File Changes for hiram

v296_preview to v296_preview2 (2014-02-10 to 2014-02-17) v296

• src/hg/hgTracks/cutterTrack.c
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    reset default priorities for wikiTrack, Short Match and Restr Enzymes refs #7343
• src/hg/hgTracks/hgTracks.c
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    reset default priorities for wikiTrack, Short Match and Restr Enzymes refs #7343
• src/hg/hgTracks/simpleTracks.c
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    default priorities for New variants track refs #7343
• src/hg/inc/hui.h
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    reset default priorities for wikiTrack, Short Match and Restr Enzymes refs #7343
• src/hg/inc/wikiTrack.h
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    reset default priorities for wikiTrack, Short Match and Restr Enzymes refs #7343
• src/hg/makeDb/doc/hg19.txt
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    running up phyloP for the 100way rework refs #12260
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    creating downloads for new 100-way refs #12260
• src/hg/makeDb/doc/hg38.txt
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    donewith rheMac3 lastz/chain/net refs #11681
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    adding analysis set construction refs #11681
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    running up the self lastz chain refs #11681
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    addingmultiz4way construction refs #12673
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    add temporary experiment with altAlignments refs #11681
• src/hg/makeDb/trackDb/human/decode.rmap.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite10.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    absent priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite2.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    absent priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    absent priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite9.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    absent priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetFr2.ra
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    correct ordering within Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetFr3.ra
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    correct ordering within Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra
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    correct ordering within Conservation group refs #7343
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    slight reordering in Conservation group refs #7343
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    doesn't matter where legacy is refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra
  • lines changed 31, context: html, text, full: html, text
    correct ordering within Conservation group refs #7343
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    slight reordering in Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra
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    correct ordering within Conservation group refs #7343
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    slight reordering in Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetSusScr2.ra
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    correct ordering within Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetSusScr3.ra
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    correct ordering within Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetTurTru1.ra
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    correct ordering within Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetTurTru2.ra
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    correct ordering within Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra
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    correct ordering within Conservation group refs #7343
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    slight reordering in Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
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    default vis tracks default priorities to get them first in their track groups refs #7343
• src/hg/makeDb/trackDb/human/hg19/hg38ContigDiff.html
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    adding hg19 to hg38 difference track on hg19 and correct label on same track on hg38 refs #11681
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
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    default vis tracks default priorities to get them first in their track groups refs #7343
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
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    correct ordering within Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
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    default priorities for Denisova track group refs #7343
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    adding hg19 to hg38 difference track on hg19 and correct label on same track on hg38 refs #11681
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    most hg19 tracks are now in alphabetic order refs #7343
  • lines changed 43, context: html, text, full: html, text
    most tracks on hg19 are now in alpha order refs #7343
  • lines changed 45, context: html, text, full: html, text
    absent priority is as good as priority 0 refs #7343
  • lines changed 7, context: html, text, full: html, text
    default vis tracks default priorities to get them first in their track groups refs #7343
  • lines changed 2, context: html, text, full: html, text
    catching a few outliers in the reorder tracks refs #7343
  • lines changed 7, context: html, text, full: html, text
    correct ordering within Conservation group refs #7343
  • lines changed 2, context: html, text, full: html, text
    slight reordering in Conservation group refs #7343
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra
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    catching a few outliers in the reorder tracks refs #7343
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
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    catching a few outliers in the reorder tracks refs #7343
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.ra
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    catching a few outliers in the reorder tracks refs #7343
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
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    remove priority 0 statements and set default vis on tracks to priorities to get them at the head of their track group refs #7343
• src/hg/makeDb/trackDb/human/hg38/analysisGap.html
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    adding track overrides and description pages for all tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/chainNetPrimate.ra
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    adding track overrides and description pages for all tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/ctgPos2.html
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    adding track overrides and description pages for all tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
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    remove priority 0 statements and set default vis on tracks to priorities to get them at the head of their track group refs #7343
• src/hg/makeDb/trackDb/human/hg38/genbankOverrides.ra
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    adding track overrides and description pages for all tracks refs #11681
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    remove priority 0 statements and set default vis on tracks to priorities to get them at the head of their track group refs #7343
• src/hg/makeDb/trackDb/human/hg38/hg38primateChainNet.html
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    adding track overrides and description pages for all tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/hmmerUnique.bed
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    file moved to hmmerUnique.html refs #11681
• src/hg/makeDb/trackDb/human/hg38/hmmerUnique.html
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    adding track overrides and description pages for all tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/multiz4way.html
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    adding track overrides and description pages for all tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskTracks.html
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    super track package of extra rmsk tracks in the Experimental group refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskTracks.ra
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    super track package of extra rmsk tracks in the Experimental group refs #11681
• src/hg/makeDb/trackDb/human/hg38/scaffolds.html
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    adding track overrides and description pages for all tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    adding chainSelf overrides refs #11681
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    turn on multiz4way track display refs #12673
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    adding track overrides and description pages for all tracks refs #11681
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    adding hg19 to hg38 difference track on hg19 and correct label on same track on hg38 refs #11681
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    remove priority 0 statements and set default vis on tracks to priorities to get them at the head of their track group refs #7343
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    super track package of extra rmsk tracks in the Experimental group refs #11681
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    shorten the shortLabel for centromeres refs #11681
• src/hg/makeDb/trackDb/human/phastBias.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/trackDb.denisova.ra
  • lines changed 2, context: html, text, full: html, text
    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
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    no priority for ENCODE Pilot to get it into alpha order refs #7343
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra
  • lines changed 1, context: html, text, full: html, text
    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 106, context: html, text, full: html, text
    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
  • lines changed 8, context: html, text, full: html, text
    remove empty override track statements refs #7343
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    catching a few outliers in the reorder tracks refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/altSeqComposite1.ra
  • lines changed 1, context: html, text, full: html, text
    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
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    setting default vis tracks with priorities to get them first in their track group refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1SuperTrack.ra
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    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 1, context: html, text, full: html, text
    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
  • lines changed 1, context: html, text, full: html, text
    setting default vis tracks with priorities to get them first in their track group refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
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    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
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    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
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    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
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    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
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    setting default vis tracks with priorities to get them first in their track group refs #7343
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    tracks on mm10 should now be in alpha order refs #7343
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    no priority is as good as 0 priority refs #7343
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    tracks on mm10 should now be in alpha order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/trackDb.genbank.new.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
  • lines changed 2, context: html, text, full: html, text
    catching a few outliers in the reorder tracks refs #7343
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 12, context: html, text, full: html, text
    most hg19 tracks are now in alphabetic order refs #7343
  • lines changed 12, context: html, text, full: html, text
    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/trackDb.nt.ra
  • lines changed 2, context: html, text, full: html, text
    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/hg/makeDb/trackDb/trackDb.ra
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    most hg19 tracks are now in alphabetic order refs #7343
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    missing priority is as good as priority 0 refs #7343
• src/utils/qa/weeklybld/buildEnv.csh
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    v296 preview2 refs #12535