All File Changes

v290_preview to v290_preview2 (2013-09-16 to 2013-09-23) v290

• src/README
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    Adding section about preventing sqli to src/README
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 7, context: html, text, full: html, text
    Making paraFetch retry an extra time. Making it only hit database once a second when checking for interrupts.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Making pooled replicates not try to find a mate.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 10, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/hgVai/hgVai.c
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    Fixing a URL (copy-paste error).
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 2, context: html, text, full: html, text
    Making corrections per code review refs #11759
• src/hg/htdocs/ENCODE/index.html
  • lines changed 4, context: html, text, full: html, text
    Making corrections per code review refs #11759
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    Adding back link to newsarchives code review 11759
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    Making corrections per code review refs #11759
  • lines changed 1, context: html, text, full: html, text
    Updating per code review refs #11759
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 296, context: html, text, full: html, text
    Publication/requested specific updates from Mike Pazin (per document) for ENCODE, RM at Stanford #562
  • lines changed 7, context: html, text, full: html, text
    Removing misplaced reference in Mike Pazin's document, refs Stanford RM #562
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 769, context: html, text, full: html, text
    Publication/requested specific updates from Mike Pazin (per document) for ENCODE, RM at Stanford #562
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 2, context: html, text, full: html, text
    Adding a frameshift SNP to pgSNP format example per request of Bob
• src/hg/htdocs/admin/mirror.html
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    because Steve said so!
• src/hg/htdocs/conditions.html
  • lines changed 32, context: html, text, full: html, text
    Made some changes to conditions.html per ref #8699. Also removed some duplicate info from indexInfo.html, but not all of it. This will improve once we revamp the static pages, but I think it's OK for now.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    Fixing link to information on PSL format, refs #11307
• src/hg/htdocs/indexInfo.html
  • lines changed 51, context: html, text, full: html, text
    Made some changes to conditions.html per ref #8699. Also removed some duplicate info from indexInfo.html, but not all of it. This will improve once we revamp the static pages, but I think it's OK for now.
• src/hg/lib/annoFormatVep.c
  • lines changed 2, context: html, text, full: html, text
    Avoid double-linebreak in VEP header when dbSNP is not included.
• src/hg/lib/haplotypes.c
  • lines changed 1, context: html, text, full: html, text
    Corrected a typo that Donna noticed.
• src/hg/lib/jsHelper.c
  • lines changed 12, context: html, text, full: html, text
    Handle IE's unique behavior of window.location.replace when the newURL (including stuff after '?') is the same as the current URL.
    fixes #11443
    
• src/hg/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 4, context: html, text, full: html, text
    Oops, forgot to correct test file after fixing intron off-by-one in 099102d. Too bad I didn't notice it in the test file to begin with...
• src/hg/makeDb/doc/hg19.txt
  • lines changed 69, context: html, text, full: html, text
    panTig1 lastz done starting letCam1 lastz refs #10272
  • lines changed 1698, context: html, text, full: html, text
    the 100-way procedure included refs #10272
  • lines changed 134, context: html, text, full: html, text
    swapping hg19 letCam1 lastz and constructing downloads for 100-way refs #10272
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 1276, context: html, text, full: html, text
    adding v73 build sequences refs #11675
• src/hg/makeDb/genbank/etc/align.dbs
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    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 29, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 5, context: html, text, full: html, text
    add more lines to this file ignore.idx which is a list of lines
• src/hg/makeDb/genbank/src/dbload/dbLoadOptions.h
  • lines changed 1, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/dbload/dbLoadPartitions.c
  • lines changed 2, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/dbload/gbAlignData.c
  • lines changed 2, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • lines changed 4, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c
  • lines changed 9, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/dbload/gbGeneTbl.h
  • lines changed 2, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
  • lines changed 8, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/dbload/gbMetaData.c
  • lines changed 5, context: html, text, full: html, text
    oops, a little fix to updating metadata to track whether to keep theversion #
    
• src/hg/makeDb/genbank/src/inc/gbDefs.h
  • lines changed 1, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Adding all dgv* tracks to tablesIgnored.
  • lines changed 1, context: html, text, full: html, text
    avoid duplicate ensGene.name errors on gadMor1 refs #11675
• src/hg/makeDb/trackDb/chicken/bgiCov.html
  • lines changed 2, context: html, text, full: html, text
    Fixing broken links on some chicken track description pages
• src/hg/makeDb/trackDb/chicken/bgiSnp.html
  • lines changed 2, context: html, text, full: html, text
    Fixing broken links on some chicken track description pages
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    added the panTro2 to panTro4 over chains as a separate track as requested by Adam/David, they want to compare the assemblies
• src/hg/makeDb/trackDb/human/dgvPlus.html
  • lines changed 9, context: html, text, full: html, text
    Incorporating corrections from Jeff MacDonald.refs #11200
    
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 108, context: html, text, full: html, text
    updated genome list for this set of 100 refs #10272
  • lines changed 4, context: html, text, full: html, text
    case and name updates updated refs #10272
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 440, context: html, text, full: html, text
    Added searchable termRegex cg######## probe items to HAIB Methyl track, with BRaney's help, refs #11754
  • lines changed 434, context: html, text, full: html, text
    bringing down search results for wgEncodeHaibMethyl450.ra to just one table of Tier1 cell line per feedback from Steve & BrianR refs #11754
• src/hg/makeDb/trackDb/human/hg19/wgRna.html
  • lines changed 11, context: html, text, full: html, text
    Fixing links to miRBase, refs #11280
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Incorporating corrections from Jeff MacDonald.refs #11200
    
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    Fixing broken download links on lamprey conservation description page
• src/hg/pslCDnaFilter/algo.txt
  • lines changed 1, context: html, text, full: html, text
    add new option -maxAlignsDrop=N to pslCDnaFilter that drops all thealignments of a query that aligns more than N times.
    
