suggest fixes
  • 1.16 lines changed: 60, context: html, text, full: html, text
    Added suggest on feature input
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Committing current changes
  • 1.14 lines changed: 163, context: html, text, full: html, text
    Committing current changes
• src/hg/instinct/bioInt2/bioIntFrontend/color.js
  • 1.1 lines changed: 723, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/bioInt2/bioIntFrontend/index.html
  • 1.16 lines changed: 14, context: html, text, full: html, text
    Added new wizard at the beginning
  • 1.15 lines changed: 7, context: html, text, full: html, text
    Added start of toolbar
  • 1.14 lines changed: 1, context: html, text, full: html, text
    A few minor suggest fixes
  • 1.13 lines changed: 27, context: html, text, full: html, text
    Committing current changes
• src/hg/instinct/bioInt2/bioIntFrontend/jquery.cookie.js
  • 1.1 lines changed: 96, context: html, text, full: html, text
    Adding cookie handler
• src/hg/instinct/bioInt2/bioIntUI.c
  • 1.14 lines changed: 125, context: html, text, full: html, text
    changed way codes were sent
  • 1.13 lines changed: 45, context: html, text, full: html, text
    updated
  • 1.12 lines changed: 7, context: html, text, full: html, text
    added files, fixed cohorts API
  • 1.11 lines changed: 59, context: html, text, full: html, text
    added cohorts api
  • 1.10 lines changed: 56, context: html, text, full: html, text
    better search results
  • 1.9 lines changed: 10, context: html, text, full: html, text
    updated
  • 1.8 lines changed: 69, context: html, text, full: html, text
    added suggestions api and changed getFeatureData api
• src/hg/instinct/bioInt2/bioLevelI.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    added cohorts api
• src/hg/instinct/bioInt2/bioSetLevel.c
  • 1.1 lines changed: 251, context: html, text, full: html, text
    added files, fixed cohorts API
• src/hg/instinct/bioInt2/grabData.c
  • 1.3 lines changed: 6, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 71, context: html, text, full: html, text
    added transpose option
  • 1.1 lines changed: 412, context: html, text, full: html, text
    added files, fixed cohorts API
• src/hg/instinct/bioInt2/makefile
  • 1.7 lines changed: 8, context: html, text, full: html, text
    added cohorts api
• src/hg/instinct/bioInt2/populateDb.c
  • 1.6 lines changed: 18, context: html, text, full: html, text
    added cohorts api
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.74 lines changed: 2, context: html, text, full: html, text
    removed a printf
• src/hg/js/hgTracks.js
  • 1.24 lines changed: 3, context: html, text, full: html, text
    Tighten the restrictions on converting links to posts
  • 1.23 lines changed: 126, context: html, text, full: html, text
    Made hgTracks expand/colapse groups work identiacally between config and image version
  • 1.22 lines changed: 2, context: html, text, full: html, text
    Oops. Reversing accidental check in of experimental code
  • 1.21 lines changed: 2, context: html, text, full: html, text
    Convert all href links to posts in order to save the users settings to the cart
  • 1.20 lines changed: 13, context: html, text, full: html, text
    Convert all href links to posts in order to save the users settings to the cart
• src/hg/js/hui.js
  • 1.24 lines changed: 19, context: html, text, full: html, text
    Partially enable desirable multi-select changes
  • 1.23 lines changed: 42, context: html, text, full: html, text
    Necessary checkin of registerOnChange to bind with jQuery.change(). Also checking in incomplete, but not yet used code.
• src/hg/js/utils.js
  • 1.17 lines changed: 1, context: html, text, full: html, text
    postTheForm must explicitly set action to POST
  • 1.16 lines changed: 5, context: html, text, full: html, text
    No longer need to convert href vars to hidden inputs when converting a link to a posted url
  • 1.15 lines changed: 131, context: html, text, full: html, text
    Added validation routines for integers and floats
• src/hg/lib/botDelay.c
  • 1.14 lines changed: 2, context: html, text, full: html, text
    use standard function in hui to get central.cookie - note RR does not set central.cookie, so it has to provide the default "hguid"
• src/hg/lib/encode/broadPeak.sql
  • 1.3 lines changed: 4, context: html, text, full: html, text
    some RNA files are > 4gb
• src/hg/lib/encode/pairedTagAlign.sql
  • 1.3 lines changed: 4, context: html, text, full: html, text
    GIS gDNA PET alignments overflow the 4GB table
• src/hg/lib/genoLay.c
  • 1.12 lines changed: 10, context: html, text, full: html, text
    removing some unneeded bits
  • 1.11 lines changed: 48, context: html, text, full: html, text
    add genoLayDbChromsExt to handle case of not abort on error, also change filtering to only include chr chroms other than chrUn and chrM
• src/hg/lib/hui.c
  • 1.184 lines changed: 4, context: html, text, full: html, text
    Fix problem where multi-view without cfgType was causing warn()
  • 1.183 lines changed: 2, context: html, text, full: html, text
    Partially enable desirable multi-select changes
  • 1.182 lines changed: 143, context: html, text, full: html, text
    Enable javascript validation of selected integer and double input controls.
