CVS changes by file

branch to review (2009-07-07 to 2009-07-15) v210

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.68 lines changed: 67, context: html, text, full: html, text
    Added two new Thermococcus genomes, still need multiz tracks
• src/hg/autoSql/makefile
  • 1.17 lines changed: 2, context: html, text, full: html, text
    fixed install rule to preserve permissions
• src/hg/encode/DAFs/CshlLongRnaSeq.daf
  • 1.2 lines changed: 2, context: html, text, full: html, text
    new datatype as this will be a separate composite track from CshlRnaSeq (short RNA-seq)
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.17 lines changed: 12, context: html, text, full: html, text
    Don't show restriction dates if they are in the past.
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.68 lines changed: 1, context: html, text, full: html, text
    dont need comment
  • 1.67 lines changed: 5, context: html, text, full: html, text
    removed deprecated warning and added check for raw directory
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.187 lines changed: 7, context: html, text, full: html, text
    Change labeling for consistency
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.88 lines changed: 13, context: html, text, full: html, text
    Run validator with -allowReloads if (a) the box is checked on the upload page, or (b) user is an admin.
  • 1.87 lines changed: 6, context: html, text, full: html, text
    Changes to list and show_user action dealing with the submitter CGI var, as well as sort defaults.
• src/hg/encode/hgEncodeSubmit/app/helpers/sort_helper.rb
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Necessary small extension to helper to add optional params to the sort link i.e. the additional submitter CGI var.
• src/hg/encode/hgEncodeSubmit/app/views/layouts/main.rhtml
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Make sure that when viewing list of submissions from a submitter, all three of the main links on the top navbar are clickable.
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/list.rhtml
  • 1.22 lines changed: 6, context: html, text, full: html, text
    Run validator with -allowReloads if (a) the box is checked on the upload page, or (b) user is an admin.
  • 1.21 lines changed: 16, context: html, text, full: html, text
    Various changes to sort links, added links to Submitter column, removed "Type" column.
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Various changes to sort links, added links to Submitter column, removed "Type" column.
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/upload.rhtml
  • 1.19 lines changed: 5, context: html, text, full: html, text
    Run validator with -allowReloads if (a) the box is checked on the upload page, or (b) user is an admin.
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.14 lines changed: 7, context: html, text, full: html, text
    Run validator with -allowReloads if (a) the box is checked on the upload page, or (b) user is an admin.
• src/hg/encode/hgEncodeSubmit/public/stylesheets/encode.css
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Made left margin 5% instead of 15%... there was just too much space on the left.
• src/hg/gigAssembler/checkAgpAndFa/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixup broken build on Solaris, add SOCKETLIB
• src/hg/gigAssembler/checkNt/checkNt.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Fixup broken build on Solaris
• src/hg/gigAssembler/checkOut/checkOut.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixup broken build on Solaris
• src/hg/gigAssembler/checkQa/checkQa.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixup broken build on Solaris
• src/hg/gigAssembler/gapper/gapper.c
  • 1.4 lines changed: 9, context: html, text, full: html, text
    Fixup broken build on Solaris
• src/hg/gigAssembler/goldToAgp/goldToAgp.c
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixup broken build on Solaris
• src/hg/gigAssembler/mendMap/mendMap.c
  • 1.11 lines changed: 39, context: html, text, full: html, text
    Fixup broken build on Solaris
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra.v3
  • 1.1 lines changed: 201, context: html, text, full: html, text
    New column.ra for the coming V3 data update.
• src/hg/hgGene/hgGene.c
  • 1.116 lines changed: 2, context: html, text, full: html, text
    use hUserAbort to prevent unneed stack track
• src/hg/hgLiftOver/hgLiftOver.c
  • 1.62 lines changed: 5, context: html, text, full: html, text
    fixed some missing closes noticed while search for a bug
• src/hg/hgTables/correlate.c
  • 1.78 lines changed: 5, context: html, text, full: html, text
    Moved connection-freeing into the block that originally allocated the connection.
• src/hg/hgTables/identifiers.c
  • 1.28 lines changed: 5, context: html, text, full: html, text
    Fix for corner case in explainIdentifiers: when xrefTable is the selected table, and its idField happens to be the same as its alias field for the main table (e.g. refLink), don't refer to the field twice (thanks Katrina).
