All File Changes

v308_preview2 to v308_base (2014-10-27 to 2014-11-03) v308

• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 5, context: html, text, full: html, text
    Made checkTableCoords skip the tests for overlapping blocks andinconsistent ends if the table name starts with bacEnd or cloneEnd,
    because it's legit for those particular tables to have some scrambled
    alignments to the reference genome.
    
  • lines changed 46, context: html, text, full: html, text
    Adding a couple exemptions to checkTableCoords for {bac,clone}End*Orphan* tracks. Moved the exemptions up to where the comparisons are made (and verbose-mode errors printed out) instead of where summaries are printed.
  • lines changed 21, context: html, text, full: html, text
    Oops, moved something up before a for loop that needed to happen afterwards -- fixed.
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 1, context: html, text, full: html, text
    hgLiftOver was missing a call to setUdcCacheDir leading to erroneoususe of /tmp/udcCache instead of hg.conf setting.
    
• src/hg/hgMirror/hgMirror
  • lines changed 1, context: html, text, full: html, text
    fix gbib bug where only one organism is shown per clade
• src/hg/hgTables/bedList.c
  • lines changed 1, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/compositeTrack.c
  • lines changed 2, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/correlate.c
  • lines changed 1, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/custom.c
  • lines changed 1, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/hgTables.c
  • lines changed 18, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/hgTables.h
  • lines changed 1, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/intersect.c
  • lines changed 2, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
    underflow errAbort because doMainPage ends with an htmlClose (which
    btw invokes popWarnHandler three times: one directly, once in
    cartWebEnd and once in webEnd). The symptom was that changes made to
    the main page form before looking up a term that returned multiple
    results were lost because the underflow errAbort prevented the cart
    from being saved. The solution is to not use doMainPage(conn, TRUE)
    but instead to call mainPageAfterOpen enclosed by push and pop of
    web warn/error handlers.
    
    Since doMainPage(conn, TRUE) caused trouble that can be avoided by
    calling mainPageAfterOpen, I removed the option.
    
    I also removed dead code doLookupPosition; dispatch is called only
    when lookupPosition() has already returned a single match, so the
    work is already done and it will default to the main page anyway.
    
    refs #12557
    
• src/hg/hgTables/userRegions.c
  • lines changed 2, context: html, text, full: html, text
    Allow start==end in hgTables' user-defined regions BED (valid for insertions).fixes #14238
    
• src/hg/hgTables/vcf.c
  • lines changed 2, context: html, text, full: html, text
    I was under the mistaken impression that VCF header ##INFO andencouraged." This change remove errors about missing descriptions
    that were causing hgTables to give up after 101 errors on a track
    hub VCF. While inspecting the code I found that hgc's vcfClick.c
    printKeysWithDescriptions had never made use of its infoDefs arg
    as intended, so descriptions from ##ALT (symbolic alternate alleles)
    and ##FILTER were not displayed -- fixed that.
    refs #14231
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 8, context: html, text, full: html, text
    adding a checkbox to bam track config to switch to bamWig mode
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 73, context: html, text, full: html, text
    Added support for gencode filter by tag and highlight by tag and annotation method. Currently only enabled in GENCODE V21.
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    making clone ends track hgc page read the psl table from the trackDb setting
• src/hg/hgc/vcfClick.c
  • lines changed 33, context: html, text, full: html, text
    I was under the mistaken impression that VCF header ##INFO andencouraged." This change remove errors about missing descriptions
    that were causing hgTables to give up after 101 errors on a track
    hub VCF. While inspecting the code I found that hgc's vcfClick.c
    printKeysWithDescriptions had never made use of its infoDefs arg
    as intended, so descriptions from ##ALT (symbolic alternate alleles)
    and ##FILTER were not displayed -- fixed that.
    refs #14231
    
