All File Changes

v276_base to v277_preview (2012-11-20 to 2012-12-03) v277

• python/lib/ucscGb/externalData/geo/soft.py
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    fixed spelling error
• src/hg/hgGene/hgGene.c
  • lines changed 29, context: html, text, full: html, text
    if we have hgg_gene, don't even bother looking for hgg_chrom in the cart because it might be grek from an earlier call. (#9668)
• src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    make mm10 the new mouse target for blastTabs (#7045)
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    make mm10 the new mouse target for blastTabs (#7045)
• src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    make mm10 the new mouse target for blastTabs (#7045)
• src/hg/hgGene/hgGeneData/Mouse/mm10/links.ra
  • lines changed 8, context: html, text, full: html, text
    add link to ExonPrimer in hgGene (#7045)
• src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    make mm10 the new mouse target for blastTabs (#7045)
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer3/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    make mm10 the new mouse target for blastTabs (#7045)
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    fix a problem in the table browser when track hubs have tables with dots in them
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    Checking in special case fix for 'affyTxnPhase2' which has been broken for a long time. This track only exists on hg15 and hg17 and these changes include changing the track name to 'affyTxnPhase2b'. The existing broken track is being dropped and the new version will be rolled out through QA. Redmine 7554.
• src/hg/hgTracks/transcriptome.c
  • lines changed 151, context: html, text, full: html, text
    Checking in special case fix for 'affyTxnPhase2' which has been broken for a long time. This track only exists on hg15 and hg17 and these changes include changing the track name to 'affyTxnPhase2b'. The existing broken track is being dropped and the new version will be rolled out through QA. Redmine 7554.
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    Missed this one old define that is now gone. Still redmine 7554.
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 3, context: html, text, full: html, text
    Making changes to FAQ about naming of releases referencing gggSss# format, also updated links for new Blue Bar organization.
  • lines changed 1, context: html, text, full: html, text
    Making edits based on feedback from Bob in adding info about names of assemblies and new pulldown menus
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 7, context: html, text, full: html, text
    Making changes to FAQ about naming of releases referencing gggSss# format, also updated links for new Blue Bar organization.
  • lines changed 2, context: html, text, full: html, text
    Making edits based on feedback from Bob in adding info about names of assemblies and new pulldown menus
  • lines changed 16, context: html, text, full: html, text
    Added several new assemblies to release list.
  • lines changed 7, context: html, text, full: html, text
    Added 5 new assemblies.
  • lines changed 7, context: html, text, full: html, text
    Added 4 new assemblies to release list.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 608, context: html, text, full: html, text
    Added credits for 12 more assemblies.
  • lines changed 228, context: html, text, full: html, text
    Added 5 new assemblies.
  • lines changed 321, context: html, text, full: html, text
    Added credits for 4 more assemblies.
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 1, context: html, text, full: html, text
    Corrected the coordinates in the description of the example (redmine #9681)
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 1, context: html, text, full: html, text
    Making changes to FAQ about naming of releases referencing gggSss# format, also updated links for new Blue Bar organization.
  • lines changed 1, context: html, text, full: html, text
    Making edits based on feedback from Bob in adding info about names of assemblies and new pulldown menus
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 2, context: html, text, full: html, text
    Making changes to FAQ about naming of releases referencing gggSss# format, also updated links for new Blue Bar organization.
  • lines changed 1, context: html, text, full: html, text
    Making edits based on feedback from Bob in adding info about names of assemblies and new pulldown menus
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 16, context: html, text, full: html, text
    Making changes to FAQ about naming of releases referencing gggSss# format, also updated links for new Blue Bar organization.
  • lines changed 10, context: html, text, full: html, text
    Making edits based on feedback from Bob in adding info about names of assemblies and new pulldown menus
  • lines changed 5, context: html, text, full: html, text
    Corrected references to old menu items in the blue top navigation bar (redmine #8900)
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 30, context: html, text, full: html, text
    added mm10 ucsc genes announcement
  • lines changed 2, context: html, text, full: html, text
    added sentence about mm10 being the new default assembly
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    removed doi designation
  • lines changed 9, context: html, text, full: html, text
    Added ENCODE NAR pub.
