Commits for hiram
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v296_preview to v296_preview2 (2014-02-10 to 2014-02-17) v296
- donewith rheMac3 lastz/chain/net refs #11681
- src/hg/makeDb/doc/hg38.txt - lines changed 61, context: html, text, full: html, text
- adding analysis set construction refs #11681
- src/hg/makeDb/doc/hg38.txt - lines changed 74, context: html, text, full: html, text
- running up phyloP for the 100way rework refs #12260
- src/hg/makeDb/doc/hg19.txt - lines changed 111, context: html, text, full: html, text
- running up the self lastz chain refs #11681
- src/hg/makeDb/doc/hg38.txt - lines changed 155, context: html, text, full: html, text
- adding chainSelf overrides refs #11681
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 9, context: html, text, full: html, text
- creating downloads for new 100-way refs #12260
- src/hg/makeDb/doc/hg19.txt - lines changed 45, context: html, text, full: html, text
- turn on multiz4way track display refs #12673
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 24, context: html, text, full: html, text
- addingmultiz4way construction refs #12673
- src/hg/makeDb/doc/hg38.txt - lines changed 171, context: html, text, full: html, text
- add temporary experiment with altAlignments refs #11681
- src/hg/makeDb/doc/hg38.txt - lines changed 94, context: html, text, full: html, text
- adding track overrides and description pages for all tracks refs #11681
- src/hg/makeDb/trackDb/human/hg38/analysisGap.html - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/chainNetPrimate.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/ctgPos2.html - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/genbankOverrides.ra - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/hg38primateChainNet.html - lines changed 202, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/hmmerUnique.html - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/multiz4way.html - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/scaffolds.html - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 12, context: html, text, full: html, text
- file moved to hmmerUnique.html refs #11681
- src/hg/makeDb/trackDb/human/hg38/hmmerUnique.bed - lines changed 12, context: html, text, full: html, text
- 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.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
- adding hg19 to hg38 difference track on hg19 and correct label on same track on hg38 refs #11681
- src/hg/makeDb/trackDb/human/hg19/hg38ContigDiff.html - lines changed 38, context: html, text, full: html, text
- most hg19 tracks are now in alphabetic order refs #7343
- src/hg/makeDb/trackDb/human/decode.rmap.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite10.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite2.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite9.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 43, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/phastBias.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.denisova.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.nt.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 106, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.genbank.new.ra - lines changed 14, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.genbank.ra - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.nt.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 154, context: html, text, full: html, text
- most tracks on hg19 are now in alpha order refs #7343
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 43, context: html, text, full: html, text
- tracks on mm10 should now be in alpha order refs #7343
- src/hg/makeDb/trackDb/mouse/mm10/altSeqComposite1.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1SuperTrack.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/trackDb.ra - lines changed 40, context: html, text, full: html, text
- missing priority is as good as priority 0 refs #7343
- src/hg/makeDb/trackDb/trackDb.genbank.new.ra - lines changed 14, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.genbank.ra - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.nt.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 155, context: html, text, full: html, text
- missing priority is as good as priority 0 refs #7343
- src/hg/makeDb/trackDb/human/decode.rmap.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/phastBias.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.denisova.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.nt.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 142, context: html, text, full: html, text
- remove empty override track statements refs #7343
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 8, context: html, text, full: html, text
- missing priority is as good as priority 0 refs #7343
- src/hg/makeDb/trackDb/mouse/trackDb.ra - lines changed 42, context: html, text, full: html, text
- absent priority is as good as priority 0 refs #7343
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite10.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite2.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite9.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 45, context: html, text, full: html, text
- default vis tracks default priorities to get them first in their track groups refs #7343
- src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 7, context: html, text, full: html, text
- no priority is as good as 0 priority refs #7343
- src/hg/makeDb/trackDb/mouse/mm10/altSeqComposite1.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1SuperTrack.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - 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/defaultPriority.ra - lines changed 25, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 8, context: html, text, full: html, text
- 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/altSequences.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/genbankOverrides.ra - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 42, context: html, text, full: html, text
- super track package of extra rmsk tracks in the Experimental group refs #11681
- src/hg/makeDb/trackDb/human/hg38/rmskTracks.html - lines changed 93, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/rmskTracks.ra - lines changed 58, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 55, context: html, text, full: html, text
- catching a few outliers in the reorder tracks refs #7343
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
- catching a few outliers in the reorder tracks refs #7343
- src/hg/makeDb/trackDb/trackDb.genbank.new.ra - lines changed 2, context: html, text, full: html, text
- reset default priorities for wikiTrack, Short Match and Restr Enzymes refs #7343
- src/hg/hgTracks/cutterTrack.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
- no priority for ENCODE Pilot to get it into alpha order refs #7343
- src/hg/makeDb/trackDb/human/trackDb.encode.ra - lines changed 1, context: html, text, full: html, text
- default priorities for New variants track refs #7343
- src/hg/hgTracks/simpleTracks.c - lines changed 2, context: html, text, full: html, text
- default priorities for Denisova track group refs #7343
- src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra - lines changed 4, context: html, text, full: html, text
- correct ordering within Conservation group refs #7343
- src/hg/makeDb/trackDb/human/hg19/chainNetFr2.ra - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetFr3.ra - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 277, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra - lines changed 31, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetSusScr2.ra - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetSusScr3.ra - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetTurTru1.ra - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetTurTru2.ra - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra - lines changed 50, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 7, context: html, text, full: html, text
- shorten the shortLabel for centromeres refs #11681
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
- slight reordering in Conservation group refs #7343
- src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
- doesn't matter where legacy is refs #7343
- src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 1, context: html, text, full: html, text
- v296 preview2 refs #12535
- src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text
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