• src/hg/htdocs/ebola/index.html
  • lines changed 66, context: html, text, full: html, text
    Removing obsolete page
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 146, context: html, text, full: html, text
    Update for maintainability: Remove treatment and vaccines sections, add Wikipedia link to cover these topics. Move antibody section to main page.
  • lines changed 26, context: html, text, full: html, text
    Add plea for samples and sequences to Ebola Portal
  • lines changed 6, context: html, text, full: html, text
    Fix email address format
  • lines changed 18, context: html, text, full: html, text
    Input from JK, and PLOS reviewer
  • lines changed 12, context: html, text, full: html, text
    A little shuffling of links
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 431, context: html, text, full: html, text
    Some more edits to this file.
  • lines changed 136, context: html, text, full: html, text
    More futzing with this file.
  • lines changed 10, context: html, text, full: html, text
    Added journal reference.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 34, context: html, text, full: html, text
    adding news blurb for GBiB
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    Fixed typo.
  • lines changed 8, context: html, text, full: html, text
    Added GBiB pub. This is an advance access citation, so doesn't yet have page numbers or pubmed ID.
• src/hg/htdocs/images/gbib-RAM.png
  • lines changed 0, context: html, text, full: html, text
    Added these images for gbib.html doc.
• src/hg/htdocs/images/gbib-terminal.png
  • lines changed 0, context: html, text, full: html, text
    Added these images for gbib.html doc.
• src/hg/htdocs/inc/ebola.topbar.html
  • lines changed 2, context: html, text, full: html, text
    Update for maintainability: Remove treatment and vaccines sections, add Wikipedia link to cover these topics. Move antibody section to main page.
• src/hg/htdocs/indexNews.html
  • lines changed 29, context: html, text, full: html, text
    adding news blurb for GBiB
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    adding a checkbox to bam track config to switch to bamWig mode
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v308
• src/hg/lib/hui.c
  • lines changed 8, context: html, text, full: html, text
    adding a checkbox to bam track config to switch to bamWig mode
  • lines changed 2, context: html, text, full: html, text
    temporarily remove check box that allows BAMs to be displayed aswiggles because right now we don't have a way to specify the wiggle
    variables like min,max, and autoscale
    