• src/hg/htdocs/images/RepeatMasker_Consensus_Sequences.png
  • lines changed 0, context: html, text, full: html, text
    first checkin for repeats2 browser
• src/hg/htdocs/indexNews.html
  • lines changed 46, context: html, text, full: html, text
    added news announcement for mm10 ucsc genes
  • lines changed 1, context: html, text, full: html, text
    Fixed link in announcement
  • lines changed 2, context: html, text, full: html, text
    added sentence about mm10 being the new default assembly
• src/hg/lib/customFactory.c
  • lines changed 156, context: html, text, full: html, text
    using threads to process bigDataUrl customTracks in parallel. Fixes bug #9680
• src/hg/lib/hgFind.c
  • lines changed 3, context: html, text, full: html, text
    fixup mouse cytoBand searching redmine 8536
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    fixed bug that was resulting in schemas for track hub tracks not being displayed from the table browser "show schema" button.
  • lines changed 2, context: html, text, full: html, text
    remove unnecessary assert that was causing hgTables to crash with super tracks in track hubs (reported by Pauline)
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 37, context: html, text, full: html, text
    liftOver to canFam2 done
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 22, context: html, text, full: html, text
    completed lastz runs to rn5 for melGal1, xenTro3 and danRer7
• src/hg/makeDb/doc/hg17.txt
  • lines changed 10, context: html, text, full: html, text
    Track #9401 (DGV update): checkTableCoords found some items with chromEnd > chrom sizefor several chroms in hg17. Truncated those.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 16, context: html, text, full: html, text
    Track #1079 (1000 Genomes Phase 1 Paired-End Accessible Regions): added missing hg19.txt entry, thanks for catching that Steve!
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 22, context: html, text, full: html, text
    completed lastz runs to rn5 for melGal1, xenTro3 and danRer7
• src/hg/makeDb/doc/rn5.txt
  • lines changed 190, context: html, text, full: html, text
    completed lastz runs to rn5 for melGal1, xenTro3 and danRer7
  • lines changed 423, context: html, text, full: html, text
    running lastz for galGal4 monDom5 bosTau7 canFam3 ailMel1 panTro4 cavPor3
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 16, context: html, text, full: html, text
    upgrade the mmBlastTab tables in the "other" species. (#7045)
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 24, context: html, text, full: html, text
    completed lastz runs to rn5 for melGal1, xenTro3 and danRer7
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 5, context: html, text, full: html, text
    Added dasNov3, ochPri2, oreNil2, otoGar3 and panTro4
  • lines changed 4, context: html, text, full: html, text
    Added felCat5, hetGla2, rheMac3 and turTru2.
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 3, context: html, text, full: html, text
    constant churn is the watch word
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 3, context: html, text, full: html, text
    constant churn is the watch word
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    Added tables for the new 1000 Genomes tracks to the tablesIgnored section (redmine #1079,7964)
  • lines changed 7, context: html, text, full: html, text
    redmine assembly #8166 Put papAnu2 into all.joiner.
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Put longLabel NumtS ...the top-level trackDb.ra for new NumtS tracks as suggested by Angie in review #9636
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 7, context: html, text, full: html, text
    adding fixes to target name
  • lines changed 2, context: html, text, full: html, text
    Fixing a search and replace that went to wide found by Brian Lee
  • lines changed 4, context: html, text, full: html, text
    Adding protocol documents for cell lines for Gilbert Lab: L1210, ES-EM5...25,IPS...4,IPS...5
  • lines changed 2, context: html, text, full: html, text
    Adding protocol links for EpiSC-7 and EpiSC-5 for Gilbert lab, RM9226
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    Renaming validation files for H3K9me3 H3K4me3_(04-745) H3K4me1 H3K27me3_(39155) H3K36me3 antibodies that were pointing to files called human when in the validation document Western Blot was done on mice, so files and pointers changed to mouse per Cricket RM#9159, also fixing pointer to correct human_H3K9me3_ab8898_validation_Ren.pdf file
  • lines changed 1, context: html, text, full: html, text
    Adding validation document for antibody NCOR
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    Changing validation antibody document name to have hyphen in order to match pdf file so link works for SETDB1
  • lines changed 91, context: html, text, full: html, text
    Dealing with missing cell growth protocols. I have added explicitly which ones are missing and commented out cell lines that do not have protocols and are not used
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 153, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra RM#9480
  • lines changed 15, context: html, text, full: html, text
    Copying alpha/cv.ra to beta, more accurate target descriptions and addition of protocols for cell lines in Gilbert lab
  • lines changed 6, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra with changes for RM#9159, correcting validation file names from human to mouse for some antibodies
  • lines changed 1, context: html, text, full: html, text
