Commits for hiram

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

• completed galGal4 geoFor1 lastz chain net
  • src/hg/makeDb/doc/galGal4.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 22, context: html, text, full: html, text
• 7-way phylo tree for Darwin Finch
  • src/hg/htdocs/images/phylo/geoFor1_7way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• done with chicken galGal4 and finch taeGut1 lastz chain net and starting 7-way
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 194, context: html, text, full: html, text
• adding chainNet definitions for galGal4
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 51, context: html, text, full: html, text
• Added chiLan1.
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
• done with genbank run and loading
  • src/hg/makeDb/doc/chiLan1.txt - lines changed 5, context: html, text, full: html, text
• looking at recipbest and synNets for all alignments
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 82, context: html, text, full: html, text
• test for table altSeqLiftOverPsl* should be startsWith not sameString
  • src/hg/hgc/hgc.c - lines changed 1, 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/altSeqComposite5.ra - lines changed 33, context: html, text, full: html, text
• featureBits on all syntenic nets and reciprocal best nets and starting 7-way alignment
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 207, context: html, text, full: html, text
• readjust budgie above mouse
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.chainNet.ra - lines changed 17, context: html, text, full: html, text
• adding the chainNet overrides
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra - lines changed 2, context: html, text, full: html, text
• adding 7-way conservation for geoFor1
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra - lines changed 193, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• adding 7-way for geoFor1
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra - lines changed 2, context: html, text, full: html, text
• adding overrides for minScore linearGap and matrix
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.chainNet.ra - lines changed 13, context: html, text, full: html, text
• adding geoFor1 chainNet and overrides for mm10
  • src/hg/makeDb/trackDb/chicken/galGal4/trackDb.chainNet.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra - lines changed 5, context: html, text, full: html, text
• adding geoFor1 and mm10 overrides
  • src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra - lines changed 11, context: html, text, full: html, text
• adding overrides for geoFor1 melGal1 and mm10
  • src/hg/makeDb/trackDb/zebraFinch/trackDb.chainNet.ra - lines changed 14, context: html, text, full: html, text
• adding overrides for geoFor1 and mm10
  • src/hg/makeDb/trackDb/birds/melUnd1/trackDb.chainNet.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• default pack for geoFor1 chain net
  • src/hg/makeDb/trackDb/birds/melUnd1/trackDb.chainNet.ra - lines changed 1, 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/mouse/trackDb.chainNet.ra - lines changed 125, context: html, text, full: html, text
• fixup phylo image reference
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra - lines changed 2, context: html, text, full: html, text
• reset default position to FOXP2 and loading the 7-way multiz
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 44, context: html, text, full: html, text
• setting default track visibilities
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.chainNet.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra - lines changed 6, context: html, text, full: html, text
• adding geoFor1 chain and net
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 19, context: html, text, full: html, text
• adding allMis0 and geoFor1 overrides
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra - lines changed 5, context: html, text, full: html, text
• done with geoFor1 chain net
  • src/hg/makeDb/doc/taeGut1.txt - lines changed 8, context: html, text, full: html, text
• 7-way annotations and frames and 4d estimation done
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 434, context: html, text, full: html, text
• the calculated 4d tree indicates fixing the original tree to start the 7-way
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 20, context: html, text, full: html, text
• correct tree diagram for geoFor1
  • src/hg/htdocs/images/phylo/geoFor1_7way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct order of species to display
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra - lines changed 1, context: html, text, full: html, text
• restarted multiz with better tree
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 27, context: html, text, full: html, text
• reloaded the 7-way with the better phylo tree
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 92, context: html, text, full: html, text
• all phastCons and phyloP tracks now on
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra - lines changed 17, context: html, text, full: html, text