All File Changes

v285_preview2 to v285_base (2013-06-11 to 2013-06-18) v285

• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 1, context: html, text, full: html, text
    removing unneeded fix-sqli functions
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
  • lines changed 1, context: html, text, full: html, text
    getting rid of unintended use of sqlEscapeString -- should be cgiEncode
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    Edited description slightly for clarity
  • lines changed 11, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/hgGene/domains.c
  • lines changed 1, context: html, text, full: html, text
    fix link-out to Interpro
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 5, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/hgTracks/pubsTracks.c
  • lines changed 15, context: html, text, full: html, text
    fixing an sqlinjection problem as suggested by galt
  • lines changed 1, context: html, text, full: html, text
    fix to fox for sql injection problem, suggested by galt
  • lines changed 1, context: html, text, full: html, text
    improving comments, making comments consistent between jksql.c,h and fixing one reference to a renamed function in pubsTracks.c
• src/hg/hgUserSuggestion/hgUserSuggestion.c
  • lines changed 5, context: html, text, full: html, text
    CAPTCHA enabled per Jonathan's suggestion
  • lines changed 2, context: html, text, full: html, text
    Remove cancel button.
  • lines changed 16, context: html, text, full: html, text
    Thank you suggestion confirmed page.
  • lines changed 5, context: html, text, full: html, text
    redmine 11003 note 21.
  • lines changed 10, context: html, text, full: html, text
    redmine 10633 notre 20
  • lines changed 16, context: html, text, full: html, text
    redmine 11003 hide genome-www address.
  • lines changed 3, context: html, text, full: html, text
    feedback 11003: run user email address thru safecpy before send it to mailViaPipe().
  • lines changed 79, context: html, text, full: html, text
    Check email format at server side, add vertical space between text box.
  • lines changed 7, context: html, text, full: html, text
    Add space between labels and text boxes.
  • lines changed 8, context: html, text, full: html, text
    Make Details input optional
  • lines changed 17, context: html, text, full: html, text
    Limit length of input fields to 256/254, details to 4096. Increase internal char arrays length accordingly.
  • lines changed 7, context: html, text, full: html, text
    Give "Email field must be filled out" when user did not provide input to email field.
  • lines changed 6, context: html, text, full: html, text
    Bug 11059 The title bar of the hgUserSuggestion page doesn't need to include our browser position.
  • lines changed 2, context: html, text, full: html, text
    Add contact.html to "contact us" link. Cite the source of Simple JavaScript CAPTCHA Generator code used.
  • lines changed 38, context: html, text, full: html, text
    ToDo 11002 Jonathan's CRAZ category hack STOOPED.
• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
  • lines changed 1, context: html, text, full: html, text
    Bugfix: forgot to pass through an argument, so all sections started up closed by default. refs #6152
  • lines changed 2, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
  • lines changed 2, context: html, text, full: html, text
    Added cgiExitTime to main.
  • lines changed 27, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 15, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
• src/hg/hgc/ccdsClick.c
  • lines changed 1, context: html, text, full: html, text
    removing unneeded cartWebEnd calls that cause the error popWarnHandler underflow
• src/hg/hgc/gencodeClick.c
  • lines changed 1, context: html, text, full: html, text
    open gencode hgc links back to browser in the same window
  • lines changed 1, context: html, text, full: html, text
    removing unneeded cartWebEnd calls that cause the error popWarnHandler underflow
• src/hg/hgc/mgcClick.c
  • lines changed 1, context: html, text, full: html, text
    removing unneeded cartWebEnd calls that cause the error popWarnHandler underflow
• src/hg/hgc/peakClusters.c
  • lines changed 1, context: html, text, full: html, text
    removing unneeded fix-sqli functions
  • lines changed 2, context: html, text, full: html, text
    removing unneeded cartWebEnd calls that cause the error popWarnHandler underflow
• src/hg/hgc/regMotif.c
  • lines changed 1, context: html, text, full: html, text
    fixed multiple NOSQLINJ tag error by using sqlSafefFrag instead of sqlSafef
• src/hg/hgc/retroClick.c
  • lines changed 1, context: html, text, full: html, text
    removing unneeded cartWebEnd calls that cause the error popWarnHandler underflow
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Adding news release and documentation for Ferret musFur1 release refs #6352
• src/hg/htdocs/contacts.html
  • lines changed 10, context: html, text, full: html, text
    Added section to link to our suggestion box cgi, refs #9142
  • lines changed 8, context: html, text, full: html, text
    Added email address for following up on suggestions, refs #11003
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 58, context: html, text, full: html, text
    Adding news release and documentation for Ferret musFur1 release refs #6352
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 2, context: html, text, full: html, text
    Fixed a couple typos in the text of haplotypes.html
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 29, context: html, text, full: html, text
    Adding news release and documentation for Ferret musFur1 release refs #6352
  • lines changed 2, context: html, text, full: html, text
    Adding missed dash to news release information on release of musFur1 refs #6352
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/htdocs/index.html
  • lines changed 2, context: html, text, full: html, text
    Move Suggestion link to contact page.
• src/hg/htdocs/indexNews.html
  • lines changed 49, context: html, text, full: html, text
    Adding news release and documentation for Ferret musFur1 release refs #6352
  • lines changed 2, context: html, text, full: html, text
    Adding missed dash to news release information on release of musFur1 refs #6352
• src/hg/inc/annoFormatVep.h
  • lines changed 2, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
• src/hg/inc/gpFx.h
  • lines changed 1, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/inc/hCommon.h
  • lines changed 3, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/inc/jksql.h
  • lines changed 20, context: html, text, full: html, text
    removing unneeded fix-sqli functions
  • lines changed 42, context: html, text, full: html, text
    improving comments, making comments consistent between jksql.c,h and fixing one reference to a renamed function in pubsTracks.c
• src/hg/inc/jsHelper.h
  • lines changed 4, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v285
• src/hg/lib/annoFormatVep.c
  • lines changed 23, context: html, text, full: html, text
    Addressing a couple VEP output issues that Jonathan found in #6152 note 46(DISTANCE sometimes off-by-1 vs Ensembl VEP; crazy long sequences reported
    for frameshifts) refs #6152
    