    Copying alpha cv.ra to beta/cv.ra, adding validation doc for antibody NCOR
  • lines changed 1, context: html, text, full: html, text
    Correcting antibody validation link for SETDB1 to correct broken link on the RR
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 171, context: html, text, full: html, text
    Moving beta to public
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    Correcting antibody validation link for SETDB1 to correct broken link on the RR
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 19, context: html, text, full: html, text
    Revoking files with Pol2(b)
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeBroadChipSeq.ra
  • lines changed 19, context: html, text, full: html, text
    Revoking an antibody in Broad experiments in hg18 BroadChipSeq and hg19 BroadHistone RM9349#note-9 and 11
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeBroadChipSeq.ra
  • lines changed 19, context: html, text, full: html, text
    Revoking an antibody in Broad experiments in hg18 BroadChipSeq and hg19 BroadHistone RM9349#note-9 and 11
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 27, context: html, text, full: html, text
    Revoking files with Pol2(b)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra
  • lines changed 9, context: html, text, full: html, text
    added accessions to hg19 FSU RepliChip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 42, context: html, text, full: html, text
    added UW accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 27, context: html, text, full: html, text
    Revoking an antibody in Broad experiments in hg18 BroadChipSeq and hg19 BroadHistone RM9349#note-9 and 11
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 89, context: html, text, full: html, text
    Removing GEO Sample Accession numbers for CaltechRnaSeq, HaibTfbs, and OpenChromDnase per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 14, context: html, text, full: html, text
    Revoking status of some metaDb files for CSHL Long RNA-seq RM#9521
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeDukeAffyExon.ra
  • lines changed 220, context: html, text, full: html, text
    Adding GEO accession information for beta/public on ENCODE DukeAffyExon and HaibMethylRrbs per RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeFsuRepliChip.ra
  • lines changed 9, context: html, text, full: html, text
    Adding Geo Sample Accession numbers fot FSU Repli Chip per RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethylRrbs.ra
  • lines changed 191, context: html, text, full: html, text
    Adding GEO accession information for beta/public on ENCODE DukeAffyExon and HaibMethylRrbs per RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    Removing GEO Sample Accession numbers for CaltechRnaSeq, HaibTfbs, and OpenChromDnase per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
  • lines changed 15, context: html, text, full: html, text
    Removing GEO Sample Accession numbers for CaltechRnaSeq, HaibTfbs, and OpenChromDnase per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 42, context: html, text, full: html, text
    Adding GEO numbers to UWAffyExonArray RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 11, context: html, text, full: html, text
    Removing from wgEncodeUwDnase 10 occurances of GSM per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
  • lines changed 51, context: html, text, full: html, text
    Dropping some Geo Sample Accession numbers and changing some md5sums RM#9359, RM9564.
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 27, context: html, text, full: html, text
    Revoking an antibody in Broad experiments in hg18 BroadChipSeq and hg19 BroadHistone RM9349#note-9 and 11
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 89, context: html, text, full: html, text
    Removing GEO Sample Accession numbers for CaltechRnaSeq, HaibTfbs, and OpenChromDnase per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 14, context: html, text, full: html, text
    Revoking status of some metaDb files for CSHL Long RNA-seq RM#9521
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeDukeAffyExon.ra
  • lines changed 220, context: html, text, full: html, text
    Adding GEO accession information for beta/public on ENCODE DukeAffyExon and HaibMethylRrbs per RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeFsuRepliChip.ra
  • lines changed 9, context: html, text, full: html, text
    Adding Geo Sample Accession numbers fot FSU Repli Chip per RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethylRrbs.ra
  • lines changed 191, context: html, text, full: html, text
    Adding GEO accession information for beta/public on ENCODE DukeAffyExon and HaibMethylRrbs per RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    Removing GEO Sample Accession numbers for CaltechRnaSeq, HaibTfbs, and OpenChromDnase per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromDnase.ra
  • lines changed 15, context: html, text, full: html, text
    Removing GEO Sample Accession numbers for CaltechRnaSeq, HaibTfbs, and OpenChromDnase per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 42, context: html, text, full: html, text
    Adding GEO numbers to UWAffyExonArray RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 11, context: html, text, full: html, text
    Removing from wgEncodeUwDnase 10 occurances of GSM per RM#9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwHistone.ra
  • lines changed 51, context: html, text, full: html, text
    Dropping some Geo Sample Accession numbers and changing some md5sums RM#9359, RM9564.