• src/hg/lib/web.c
  • 1.160 lines changed: 1, context: html, text, full: html, text
    Moved call to commonCssStyles to here. Now we should expand CSS styles in one place.
• src/hg/makeDb/doc/dp4.txt
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Added comment that 12fly dpse_caf1 is the same assembly as FlyBase dpse_r2.1_FB2008_02.
• src/hg/makeDb/doc/droAna3.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droEre2.txt
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droGri2.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droMoj3.txt
  • 1.4 lines changed: 11, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droVir3.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/droWil1.txt
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Swapped chains/nets from dm3 to get liftOver chains to dm3 -- user request.
• src/hg/makeDb/doc/hg19.txt
  • 1.4 lines changed: 356, context: html, text, full: html, text
    venter1 chain and net, self lastz chain, chimp lastz chain and net, pushQ entry, PAR region, Gorilla lastz chain and net, lineage specific repeats
• src/hg/makeDb/doc/mm9.txt
  • 1.91 lines changed: 167, context: html, text, full: html, text
    added Human Proteins track
• src/hg/makeDb/doc/sacCer1.txt
  • 1.9 lines changed: 1, context: html, text, full: html, text
    loaded UW yeast footprint tracks
  • 1.8 lines changed: 29, context: html, text, full: html, text
    added UW footprint tracks to sacCer1
• src/hg/makeDb/doc/sacCer2.txt
  • 1.6 lines changed: 29, context: html, text, full: html, text
    loaded UW yeast footprint tracks
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.334 lines changed: 4, context: html, text, full: html, text
    reenabled ccds, but was false alarm
  • 1.333 lines changed: 4, context: html, text, full: html, text
    disable CCDS update until a bug is fixed
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.67 lines changed: 2, context: html, text, full: html, text
    fixed ordering of lin cnv set
• src/hg/makeDb/schema/all.joiner
  • 1.701 lines changed: 2, context: html, text, full: html, text
    add human proteins to mm9
• src/hg/makeDb/trackDb/README
  • 1.69 lines changed: 3, context: html, text, full: html, text
    fixed some punctuation
• src/hg/makeDb/trackDb/hiv/trackDb.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    changed priorities so they would order correclty
  • 1.2 lines changed: 10, context: html, text, full: html, text
    removed duplicate entry
• src/hg/makeDb/trackDb/hiv/vax003PosSel.html
  • 1.9 lines changed: 117, context: html, text, full: html, text
    swapped order of sections
  • 1.8 lines changed: 385, context: html, text, full: html, text
    added last section
  • 1.7 lines changed: 571, context: html, text, full: html, text
    cleaned up table
  • 1.6 lines changed: 13, context: html, text, full: html, text
    substituting some html characters.
  • 1.5 lines changed: 40, context: html, text, full: html, text
    continuing major cleanup of MS Word cruft
  • 1.4 lines changed: 171, context: html, text, full: html, text
    continuing major cleanup of MS Word cruft
  • 1.3 lines changed: 171, context: html, text, full: html, text
    starting major cleanup of MS Word cruft
  • 1.2 lines changed: 54, context: html, text, full: html, text
    corrected Reference section
• src/hg/makeDb/trackDb/hiv/vax004PosSelLoc.html
  • 1.4 lines changed: 53, context: html, text, full: html, text
    corrected Reference section
• src/hg/makeDb/trackDb/hiv/vax004PosSelRace.html
  • 1.4 lines changed: 53, context: html, text, full: html, text
    corrected Reference section
• src/hg/makeDb/trackDb/hiv/vax004PosSelVac.html
  • 1.4 lines changed: 53, context: html, text, full: html, text
    corrected Reference section
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.240 lines changed: 55, context: html, text, full: html, text
    Reworked some CalTech settings to get rid of confusing dimensionZ
  • 1.239 lines changed: 83, context: html, text, full: html, text
    Added UNC FAIRE HeLa
  • 1.238 lines changed: 71, context: html, text, full: html, text
    first 3 projects of GIS DNA PET
  • 1.237 lines changed: 1, context: html, text, full: html, text
    GIS RNAseq extra views
  • 1.236 lines changed: 133, context: html, text, full: html, text
    GIS RNAseq initial load
  • 1.235 lines changed: 2, context: html, text, full: html, text
    fix Methyl27K56 long labels
  • 1.234 lines changed: 206, context: html, text, full: html, text
    Added resubmitted Yale inputs as bedGrahps (InputBg) restricting to alpha while wigs restricted to beta. Also some Duke label formatting.