  • lines changed 251, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
  • lines changed 22, context: html, text, full: html, text
    As Jonathan pointed out, to be consistent with VEP we should uppercase only the varying bases in the codon change column. refs #6152
• src/hg/lib/annoGratorGpVar.c
  • lines changed 8, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/annoStreamDb.c
  • lines changed 17, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
  • lines changed 9, context: html, text, full: html, text
    Fixing code review bugs -- Tim noticed I was not using lm when I meant to, and pointed out a contradiction in the way I was using nextChunkStart. refs #11034
  • lines changed 1, context: html, text, full: html, text
    oops, one more thing that Tim caught. refs #11034
  • lines changed 17, context: html, text, full: html, text
    More bugfixing after testing with artificially low ASD_CHUNK_SIZE.
  • lines changed 7, context: html, text, full: html, text
    Fixing bug w/interaction of merge state and chrom-skipping queries.
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    removing unneeded fix-sqli functions
• src/hg/lib/ccdsInfo.c
  • lines changed 3, context: html, text, full: html, text
    needed %-s for where clause
• src/hg/lib/gpFx.c
  • lines changed 238, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 58, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/hCommon.c
  • lines changed 7, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/lib/hgFind.c
  • lines changed 17, context: html, text, full: html, text
    cleanup debug stuff
  • lines changed 3, context: html, text, full: html, text
    Bugfixes and improvements suggested by Brooke in #6152 notes 36, 38, 42. refs #6152
• src/hg/lib/jksql.c
  • lines changed 10, context: html, text, full: html, text
    not getting the desired behavior on stackdump
  • lines changed 145, context: html, text, full: html, text
    removing unneeded fix-sqli functions
  • lines changed 34, context: html, text, full: html, text
    extending sqlCheckIdentifiersList to support just one literal '.' since it is used by hgTables/bedList.c::bedSqlFieldsExceptForChrom()
  • lines changed 37, context: html, text, full: html, text
    improving comments, making comments consistent between jksql.c,h and fixing one reference to a renamed function in pubsTracks.c
• src/hg/lib/joiner.c
  • lines changed 3, context: html, text, full: html, text
    fixing bug related to incorrect detection of wildcards in table names and prefixes
• src/hg/lib/jsHelper.c
  • lines changed 23, context: html, text, full: html, text
    Libifying a javascript trick to detect that the back button has been pressed, and reload the page to redraw with the latest cart vars. refs #6152
• src/hg/lib/mdb.c
  • lines changed 2, context: html, text, full: html, text
    removing unneeded fix-sqli functions
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 2, context: html, text, full: html, text
    Adding HTML version of VEP output format. refs #6152
• src/hg/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 1, context: html, text, full: html, text
    Addressing a couple VEP output issues that Jonathan found in #6152 note 46(DISTANCE sometimes off-by-1 vs Ensembl VEP; crazy long sequences reported
    for frameshifts) refs #6152
    