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
  • lines changed 30, context: html, text, full: html, text
    Made minor formatting corrections; fixed References section (redmine #7964)
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html
  • lines changed 49, context: html, text, full: html, text
    Made minor corrections, added software links, reformatted references (redmine #1079)
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    Changed number of individuals described in Methods section to 1,092 to match the journal title in the References section per Tom Blackwell (redmine #1079)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed the track long label for 1000 Genomes Phase 1 Variant Calls - changed 'InDels' to 'Indels' (redmine #7964)
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    Shortened the long label for 1000 Genomes Accessibility Pilot Criteria subtrack so it was under 80 characters (redmine #1079)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.ra
  • lines changed 40, context: html, text, full: html, text
    Revoking files ticket 9521
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 392, context: html, text, full: html, text
    Checking in special case fix for 'affyTxnPhase2' which has been broken for a long time. This track only exists on hg15 and hg17 and these changes include changing the track name to 'affyTxnPhase2b'. The existing broken track is being dropped and the new version will be rolled out through QA. Redmine 7554.
• src/hg/makeDb/trackDb/makefile
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    first checkin for repeats2 browser
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 5, context: html, text, full: html, text
    Updated mouse miRNA tracks to point to miRBase per Rachel (redmine #9598)
• src/hg/makeDb/trackDb/mouse/mm8/miRNA.html
  • lines changed 7, context: html, text, full: html, text
    Updated mouse miRNA tracks to point to miRBase per Rachel (redmine #9598)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliChip.ra
  • lines changed 28, context: html, text, full: html, text
    added accessions to mm9 FSU
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeFsuRepliChip.ra
  • lines changed 28, context: html, text, full: html, text
    Adding GEO numbers for mm9 wgEncodeFsu RepliChip RM#9359
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeFsuRepliChip.ra
  • lines changed 28, context: html, text, full: html, text
    Adding GEO numbers for mm9 wgEncodeFsu RepliChip RM#9359
• src/hg/makeDb/trackDb/mouse/mm9/miRNA.html
  • lines changed 7, context: html, text, full: html, text
    Updated mouse miRNA tracks to point to miRBase per Rachel (redmine #9598)
• src/hg/makeDb/trackDb/other/centromers1/description.html
  • lines changed 9, context: html, text, full: html, text
    centromers html updates
• src/hg/makeDb/trackDb/other/repeats2/description.html
  • lines changed 48, context: html, text, full: html, text
    first checkin for repeats2 browser
• src/hg/makeDb/trackDb/other/repeats2/gap.html
  • lines changed 3, context: html, text, full: html, text
    first checkin for repeats2 browser
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    minor edits to track files
• src/hg/makeDb/trackDb/other/repeats2/gold.html
  • lines changed 29, context: html, text, full: html, text
    first checkin for repeats2 browser
  • lines changed 25, context: html, text, full: html, text
    minor edits to track files
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    first checkin for repeats2 browser
  • lines changed 8, context: html, text, full: html, text
    minor edits to track files
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Put longLabel NumtS ...the top-level trackDb.ra for new NumtS tracks as suggested by Angie in review #9636
• src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
  • lines changed 1, context: html, text, full: html, text
    Changed image name to match the file that exists on the RR.
• src/hg/makeDb/trackDb/tenrec/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Adding override line to have correct matrix values (default) for tenrec (echTel1) trackDb so matches output from getMatrixLines
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    Put longLabel NumtS ...the top-level trackDb.ra for new NumtS tracks as suggested by Angie in review #9636
• src/hg/mouseStuff/chainSort/chainSort.c
  • lines changed 2, context: html, text, full: html, text
    Clarified chainMergeSort directions in usage statement. (RM #9603, notes 13-14.) Thank you, braney.