• src/hg/hgTracks/config.c
  • 1.82 lines changed: 27, context: html, text, full: html, text
    re-enable drag-and-droom for AppleWebKit >= 531
• src/hg/hgTracks/hgTracks.c
  • 1.1584 lines changed: 1, context: html, text, full: html, text
    removed unneeded stackdump
  • 1.1583 lines changed: 1, context: html, text, full: html, text
    Fixed bug in leftLabel size under imageV2 logic
  • 1.1582 lines changed: 81, context: html, text, full: html, text
    Next rouund of imageV2 development. dragScroll is working.
  • 1.1581 lines changed: 1, context: html, text, full: html, text
    use hUserAbort to prevent unneed stack track
• src/hg/hgTracks/imageV2.c
  • 1.5 lines changed: 165, context: html, text, full: html, text
    Next rouund of imageV2 development. dragScroll is working.
• src/hg/hgTracks/imageV2.h
  • 1.4 lines changed: 27, context: html, text, full: html, text
    Next rouund of imageV2 development. dragScroll is working.
• src/hg/hgTracks/transMapTracks.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    allow transMap tracks to work with composite tracks
• src/hg/hgc/hgc.c
  • 1.1560 lines changed: 1, context: html, text, full: html, text
    Updated link to IUPAC codes to Ann's new goldenPath/help page.
  • 1.1559 lines changed: 2, context: html, text, full: html, text
    In printSnpAlleleRows, don't reverse-complement refUCSC if it is like '(1000bp insertion)'.
• src/hg/hgc/regMotif.c
  • 1.21 lines changed: 4, context: html, text, full: html, text
    Print track description html page for transRegCodeProbe table
• src/hg/inc/hCommon.h
  • 1.26 lines changed: 25, context: html, text, full: html, text
    moved stackDump stuff to hCommon; added function for user errAbort
• src/hg/inc/hui.h
  • 1.134 lines changed: 0, context: html, text, full: html, text
    moved stackDump stuff to hCommon; added function for user errAbort
• src/hg/inc/web.h
  • 1.45 lines changed: 13, context: html, text, full: html, text
    moved stackDump stuff to hCommon; added function for user errAbort
• src/hg/js/hgTracks.js
  • 1.30 lines changed: 140, context: html, text, full: html, text
    Next rouund of imageV2 development. dragScroll is working.
• src/hg/lib/botDelay.c
  • 1.15 lines changed: 3, context: html, text, full: html, text
    don't dump stack on bot trap
• src/hg/lib/cart.c
  • 1.111 lines changed: 3, context: html, text, full: html, text
    moved stackDump stuff to hCommon; added function for user errAbort
• src/hg/lib/ensFace.c
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Ensembl human release v55 today, no longer need to go to pre.ensembl for hg19
• src/hg/lib/hCommon.c
  • 1.39 lines changed: 65, context: html, text, full: html, text
    moved stackDump stuff to hCommon; added function for user errAbort
• src/hg/lib/hVarSubst.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Properly fill an empty cell in a table with nbsp
• src/hg/lib/hdb.c
  • 1.406 lines changed: 5, context: html, text, full: html, text
    generate useful error message when there is a huge chromosome name, most likely caused by an invalid table name
  • 1.405 lines changed: 23, context: html, text, full: html, text
    Oops, backing out the previous changes because they trigger both mrna and all_mrna trackDb records to display, and an upstream fix in hgFind.c fixed the original problem.
  • 1.404 lines changed: 29, context: html, text, full: html, text
    Added some special cases to support tracks all_{mrna,est} in a database that could have split tables.
• src/hg/lib/hgFind.c
  • 1.221 lines changed: 25, context: html, text, full: html, text
    moved stackDump stuff to hCommon; added function for user errAbort
  • 1.220 lines changed: 11, context: html, text, full: html, text
    When searching all_{mrna,est}, strip off the all_ only if there are split tables; otherwise all_{mrna,est} is the trackDb track name too.
• src/hg/lib/hui.c
  • 1.222 lines changed: 16, context: html, text, full: html, text
    check trackDb for species that should be off rather than depending on the cart having this.
• src/hg/lib/jaxAllelePheno.as
  • 1.1 lines changed: 7, context: html, text, full: html, text
    Meant to check these in a long time ago (thanks Brooke!).