  • lines changed 6, context: html, text, full: html, text
    Oops, catching up VEP output test cases with that last commit.
  • lines changed 13, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 13, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 13, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 1, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 2, context: html, text, full: html, text
    Addressing a couple VEP output issues that Jonathan found in #6152 note 46(DISTANCE sometimes off-by-1 vs Ensembl VEP; crazy long sequences reported
    for frameshifts) refs #6152
    
  • lines changed 2, context: html, text, full: html, text
    Oops, catching up VEP output test cases with that last commit.
  • lines changed 13, context: html, text, full: html, text
    As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
    refs #6152
    
• src/hg/lib/tests/expected/sqlCheck/sqlCheck.5
  • lines changed 1, context: html, text, full: html, text
    removing unneeded fix-sqli functions
• src/hg/lib/tests/expected/sqlCheck/sqlCheck.6
  • lines changed 3, context: html, text, full: html, text
    removing unneeded fix-sqli functions
• src/hg/lib/tests/expected/sqlCheck/sqlCheck.9
  • lines changed 1, context: html, text, full: html, text
    extending sqlCheckIdentifiersList to support just one literal '.' since it is used by hgTables/bedList.c::bedSqlFieldsExceptForChrom()
• src/hg/lib/tests/sqlCheck.c
  • lines changed 6, context: html, text, full: html, text
    removing unneeded fix-sqli functions
  • lines changed 5, context: html, text, full: html, text
    extending sqlCheckIdentifiersList to support just one literal '.' since it is used by hgTables/bedList.c::bedSqlFieldsExceptForChrom()
• src/hg/lib/tests/sqlCheck.mk
  • lines changed 4, context: html, text, full: html, text
    removing unneeded fix-sqli functions
  • lines changed 2, context: html, text, full: html, text
    extending sqlCheckIdentifiersList to support just one literal '.' since it is used by hgTables/bedList.c::bedSqlFieldsExceptForChrom()
• src/hg/lib/trackHub.c
  • lines changed 28, context: html, text, full: html, text
    add the ability to list more than one index for bigBed's to support track hub item search
• src/hg/lib/variant.c
  • lines changed 28, context: html, text, full: html, text
    Changing how gpFx determines indel changes. Instead of padding the non-reference allele with hyphens, and using string comparison of CDS containing
    hyphens to determine effects on genes, use the genePred information directly
    to determine the variant's offset in CDS, and how many CDS bases are
    added/deleted. This solves two problems: 1) the reference was never padded,
    so the method didn't work for insertions because string comparison could not
    pick up the trail of identical bases again; 2) the hyphens were messing up
    protein translation.
    
  • lines changed 7, context: html, text, full: html, text
    Fix corner case (deletion falls across exon boundary; normally we wantto trim the part of the allele that falls outside, but for the deletion
    the allele is "").
    
