pchan: changes by file

branch to review (2009-09-15 to 2009-09-22) v216

• src/hg/archaeStuff/data/Genome-info-meta
  • 1.10 lines changed: 3, context: html, text, full: html, text
    add cold cren to BED alignments
  • 1.9 lines changed: 204, context: html, text, full: html, text
    add site 3, 4, 8, 14, 19, and BED
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.80 lines changed: 4, context: html, text, full: html, text
    align ospSpri14_050609_1 with hydrogenobaculum
• src/hg/archaeStuff/data/blat-servers.tab
  • 1.4 lines changed: 1, context: html, text, full: html, text
    add Metagenome to lowepub
  • 1.3 lines changed: 2, context: html, text, full: html, text
    put blat server of Gammaproteobacteria onto lowedev
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.47 lines changed: 4, context: html, text, full: html, text
    add rRNA_Blat track
  • 1.46 lines changed: 15, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.23 lines changed: 1, context: html, text, full: html, text
    set max displayed hits of blastx
  • 1.22 lines changed: 0, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
  • 1.21 lines changed: 3, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.35 lines changed: 11, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
• src/hg/archaeStuff/scripts/archaeBrowser/GenePrediction.pm
  • 1.8 lines changed: 72, context: html, text, full: html, text
    add Andrew's gene prediction tracks; minor bug fixes; add common bin dir to Constants.pm; add gene finder prefix to predicted gene names
• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.15 lines changed: 15, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.9 lines changed: 8, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.41 lines changed: 90, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/Utils.pm
  • 1.3 lines changed: 15, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.19 lines changed: 155, context: html, text, full: html, text
    add rRNA_Blat track
  • 1.18 lines changed: 1, context: html, text, full: html, text
    add code to support YNP metagenomes
• src/hg/hgc/lowelab.c
  • 1.35 lines changed: 2, context: html, text, full: html, text
    check existence of scaffolds table for metagenome blastx track
• src/hg/makeDb/trackDb/lowelab/description-template.html
  • 1.12 lines changed: 1, context: html, text, full: html, text
    add rRNA_BlatRegion list
• src/hg/makeDb/trackDb/lowelab/acidBott_VIRUS/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_2/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_3/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_6/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_7/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_8/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidFila_VIRUS_9/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidRods_VIRUS_1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/acidTwot_VIRUS/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/aerPer1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/archBJ1_VIRUS/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/archFulg1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/beowSpri_East_D_072007_1/multizCrenNanoYNP.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    Details page for multiz track
• src/hg/makeDb/trackDb/lowelab/beowSpri_East_D_072007_1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update multiz track
  • 1.1 lines changed: 16, context: html, text, full: html, text
    New multiz track
• src/hg/makeDb/trackDb/lowelab/caldMaqu1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/cenaSymb1/trackDb.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/desuKamc1/trackDb.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/ferrAcid1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloHF1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloPhag_SH1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloSali1/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloUtah1/trackDb.ra
  • 1.1 lines changed: 13, context: html, text, full: html, text
    New selfz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1/trackDb.ra
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/haloWals1/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/his1Viru/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/his2Viru/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/hydrSp_128_5R1/multizAquificales.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    Details page for multiz track
• src/hg/makeDb/trackDb/lowelab/hydrSp_128_5R1/trackDb.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    New multiz track
• src/hg/makeDb/trackDb/lowelab/hydrY04A/trackDb.ra
  • 1.3 lines changed: 10, context: html, text, full: html, text
    Update ultraConserved track
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/hydrY04A/ultraConserved.html
  • 1.1 lines changed: 3, context: html, text, full: html, text
    New ultraConserved track
• src/hg/makeDb/trackDb/lowelab/hypeButy1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/igniHosp1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/koraCryp1/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/mculMari1/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/metAce1/trackDb.ra
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/metMar1/trackDb.ra
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/metaSedu/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methAeol1/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methBark1/trackDb.ra
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methBoon1/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methBurt2/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methFerv0/trackDb.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methHung1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methInfe0/trackDb.ra
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methJann1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methKand1/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methLabrZ_1/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methMari_C5_1/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methMari_C6/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methMari_C7/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methMaze1/trackDb.ra
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methPhag_PSIM2/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methSmit1/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methStad1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methTher1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methTherPT1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methVann1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/methVulc0/trackDb.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/nanEqu1/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/natrMaga0/trackDb.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/natrPhag_PHICH1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/natrPhar1/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/nitrMari1/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/picrTorr1/trackDb.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyrAby1/trackDb.ra
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyrAer1/trackDb.ra
  • 1.54 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyrFur2/trackDb.ra
  • 1.31 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyrHor1/trackDb.ra
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyroAbys_VIRUS_1/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyroArse1/trackDb.ra
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyroIsla1/trackDb.ra
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/pyroSphe_VIRUS/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/stapHell0/trackDb.ra
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/stapMari1/trackDb.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulSol1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfAcid1/trackDb.ra
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_FILAMENTOUS/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_L_S_2_15/trackDb.ra
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_14_25/trackDb.ra
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_27/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_M_16_4/trackDb.ra
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_ROD_SHAPED_V/trackDb.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_ROD_SHAPED_VIRUS_2/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_G_57_14/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfIsla_Y_N_15_51/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfSpin_VIRUS_4/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfToko1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfTurr_ICOSAHEDRAL/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfViru_1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfViru_KAMCHATKA_1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/sulfViru_STSV1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therAcid1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therBaro0/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therGamm1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therKoda1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therNeut1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therOnnu1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therPend1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therSibi1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therTena1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therTena_SPHERICAL_VI/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/therVolc1/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/uncuMeth_RCI/trackDb.ra
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    Update self blastz track
• src/hg/makeDb/trackDb/lowelab/vulcDist0/trackDb.ra
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    Update self blastz track