• src/hg/lib/jaxAllelePheno.sql
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Meant to check these in a long time ago (thanks Brooke!).
• src/hg/lib/jsHelper.c
  • 1.28 lines changed: 16, context: html, text, full: html, text
    errAbort if we can't create symlinks in js directory
  • 1.27 lines changed: 60, context: html, text, full: html, text
    implement javascript versioning with symlinks
• src/hg/lib/liftOver.c
  • 1.44 lines changed: 2, context: html, text, full: html, text
    don't close files that function didn't open, which lead to double-free crash
• src/hg/lib/snp125Coding.as
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Functional annotations including mapped coords.
• src/hg/lib/snp125Coding.sql
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Functional annotations including mapped coords.
• src/hg/lib/web.c
  • 1.169 lines changed: 48, context: html, text, full: html, text
    moved stackDump stuff to hCommon; added function for user errAbort
• src/hg/makeDb/doc/danRer6.txt
  • 1.4 lines changed: 164, context: html, text, full: html, text
    added human proteins track
  • 1.3 lines changed: 100, context: html, text, full: html, text
    genbank, blatserver, downloads
  • 1.2 lines changed: 337, context: html, text, full: html, text
    final agp, browser default position, repeat masking, simple repeats, cluster data prep, cpgIsland
• src/hg/makeDb/doc/hg19.txt
  • 1.30 lines changed: 204, context: html, text, full: html, text
    danRer6 lastz done, phylo tree 4d site prediction done for 46 way, biocyc data obtained
  • 1.29 lines changed: 1, context: html, text, full: html, text
    fixed wrong path for genbank liftfile
• src/hg/makeDb/doc/sacCer2.txt
  • 1.13 lines changed: 3, context: html, text, full: html, text
    made comment in makeDoc about removing sgdToSgd table
  • 1.12 lines changed: 17, context: html, text, full: html, text
    Added info about removing records from sgdToName
  • 1.11 lines changed: 29, context: html, text, full: html, text
    Fixup sgdToName table
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes11.csh
  • 1.4 lines changed: 142, context: html, text, full: html, text
    Done with enough tables to get full hgGene click through to work
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.97 lines changed: 1, context: html, text, full: html, text
    Added danRer6.
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.341 lines changed: 1, context: html, text, full: html, text
    Added danRer6.
  • 1.340 lines changed: 1, context: html, text, full: html, text
    Added danRer6.
  • 1.339 lines changed: 15, context: html, text, full: html, text
    Added danRer6.
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.102 lines changed: 1, context: html, text, full: html, text
    Added danRer6.
• src/hg/makeDb/hgLoadBed/makefile
  • 1.23 lines changed: 4, context: html, text, full: html, text
    fixing same problem with g+w, teh fiels are alrady this permission
  • 1.22 lines changed: 4, context: html, text, full: html, text
    merging fix for weekly build, stops make failing with error if done sequentially by 2 different people
• src/hg/makeDb/outside/allenBrain/allenCollectSeq/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Add SOCKETLIB for Solaris build
• src/hg/makeDb/schema/all.joiner
  • 1.727 lines changed: 2, context: html, text, full: html, text
    dropped mantin of cgdToSgd
  • 1.726 lines changed: 1, context: html, text, full: html, text
    added MicMur1 to list of chains
  • 1.725 lines changed: 1, context: html, text, full: html, text
    added OtoGar1 to list of chains
  • 1.724 lines changed: 1, context: html, text, full: html, text
    added snp130 (for hg18)
  • 1.723 lines changed: 1, context: html, text, full: html, text
    added TarSyr1 to list of chains
  • 1.722 lines changed: 1, context: html, text, full: html, text
    added PapHam1 to chainlist and capitalized AplCal1
• src/hg/makeDb/trackDb/chimp/panTro1/description.html
  • 1.30 lines changed: 1, context: html, text, full: html, text
    Fixed links to wustl.