• src/hg/makeDb/doc/canFam2.txt
  • lines changed 26, context: html, text, full: html, text
    Initial NumtS track for canFam2, equCap2, monDom5, ornAna1, oryCun.2 and rn4.
• src/hg/makeDb/doc/echTel1.txt
  • lines changed 20, context: html, text, full: html, text
    liftOver from echTel1 to echTel2 is complete refs #9693
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 111, context: html, text, full: html, text
    Add downloads file combining clusters with cell types represented. Also, the script to produce it. refs #10097
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 1, context: html, text, full: html, text
    Initial NumtS track for canFam2, equCap2, monDom5, ornAna1, oryCun.2 and rn4.
• src/hg/makeDb/doc/eriEur2.txt
  • lines changed 43, context: html, text, full: html, text
    stalled on RepeatMasker nestedRepeats problem refs #9419
• src/hg/makeDb/doc/galGal3.txt
  • lines changed 29, context: html, text, full: html, text
    Track 8533 NumtS 2012 track ra entries move to top level.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 64, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
  • lines changed 12, context: html, text, full: html, text
    finished work on gencode v16
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 29, context: html, text, full: html, text
    Initial NumtS track for canFam2, equCap2, monDom5, ornAna1, oryCun.2 and rn4.
• src/hg/makeDb/doc/ornAna1.txt
  • lines changed 27, context: html, text, full: html, text
    Initial NumtS track for canFam2, equCap2, monDom5, ornAna1, oryCun.2 and rn4.
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 26, context: html, text, full: html, text
    Initial NumtS track for canFam2, equCap2, monDom5, ornAna1, oryCun.2 and rn4.
• src/hg/makeDb/doc/rn4.txt
  • lines changed 27, context: html, text, full: html, text
    Initial NumtS track for canFam2, equCap2, monDom5, ornAna1, oryCun.2 and rn4.
• src/hg/makeDb/doc/sorAra1.txt
  • lines changed 20, context: html, text, full: html, text
    liftOver from sorAra1 to sorAra2 refs #9348
• src/hg/makeDb/doc/vicPac1.txt
  • lines changed 20, context: html, text, full: html, text
    construct liftOver from vicPac1 to vicPac2 refs #10833
• src/hg/makeDb/doc/xenTro7.txt
  • lines changed 459, context: html, text, full: html, text
    initial 2bit file done starting masking refs #9868
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    fixup taeGut2 to be no perChromTables refs #10190
  • lines changed 1, context: html, text, full: html, text
    incorrect ooc file path for allMis1 refs #8750
• src/hg/makeDb/schema/all.joiner
  • lines changed 16, context: html, text, full: html, text
    adding rules for echTel2 refs #9693
  • lines changed 17, context: html, text, full: html, text
    adding sorAra2 rules refs #9348
  • lines changed 80, context: html, text, full: html, text
    finished work on gencode v16
• src/hg/makeDb/trackDb/ferret/musFur1/description.html
  • lines changed 5, context: html, text, full: html, text
    Adding news release and documentation for Ferret musFur1 release refs #6352
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegTfbsClustered.ra
  • lines changed 2, context: html, text, full: html, text
    Fix incorrect tablename in metadata. refs #10097
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegTfbsClustered.ra
  • lines changed 28, context: html, text, full: html, text
    Staging metaData for wgEncodeRegTfbsClusteredInputsV3 on beta refs #10097
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 7, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
  • lines changed 224, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.release3.ra
  • lines changed 12, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra
  • lines changed 12, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.ra
  • lines changed 224, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.release3.ra
  • lines changed 12, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.release4.ra
  • lines changed 227, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.ra
  • lines changed 12, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.ra
  • lines changed 17, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.release2.ra
  • lines changed 18, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.ra
  • lines changed 17, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.html
  • lines changed 342, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.ra
  • lines changed 263, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
  • lines changed 6, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
  • lines changed 1, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 189, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release3.ra
  • lines changed 12, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release4.ra
  • lines changed 223, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 12, context: html, text, full: html, text
    GENCODE V16 import. Corrected search results order to show newest gencode first
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Tweak short label for consistency. refs #10097
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    Tweak labels and priorities of tracks within supertrack to clarify relationships and to highlight new track. refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
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    Updates and expansion of track description. refs #10097
• src/hg/makeDb/trackDb/human/hgmd.html
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    rewording of the hgmd description
• src/hg/makeDb/trackDb/makefile
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    adding xenTro7 to the build refs #9868
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
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    adding some temporary testing tracks to repeats2
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
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    Track 8533 NumtS 2012 track ra entries move to top level.
• src/hg/makeDb/trackDb/xenTro/xenTro7/description.html
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    initial set of files from makeGenomeDb.pl refs #9868
• src/hg/makeDb/trackDb/xenTro/xenTro7/gap.html
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    initial set of files from makeGenomeDb.pl refs #9868
• src/hg/makeDb/trackDb/xenTro/xenTro7/gold.html
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    initial set of files from makeGenomeDb.pl refs #9868
• src/hg/makeDb/trackDb/xenTro/xenTro7/trackDb.ra
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    initial set of files from makeGenomeDb.pl refs #9868
• src/hg/regulate/wgEncodeReg/clusterAddSources.pl
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    Extra downloads file for TFBS clusters is generated by this script. It combines two tables to create a user-friendly download (answer to repeated ML users). refs #10097
• src/product/ex.hg.conf
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    Added hgUserSuggestion lines to ex.hg.conf, refs #11017
• src/utils/qa/weeklybld/buildEnv.csh
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    v285 preview2
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    v284 final build

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