• src/hg/makeDb/doc/bosTau6.txt
  • lines changed 72, context: html, text, full: html, text
    finished equCab2 lastz refs #14221
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 118, context: html, text, full: html, text
    running up lastz to equCab2 refs #14221
  • lines changed 26, context: html, text, full: html, text
    finished equCab2 lastz refs #14221
• src/hg/makeDb/doc/eboVir3/muPIT.txt
  • lines changed 27, context: html, text, full: html, text
    completed muPIT track refs #14267
• src/hg/makeDb/doc/eboVir3/phastCons160way.txt
  • lines changed 9, context: html, text, full: html, text
    fixup mostConserved construction refs #14254
• src/hg/makeDb/doc/eboVir3/threeBaseAATrack.pl
  • lines changed 65, context: html, text, full: html, text
    completed muPIT track refs #14267
• src/hg/makeDb/doc/hg38.txt
  • lines changed 6499, context: html, text, full: html, text
    Add subdir of doc directory for hg38 make docs
• src/hg/makeDb/doc/hg38/README
  • lines changed 7, context: html, text, full: html, text
    Add subdir of doc directory for hg38 make docs
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 6499, context: html, text, full: html, text
    Add subdir of doc directory for hg38 make docs
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    ignore muPIT and check all dbs for rmskJoined refs #14267 #9741
• src/hg/makeDb/trackDb/cow/bosTau8/description.html
  • lines changed 8, context: html, text, full: html, text
    Added note about difference between UMD 3.1 and UMD 3.1.1; refs #13852
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 164, context: html, text, full: html, text
    Adding phastCons/phyloP sections and info to Conservation track description page. Changing shortLabel for 160 Acessions phyloP track. refs #14254
• src/hg/makeDb/trackDb/ebola/eboVir3/muPIT.html
  • lines changed 3, context: html, text, full: html, text
    Changing some awkward sentence wordings. refs #14267
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra
  • lines changed 2, context: html, text, full: html, text
    readjust default viz phastCons phyloP refs #14254
  • lines changed 1, context: html, text, full: html, text
    Adding phastCons/phyloP sections and info to Conservation track description page. Changing shortLabel for 160 Acessions phyloP track. refs #14254
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra
  • lines changed 2, context: html, text, full: html, text
    readjust default viz phastCons phyloP refs #14254
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 4, context: html, text, full: html, text
    making clinvar ottomatic, refs #14045
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 1, context: html, text, full: html, text
    Fixing typo regarding OC = 3, refs #14208
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing typo regarding OC = 3, refs #14208
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing html description for DNase clustered V1 track
  • lines changed 5, context: html, text, full: html, text
    Changing three-state flags for beta check of ENCODE Dnase Clustered V3, refs #13490
  • lines changed 32, context: html, text, full: html, text
    Public release of encode reg dnase clusters v3, removing v1 and v2 to genome-preview
  • lines changed 1, context: html, text, full: html, text
    Add version indicator to label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClusteredV2.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link to point to V1 track on genome-preview
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClusteredV3.html
  • lines changed 1, context: html, text, full: html, text
    Fix incomplete URL
  • lines changed 3, context: html, text, full: html, text
    Fix links
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV21.ra
  • lines changed 9, context: html, text, full: html, text
    Added support for gencode filter by tag and highlight by tag and annotation method. Currently only enabled in GENCODE V21.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    making clinvar ottomatic, refs #14045
• src/hg/makeDb/trackDb/joinedRmsk.html
  • lines changed 14, context: html, text, full: html, text
    Chaning reference format. Making external links open new tabs. refs #9741
  • lines changed 37, context: html, text, full: html, text
    Made et al in Wheeler citation italic. Primarily white space changes, refs #9741
• src/hg/makeDb/trackDb/joinedRmsk.ra
  • lines changed 11, context: html, text, full: html, text
    joinedRmsk composite only on alpha, single track on beta public refs #9741
  • lines changed 1, context: html, text, full: html, text
    shorter short label refs #9741
• src/hg/makeDb/trackDb/joinedRmskComposite.ra
  • lines changed 22, context: html, text, full: html, text
    joinedRmsk composite only on alpha, single track on beta public refs #9741
  • lines changed 1, context: html, text, full: html, text
    shorter short label refs #9741
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    making gencode VM3 a default track
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM2.ra
  • lines changed 1, context: html, text, full: html, text
    making gencode vm2 hidden by default
• src/hg/makeDb/trackDb/pubs.html
  • lines changed 3, context: html, text, full: html, text
    removing historical info from pubs page
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 2, context: html, text, full: html, text
    Changing comma to period at end of sentence
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    joinedRmsk composite only on alpha, single track on beta public refs #9741
• src/hg/near/hgNear/hgNear.c
  • lines changed 1, context: html, text, full: html, text
    hgNear, hgVisiGene and phyloGif were missing a call to setUdcCacheDir leading to erroneous use of /tmp/udcCache instead of hg.conf setting.
• src/hg/phyloGif/phyloGif.c
  • lines changed 1, context: html, text, full: html, text
    hgNear, hgVisiGene and phyloGif were missing a call to setUdcCacheDir leading to erroneous use of /tmp/udcCache instead of hg.conf setting.
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 190, context: html, text, full: html, text
    making clinvar ottomatic, refs #14045
• src/hg/utils/otto/clinvar/clinvar.as
  • lines changed 36, context: html, text, full: html, text
    making clinvar ottomatic, refs #14045
• src/hg/utils/otto/clinvar/doUpdate.sh
  • lines changed 8, context: html, text, full: html, text
    making clinvar ottomatic, refs #14045
• src/hg/utils/otto/clinvar/makefile
  • lines changed 5, context: html, text, full: html, text
    making clinvar ottomatic, refs #14045
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 1, context: html, text, full: html, text
    hgNear, hgVisiGene and phyloGif were missing a call to setUdcCacheDir leading to erroneous use of /tmp/udcCache instead of hg.conf setting.
• src/lib/tests/expected/vcfParseOldV3.out
  • lines changed 28, context: html, text, full: html, text
    Removing errors from expected output, after errors were removed from vcf.c in 294e289 because they're not actually errors.
• src/lib/vcf.c
  • lines changed 16, context: html, text, full: html, text
    I was under the mistaken impression that VCF header ##INFO andencouraged." This change remove errors about missing descriptions
    that were causing hgTables to give up after 101 errors on a track
    hub VCF. While inspecting the code I found that hgc's vcfClick.c
    printKeysWithDescriptions had never made use of its infoDefs arg
    as intended, so descriptions from ##ALT (symbolic alternate alleles)
    and ##FILTER were not displayed -- fixed that.
    refs #14231
    
• src/test/buildTableDescriptions.pl
  • lines changed 3, context: html, text, full: html, text
    At Jorge's request, adding a FLUSH TABLES to the end of the temporarySQL file that creates tableDescriptions, in hopes that this will end
    myisamchk errors about the table not being closed properly.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v308 final build refs #14194

• lines changed: 15142
• files changed: 90