• src/hg/makeDb/trackDb/chimp/panTro2/description.html
  • 1.19 lines changed: 4, context: html, text, full: html, text
    Fixed links to wustl.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.419 lines changed: 31, context: html, text, full: html, text
    new GIS RnaSeq data
  • 1.418 lines changed: 220, context: html, text, full: html, text
    added USF-1 Egr-1 Sin3Ak-20 to HudsonAlpha ChIP-Seq
  • 1.417 lines changed: 210, context: html, text, full: html, text
    GIS PET new tracks loaded
  • 1.416 lines changed: 689, context: html, text, full: html, text
    Put UW DNase tracks back into trackDb. Will work around validation stuff another way i.e. adding -allowReloads validate capability in the pipeline.
  • 1.415 lines changed: 59, context: html, text, full: html, text
    fixed up coloring and track short/long labels to all be standard for CSHL and Affy and fixed up track settings for Transfrags
  • 1.414 lines changed: 691, context: html, text, full: html, text
    Removed UW DNase-seq in prep for reload (to avoid validation errors)
  • 1.413 lines changed: 26, context: html, text, full: html, text
    CSHL Long RNA-seq is a new composite type
  • 1.412 lines changed: 18, context: html, text, full: html, text
    Long RNA Seq for CSHL
  • 1.411 lines changed: 95, context: html, text, full: html, text
    Clarify labels, and used preferred terms of submitting lab, UW Dnase
  • 1.410 lines changed: 42, context: html, text, full: html, text
    Add subtrack coloring by cell type and set default on for Rep1 of Tier 1 and Tier2 subtracks, UW Dnase track
  • 1.409 lines changed: 12, context: html, text, full: html, text
    Set dateUnrestricted to dateSubmitted for ENCODE Mapability tracks
  • 1.408 lines changed: 6, context: html, text, full: html, text
    Add lab to mapability subtrack short labels to distinguish methods
  • 1.407 lines changed: 4, context: html, text, full: html, text
    Clarify some labels, prune others to fit length limits
  • 1.406 lines changed: 5, context: html, text, full: html, text
    Adjust defaults as requested by John Stam at UW
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
  • 1.15 lines changed: 1, context: html, text, full: html, text
    fixed obfuscated email address (thanks Kayla)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLoRnaSeq.html
  • 1.3 lines changed: 8, context: html, text, full: html, text
    updated documentation
  • 1.2 lines changed: 22, context: html, text, full: html, text
    formatting
  • 1.1 lines changed: 115, context: html, text, full: html, text
    first version of doc for CSHL Long RNA-seq
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html
  • 1.7 lines changed: 60, context: html, text, full: html, text
    updated documentation
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.13 lines changed: 34, context: html, text, full: html, text
    Add data release blurb. Minor fixes and remove comments
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • 1.12 lines changed: 8, context: html, text, full: html, text
    Added note of caution concerning Gencode, Havana and Ensembl release cycles
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • 1.8 lines changed: 25, context: html, text, full: html, text
    Update to display conventions section
• src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    adjusted BLOCKQUOTE tag to put text over matrix tables
  • 1.2 lines changed: 38, context: html, text, full: html, text
    Adding the lastz matrices and chain matrices to details page
• src/hg/makeDb/trackDb/human/hg19/hg19mammalChainNet.html
  • 1.2 lines changed: 32, context: html, text, full: html, text
    Fixup the multiple lastz and axtChain matrix displays
  • 1.1 lines changed: 191, context: html, text, full: html, text
    made separate files for the three chain/net tracks
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Fixup the multiple lastz and axtChain matrix displays
  • 1.1 lines changed: 191, context: html, text, full: html, text
    made separate files for the three chain/net tracks
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
  • 1.2 lines changed: 35, context: html, text, full: html, text
    Fixup the multiple lastz and axtChain matrix displays
  • 1.1 lines changed: 191, context: html, text, full: html, text
    made separate files for the three chain/net tracks
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.36 lines changed: 8, context: html, text, full: html, text
    Fixup the multiple lastz and axtChain matrix displays
  • 1.35 lines changed: 24, context: html, text, full: html, text
    added release alphas to control push to beta. made new html files for three chain/net sets. reversed order of three chain/net tracks to match order in Conservation track. adjusted order of views on details pages
  • 1.34 lines changed: 12, context: html, text, full: html, text
    Adding the lastz matrices and chain matrices to details page
• src/hg/makeDb/trackDb/lowelab/description-template.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Fixed missing space after # of genes (just added one blank space).