• src/hg/pslCDnaFilter/cDnaAligns.h
  • lines changed 2, context: html, text, full: html, text
    add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
    
• src/hg/pslCDnaFilter/cDnaReader.c
  • lines changed 6, context: html, text, full: html, text
    add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
    
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 37, context: html, text, full: html, text
    add new option -maxAlignsDrop=N to pslCDnaFilter that drops all thealignments of a query that aligns more than N times.
    
  • lines changed 3, context: html, text, full: html, text
    add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
    
• src/hg/pslCDnaFilter/usage.txt
  • lines changed 4, context: html, text, full: html, text
    add new option -maxAlignsDrop=N to pslCDnaFilter that drops all thealignments of a query that aligns more than N times.
    
  • lines changed 2, context: html, text, full: html, text
    add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
    
• src/hg/utils/phyloTrees/benchMark100.commonNames.nh
  • lines changed 100, context: html, text, full: html, text
    updated distances from 4D measurement on the 100-way MAF files refs #10272
• src/hg/utils/phyloTrees/benchMark100.nh
  • lines changed 100, context: html, text, full: html, text
    updated distances from 4D measurement on the 100-way MAF files refs #10272
• src/hg/utils/phyloTrees/benchMark100.scientificNames.nh
  • lines changed 100, context: html, text, full: html, text
    updated distances from 4D measurement on the 100-way MAF files refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 12, context: html, text, full: html, text
    cleaning up the commonNames.sh name listing refs #10272
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 115, context: html, text, full: html, text
    tab separated listing for dbDb entries refs #10272
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    correct clade from the clade table in hgcentral refs #10272
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    update case and naming consistency refs #10272
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    cleaning up the commonNames.sh name listing refs #10272
• src/hg/utils/pslMap/tests/expected/mrnaChainMapBug.mapinfo
  • lines changed 2, context: html, text, full: html, text
    fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
• src/hg/utils/pslMap/tests/expected/mrnaChainMapBug.psl
  • lines changed 1, context: html, text, full: html, text
    fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
• src/hg/utils/pslMap/tests/input/mrnaChainMapRefSeq.chain
  • lines changed 610956, context: html, text, full: html, text
    fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
• src/hg/utils/pslMap/tests/input/mrnaChainMapRefSeq.psl
  • lines changed 1, context: html, text, full: html, text
    fixed bug where mappings would be missed if multiple mapping alignments mapped to the same rangetree node
• src/lib/annoStreamVcf.c
  • lines changed 1, context: html, text, full: html, text
    Yikes, when querying at the cart position instead of the whole genome,annoStreamVcf was skipping rows that it shouldn't have!
    
  • lines changed 149, context: html, text, full: html, text
    Fixing bug reported by user in MLQ #11775: VCF that is sorted bystart position might not be sorted by UCSC-start position, specifically
    when at the same VCF start position there is an indel followed by a
    substitution. VCF start coords for indels are actually one base to
    the left of the actual inserted or deleted bases. So we internally
    adjust those to be one base to the right, which can make them out-of-order
    when followed by a non-indel variant.
    
    To restore sorting order, indels are now saved aside in a queue until
    we know it's safe to let them out because either
    a) we got a substitution whose start is greater than the indel start
    b) we got an indel whose start is greater than the queued indel start
    c) we hit EOF.
    When condition (a) or (b) is met, we have to do something with the
    new record while the indel queue drains, so it's saved aside in the
    nextPosQ (which never holds more than one row). If it's (b), then
    when indelQ is empty, we move the nextPosQ indel to indelQ because
    we can't let that indel out until one of the 3 conditions is met.
    
    fixes #11787
    
• src/lib/paraFetch.c
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    fixing progress indicator
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    removed return FALSE that was unneeded and just causing it to be unable to retry
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    improving timeout and retry handling based in Jims suggestions
• src/product/ex.hg.conf
  • lines changed 9, context: html, text, full: html, text
    adding documentation for db.neverLocal
• src/utils/git-reports/git-reports.c
  • lines changed 24, context: html, text, full: html, text
    I am reverting Hirams changes and doing the same thing a different way. Fixes the double-free error.
  • lines changed 7, context: html, text, full: html, text
    Changing the plain text diffs to add file/link extension ".txt" which seems to help more than hurt, as most browsers support the .txt as text automatically. Of course there is a small chance that some software somewhere did automatically recognize the .diff extension properly and show it nicely colored in that way.
• src/utils/qa/2bitCompare
  • lines changed 175, context: html, text, full: html, text
    New script to compare md5sums of assembly 2bit files (redmine #6508)
  • lines changed 24, context: html, text, full: html, text
    Modified the script to also output the date and filesize of all 2bit files if applicable (redmine #6508)
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Modified makefile to include new 2bitCompare script (redmine #6508)
• src/utils/qa/weeklybld/buildEnv.csh
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    v290 preview2
• src/utils/raToStructGen/testOut/test.as
  • lines changed 1, context: html, text, full: html, text
    eliminate duplicate sql definition to src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as refs #11756

• lines changed: 617465
• files changed: 84