  • 1.233 lines changed: 374, context: html, text, full: html, text
    Added Duke Hela-S3, UT HeLa-S2 and UT HepG2
  • 1.232 lines changed: 20, context: html, text, full: html, text
    removing release alpha from Raw Signals for Gm12878 cell line
  • 1.231 lines changed: 39, context: html, text, full: html, text
    recovered two wiggle tracks for Affy
  • 1.230 lines changed: 4, context: html, text, full: html, text
    temporary fix to avoid bug with scoreMax being set to anything but 1000
  • 1.229 lines changed: 1, context: html, text, full: html, text
    Change vis defaults on Yale for consistency
  • 1.228 lines changed: 1, context: html, text, full: html, text
    fixing cell-line antibody mixup
  • 1.227 lines changed: 2, context: html, text, full: html, text
    Fixed sloppy sortOrder settings for Broad and Yale
  • 1.226 lines changed: 20, context: html, text, full: html, text
    decided (for the final time) to not release with the Raw Signals -- as there is currently no access to the gbdb supporting files
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.13 lines changed: 5, context: html, text, full: html, text
    mostly html tags
  • 1.12 lines changed: 16, context: html, text, full: html, text
    Add material about signal and pvalue
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • 1.6 lines changed: 94, context: html, text, full: html, text
    cleanup
  • 1.5 lines changed: 30, context: html, text, full: html, text
    cleanup and fix typos
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Removing inacurrate replicate info after all
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Add info about replicates
  • 1.14 lines changed: 40, context: html, text, full: html, text
    Fleshing out Methods a bit to summarize analysis and meaning of scoring; expanding acronyms; removing repetitious parts
  • 1.13 lines changed: 2, context: html, text, full: html, text
    added <EM> tags and commas to et al
  • 1.12 lines changed: 1, context: html, text, full: html, text
    added a space betw refs
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changed text slightly on search terms
• src/hg/makeDb/trackDb/human/hgdpFst.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Changed wording in methods section.
  • 1.2 lines changed: 15, context: html, text, full: html, text
    Refined references.
• src/hg/makeDb/trackDb/human/hgdpGeo.html
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Changed wording in methods section.
  • 1.6 lines changed: 15, context: html, text, full: html, text
    Refined references.
• src/hg/makeDb/trackDb/human/hgdpHzy.html
  • 1.8 lines changed: 7, context: html, text, full: html, text
    HGDP Heterozygosity label and description tweaks after more info from Joe.
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Changed wording in methods section.
  • 1.6 lines changed: 14, context: html, text, full: html, text
    Changed note about all Africa and Bantu only populations.
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Refined references.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Removed a "the".
  • 1.3 lines changed: 14, context: html, text, full: html, text
    Edits to references.
• src/hg/makeDb/trackDb/human/hgdpIhs.html
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    Changed wording in methods section.
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    Refined references.
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
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    Removed some parens.
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    Changed wording in methods section.
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    Refined references.
• src/hg/makeDb/trackDb/human/omimGene.html
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    made the disclaimer NOTE red
• src/hg/makeDb/trackDb/human/trackDb.ra
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    Added "Smoothed" to hgdpFst labels.
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    HGDP Heterozygosity label and description tweaks after more info from Joe.
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    Shortened HGDP analysis track labels to fit in 80 chars for longLabel, 16 for shortLabel.
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    Added minLimit and maxLimit settings to HGDP bedGraph tracks.
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
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    added UW footprint tracks to sacCer1
• src/hg/makeDb/trackDb/sacCer/uwFootprints.html
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    loaded UW yeast footprint tracks
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    added UW footprint tracks to sacCer1
• src/hg/orthoMap/makefile
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    added L flag to linker
• src/hg/utils/automation/Encode.pm
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    Update freeze date
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    add dcc to downloadDir
• src/hg/utils/bedExtendRanges/bedExtendRanges.c
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    fix typo in usage
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    allow user to use remote db (e.g. mysql.cse.ucsc.edu)
• src/inc/cheapcgi.h
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    Added controls for int and double which valdate using javascript. Requires utils.js and jQuery.js
• src/inc/common.mk
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    reversing ourselves to have USE_SSL=0 be the default since some mirror sites have difficulty
• src/lib/cheapcgi.c
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    Fix for printf format in cgiMakeDoubleVarInRange so value doesn't get truncated to int.
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    Added controls for int and double which valdate using javascript. Requires utils.js and jQuery.js
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    making post action URI query params available to cgi hash, and they take precedence over form vars
• src/lib/pipeline.c
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    ignore SIGPIPE in child to avoid timing issue on process completion
• src/makefile
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    add bedItemOverlapCount and bedExtendRanges to userApps list
• src/utils/faCount/makefile
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    add the mkdir business
• src/utils/qa/countPerChrom.csh
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    removed some commas from usage statement
• src/utils/qa/retirePushQ.csh
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    Changed host hgofbeta back to host hgwbeta.
• src/utils/qa/weeklybld/buildCvsReports.csh
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    adding comments about symlinks in htdocs
• src/utils/qa/weeklybld/buildEnv.csh
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    v204 preview
• src/utils/qa/weeklybld/coBranch.csh
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    useing ssl stuff
• src/utils/userApps/bigBedWigs.txt
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    Updated with an introduction
• src/utils/userApps/mkREADME.sh
  • 1.2 lines changed: 34, context: html, text, full: html, text
    Make it work from parameters

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• files changed: 99