• src/hg/makeDb/trackDb/lowelab/haloHalo1/EMSeffects.html
  • 1.2 lines changed: 8, context: html, text, full: html, text
    microarray tracks updated by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/H2O2effects.html
  • 1.2 lines changed: 10, context: html, text, full: html, text
    microarray tracks updated by Andrew Holmes
• src/hg/makeDb/trackDb/lowelab/haloHalo1/TransitionMetal.html
  • 1.2 lines changed: 150, context: html, text, full: html, text
    microarray tracks updated by Andrew Holmes
• src/hg/makeDb/trackDb/makefile
  • 1.271 lines changed: 1, context: html, text, full: html, text
    Adding loxAfr3 to the build
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.156 lines changed: 6, context: html, text, full: html, text
    Adding search on jaxQtl (just like the old one on jaxQTL, thanks Brooke).
  • 1.155 lines changed: 1, context: html, text, full: html, text
    Shortening shortLabel of jaxRepTranscript to 16 chars.
• src/hg/makeDb/trackDb/opossum/monDom4/description.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed error in sample position search.
• src/hg/makeDb/trackDb/opossum/monDom5/description.html
  • 1.6 lines changed: 5, context: html, text, full: html, text
    Added explanation of chrM and chrUn, and noticed there are 8 autosomal chroms, not 7
  • 1.5 lines changed: 36, context: html, text, full: html, text
    Edited sample searches so that they are more like monDom4 searches.
• src/hg/makeDb/trackDb/sacCer/sacCer2/sgdGene.html
  • 1.1 lines changed: 14, context: html, text, full: html, text
    Update date/time for fetch of this data
• src/hg/makeDb/trackDb/snp128.html
  • 1.14 lines changed: 7, context: html, text, full: html, text
    point to new iupac.html page
• src/hg/makeDb/trackDb/snp129.html
  • 1.12 lines changed: 7, context: html, text, full: html, text
    point to new iupac.html page
• src/hg/makeDb/trackDb/snp130.html
  • 1.8 lines changed: 7, context: html, text, full: html, text
    point to new iupac.html page
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.520 lines changed: 59, context: html, text, full: html, text
    the ChainNet tracks should be specified by their db name
  • 1.519 lines changed: 12, context: html, text, full: html, text
    composite track was premature, switch back to super tracks until controls figured out
  • 1.518 lines changed: 12, context: html, text, full: html, text
    convert transMap to composite tracks
• src/hg/makeDb/trackDb/transMap.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    updated description
• src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Mary Q. Yang
• src/hg/makeDb/trackDb/worm/caeJap1/ctgPos2.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/caeJap1/description.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/caeRem2/ctgPos2.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.edu.
• src/hg/makeDb/trackDb/worm/caeRem2/description.html
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Fixed broken links to wustl.edu.
• src/hg/makeDb/trackDb/worm/caeRem2/gap.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.edu.
• src/hg/makeDb/trackDb/worm/caeRem2/gold.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.edu.
• src/hg/mouseStuff/axtChain/makefile
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Add SOCKETLIB for Solaris build
• src/hg/mouseStuff/chainAntiRepeat/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Add SOCKETLIB for Solaris build
• src/hg/mouseStuff/makefile
  • 1.21 lines changed: 1, context: html, text, full: html, text
    build mafToPsl as part of std make
• src/hg/perf/hgTracksRandom.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    notify the database being queried unless -quiet
  • 1.15 lines changed: 5, context: html, text, full: html, text
    get default database from default genome instead of hg17
• src/hg/protein/kgBestMrna/makefile
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Should be using MAKE not make in sub-makes
• src/hg/protein/kgBestMrna2/makefile
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Should be using MAKE, not make in sub-makes
• src/hg/protein/kgBestRef2/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Should be using MAKE, not make in sub-makes
• src/hg/protein/pbGlobal/pbGlobal.c
  • 1.45 lines changed: 1, context: html, text, full: html, text
    use hUserAbort to prevent unneed stack track
• src/hg/protein/pbTracks/pbTracks.c
  • 1.57 lines changed: 1, context: html, text, full: html, text
    use hUserAbort to prevent unneed stack track
• src/hg/pslCheck/pslCheck.c
  • 1.13 lines changed: 19, context: html, text, full: html, text
    fixed segv when file doesn't exists and no database was supplied
• src/hg/pslMap/pslMap.c
  • 1.17 lines changed: 13, context: html, text, full: html, text
    added option to output mapping chain that was used
• src/hg/pslMap/tests/expected/mrnaMapOverChain.mapping.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    added option to output mapping chain that was used
• src/hg/pslMap/tests/expected/mrnaMapOverSwap.mapping.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    added option to output mapping chain that was used
• src/hg/pslMap/tests/input/mm6ToHg17.psl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    added option to output mapping chain that was used
• src/hg/pslMap/tests/makefile
  • 1.11 lines changed: 6, context: html, text, full: html, text
    added option to output mapping chain that was used
• src/hg/pslMap/usage.txt
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    added option to output mapping chain that was used
• src/hg/qaPushQ/formPushQ.html
  • 1.24 lines changed: 5, context: html, text, full: html, text
    ann requested some fields be enlarged
• src/hg/ratStuff/mafFrags/mafFrags.c
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    added option to preserve reference coordinates
• src/hg/utils/automation/EnsGeneAutomate.pm
  • 1.18 lines changed: 168, context: html, text, full: html, text
    Updated with version 55 gene set pointers
• src/hg/utils/automation/doHgNearBlastp.pl
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Correcting comment.
