File Changes for hiram

v271_preview2 to v271_base (2012-07-31 to 2012-08-07) v271

• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    test for table altSeqLiftOverPsl* should be startsWith not sameString
• src/hg/htdocs/images/phylo/geoFor1_7way.png
  • lines changed 0, context: html, text, full: html, text
    7-way phylo tree for Darwin Finch
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    correct tree diagram for geoFor1
• src/hg/makeDb/doc/chiLan1.txt
  • lines changed 5, context: html, text, full: html, text
    done with genbank run and loading
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 7, context: html, text, full: html, text
    completed galGal4 geoFor1 lastz chain net
• src/hg/makeDb/doc/geoFor1.txt
  • lines changed 22, context: html, text, full: html, text
    completed galGal4 geoFor1 lastz chain net
  • lines changed 194, context: html, text, full: html, text
    done with chicken galGal4 and finch taeGut1 lastz chain net and starting 7-way
  • lines changed 82, context: html, text, full: html, text
    looking at recipbest and synNets for all alignments
  • lines changed 207, context: html, text, full: html, text
    featureBits on all syntenic nets and reciprocal best nets and starting 7-way alignment
  • lines changed 44, context: html, text, full: html, text
    reset default position to FOXP2 and loading the 7-way multiz
  • lines changed 434, context: html, text, full: html, text
    7-way annotations and frames and 4d estimation done
  • lines changed 20, context: html, text, full: html, text
    the calculated 4d tree indicates fixing the original tree to start the 7-way
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    restarted multiz with better tree
  • lines changed 92, context: html, text, full: html, text
    reloaded the 7-way with the better phylo tree
• src/hg/makeDb/doc/taeGut1.txt
  • lines changed 8, context: html, text, full: html, text
    done with geoFor1 chain net
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added chiLan1.
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added chiLan1.
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra
  • lines changed 193, context: html, text, full: html, text
    adding 7-way conservation for geoFor1
  • lines changed 2, context: html, text, full: html, text
    fixup phylo image reference
  • lines changed 1, context: html, text, full: html, text
    setting default track visibilities
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    correct order of species to display
  • lines changed 17, context: html, text, full: html, text
    all phastCons and phyloP tracks now on
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.chainNet.ra
  • lines changed 17, context: html, text, full: html, text
    readjust budgie above mouse
  • lines changed 13, context: html, text, full: html, text
    adding overrides for minScore linearGap and matrix
  • lines changed 24, context: html, text, full: html, text
    setting default track visibilities
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding the chainNet overrides
  • lines changed 2, context: html, text, full: html, text
    adding 7-way for geoFor1
  • lines changed 6, context: html, text, full: html, text
    setting default track visibilities
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.chainNet.ra
  • lines changed 10, context: html, text, full: html, text
    adding overrides for geoFor1 and mm10
  • lines changed 1, context: html, text, full: html, text
    default pack for geoFor1 chain net
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding overrides for geoFor1 and mm10
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.chainNet.ra
  • lines changed 8, context: html, text, full: html, text
    adding geoFor1 chainNet and overrides for mm10
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding geoFor1 chainNet and overrides for mm10
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra
  • lines changed 33, context: html, text, full: html, text
    this version ages out as patch9 replaces it, preserve at P5 for hgwdev viewing
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    adding geoFor1 chain and net
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    adding allMis0 and geoFor1 overrides
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 125, context: html, text, full: html, text
    adding overrides for Rn5 DipOrd1 HetGla2 HetGla1 SpeTri2 OchPri2 OtoGar3 MicMur1 TarSyr1 SaiBol1 PapHam1 RheMac3 NomLeu1 NomLeu2 GorGor3 PteVam1 MyoLuc2 CanFam3 FelCat5 FelCat4 OviAri1 TurTru1 TurTru2 VicPac1 SusScr1 ChoHof1 DasNov3 DasNov2 TriMan1 ProCap1 MacEug2 SarHar1 ChrPic1 MelUnd1 TaeGut1 GeoFor1 GalGal4 MelGal1 LatCha1 OreNil1 OreNil2 Fr3
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    adding 7-way conservation for geoFor1
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding chainNet definitions for galGal4
• src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
  • lines changed 11, context: html, text, full: html, text
    adding geoFor1 and mm10 overrides
• src/hg/makeDb/trackDb/zebraFinch/trackDb.chainNet.ra
  • lines changed 14, context: html, text, full: html, text
    adding overrides for geoFor1 melGal1 and mm10