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 198, context: html, text, full: html, text
    redmine #9409 Ensembl Genes v69 - Create list of organisms with v69 ensemble genes.
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 12, context: html, text, full: html, text
    added doNotCheckDuplicates option to makeGenomeDb.pl
  • lines changed 2, context: html, text, full: html, text
    fixing a bug in makeGenomeDb.pl where .ra files are missing
• src/hg/utils/automation/synBlastp.csh
  • lines changed 17, context: html, text, full: html, text
    upgrade synBlastp.csh to allow specification of gene table on both databases. Required since rn4 has funky rgdGene2 (#7045)
• src/hg/utils/bedToPsl/bedToPsl.c
  • lines changed 17, context: html, text, full: html, text
    added option to bedToPsl to keep original coordinates in target side of psl
  • lines changed 6, context: html, text, full: html, text
    correction to previous commit: I meant the query, not the target
  • lines changed 11, context: html, text, full: html, text
    bedToPsl: copying blocksizes for keepQuery option
  • lines changed 1, context: html, text, full: html, text
    Stricter-compiler warning: true is not defined, so use TRUE (common.h).
• src/hg/utils/pslMap/usage.txt
  • lines changed 3, context: html, text, full: html, text
    tiny change to pslMap help message
• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 6, context: html, text, full: html, text
    Adding some more error checking and diagnostic messages.
  • lines changed 2, context: html, text, full: html, text
    Detecting and aborting on empty input.
  • lines changed 2, context: html, text, full: html, text
    Adding one more error check on input.
• src/kehayden/alphaAsm/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding a new test case.
• src/kehayden/alphaChain/alphaChain.c
  • lines changed 3, context: html, text, full: html, text
    Handling an edge condition to avoid a crash.
  • lines changed 1, context: html, text, full: html, text
    Putting warning message redirecting people to alphaAsm.
• src/lib/htmlPage.c
  • lines changed 2, context: html, text, full: html, text
    Making htmlCheck not warn about missing NAME tags for INPUT tags if they have an ONCHANGE.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    fix typo that broke userApps
• src/product/README.customTracks.dataBase
  • lines changed 1, context: html, text, full: html, text
    needst to be customTrash.* for the grant statement
• src/utils/qa/checkAllStaticLinks.csh
  • lines changed 29, context: html, text, full: html, text
    fixed two check*Static scripts to run with htmlCheck instead of LinkCheck and streamlined them a bit
  • lines changed 36, context: html, text, full: html, text
    extensive modifications to both static links checking scripts
  • lines changed 14, context: html, text, full: html, text
    added two levels of backup protection in genecats directory because script writes directly there
• src/utils/qa/checkStaticLinks.csh
  • lines changed 84, context: html, text, full: html, text
    fixed two check*Static scripts to run with htmlCheck instead of LinkCheck and streamlined them a bit
  • lines changed 35, context: html, text, full: html, text
    extensive modifications to both static links checking scripts
• src/utils/qa/checkTrackUiLinks.csh
  • lines changed 12, context: html, text, full: html, text
    Modified script so it doesn't print output unless it actually finds broken links; will make the output much easier to interpret for assemblies with a large number of tables
  • lines changed 6, context: html, text, full: html, text
    Also edited the section that checks the description page to only print output if it finds broken links
  • lines changed 15, context: html, text, full: html, text
    Added an error counter and a summary line in the output so in the event of no errors, there wouldn't just be a blank output file
  • lines changed 6, context: html, text, full: html, text
    Moved line to delete error file outside of if-statement - otherwise, the error file only gets deleted if there is an error; also added a line to ignore '403 from http://hgwbeta.cse.ucsc.edu/cgi-bin/' as a valid error
  • lines changed 5, context: html, text, full: html, text
    removed reporting of internal anchors not found
  • lines changed 7, context: html, text, full: html, text
    Added a table counter and added the total table count to the summary section
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v277 preview1
• src/utils/qa/whoMadeIt.csh
  • lines changed 23, context: html, text, full: html, text
    updated to work with git
  • lines changed 43, context: html, text, full: html, text
    fixed to combine dual occurances of same person: e.g., kent and Jim Kent
  • lines changed 1, context: html, text, full: html, text
    adjusted usage statement to note that it works on a directory

• lines changed: 5843
• files changed: 161