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    Added back the varying blastp -e params that I lost when writing this. Have been using 0.01 for all blastp runs, but the original process used 0.001, 0.005, 0.01 depending on clade distance. Thanks Hiram and b0b!
• src/hg/utils/automation/findEnsFtpNames.sh
  • 1.1 lines changed: 79, context: html, text, full: html, text
    Initial source used for the past couple of Ensembl updates
• src/inc/common.mk
  • 1.62 lines changed: 6, context: html, text, full: html, text
    Fix to SAMPATH setting: for MACHTYPE other than x86_64, look for a MACHTYPE subdir lib. Also let user's SAMPATH env variable take preference if set.
• src/inc/portable.h
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    add listDirRegEx
• src/lib/htmlPage.c
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    allow INPUT tags inside SCRIPT tags for where we have javascript modifying FORM controls
• src/lib/htmshell.c
  • 1.59 lines changed: 2, context: html, text, full: html, text
    FF 2.0 had problems with inline-box. So the box resizing must be more primative.
  • 1.58 lines changed: 23, context: html, text, full: html, text
    Replaced input type submit with BoB's new OK button image. Removed obsolete, ifdef'd out code for warnBox using real HTML alert()
  • 1.57 lines changed: 1, context: html, text, full: html, text
    I surrender.
  • 1.56 lines changed: 3, context: html, text, full: html, text
    No blinking for the warn box title
• src/lib/osunix.c
  • 1.43 lines changed: 1, context: html, text, full: html, text
    flush stdout before forking
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    add listDirRegEx
• src/parasol/parasol/parasol.c
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    use contstant for max file path
• src/utils/bigWigSummary/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    corrected link library handling
• src/utils/bigWigToBedGraph/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    corrected link library handling
• src/utils/qa/chain2.csh
  • 1.12 lines changed: 2, context: html, text, full: html, text
    dropped exit command that was in there for debugging
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    added sort check for chain and net tables
• src/utils/qa/net.csh
  • 1.20 lines changed: 28, context: html, text, full: html, text
    added sort check for chain and net tables
• src/utils/qa/realTime.csh
  • 1.13 lines changed: 2, context: html, text, full: html, text
    changed to hgw8 for now, as hgw1 is out for upgrade
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    adjusted to only check one RR machine, as they all now share hgsqlrr
• src/utils/qa/weeklybld/buildBeta.csh
  • 1.18 lines changed: 1, context: html, text, full: html, text
    better errror message
• src/utils/qa/weeklybld/buildCgi32.csh
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    different link line with gbWarn in it
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.68 lines changed: 2, context: html, text, full: html, text
    v211 preview
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    to build with SSL and BAM
• src/utils/qa/weeklybld/buildUtils.csh
  • 1.16 lines changed: 1, context: html, text, full: html, text
    colon after variable is interpreted by CSH, oops
• src/utils/qa/weeklybld/cvs-reports-d
  • 1.12 lines changed: 1, context: html, text, full: html, text
    fixed comment

• lines changed: 6305
• files changed: 134