Commits for hiram

v345_preview to v345_preview2 (2017-02-06 to 2017-02-13) v345

6d0afe71c48f9ea0fd464ab0a4cfe4cf7f3aa95e Mon Feb 6 13:22:02 2017 -0800

• wrapping up refs #16036
  • src/hg/makeDb/doc/panPan2/initialBuild.txt - lines changed 43, context: html, text, full: html, text

72252f95a1d883e51ac99325b19a3341caeee3c0 Tue Feb 7 10:20:56 2017 -0800

• attempt to fixup search results, does not help refs #13673
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 13, context: html, text, full: html, text

eb2a370147a1a6baee620ffed257e254bf7be331 Tue Feb 7 10:26:49 2017 -0800

• fixup track color for refGene and search result refs #13673
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 1, context: html, text, full: html, text

4d1dbb0bb39503121c09cfcc2ebe1d2947a190fa Wed Feb 8 14:39:34 2017 -0800

• fixing up track colors refs #13673
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 7, context: html, text, full: html, text

5a594eb0bea5287a1751e62f2929d6f206e7d5eb Thu Feb 9 11:43:17 2017 -0800

• fixing up search rules for ncbiRefSeq tracks refs #13673
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 24, context: html, text, full: html, text

2f1ea1224e1733ea281a5fc12d3de1c8d434900d Thu Feb 9 13:12:40 2017 -0800

• fixup ncbiRefSeqOther clicks refs #13673
  • src/hg/hgc/hgc.c - lines changed 6, context: html, text, full: html, text

6eaeb14754e63042fad7370fc49c4c12274c74a8 Fri Feb 10 10:59:25 2017 -0800

• eliminate the dbAlias option for snake hal tracks not completely useful at this time refs #18440
  • src/hg/hgTracks/snakeTrack.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/GCA_001624535.1_FVB_NJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/GCA_001624745.1_NZO_HlLtJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/GCA_001624775.1_PWK_PhJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/GCA_001624835.1_WSB_EiJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1_C57BL_6NJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.cactus.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/mouseStrains.cactus.trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

a2e2b1a9f8cb87c36c28acb2a6fc28d98c66fda9 Fri Feb 10 13:51:08 2017 -0800

• updated lastz/chain/net alignments to danRer10 refs #18809
  • src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.chainNet.ra - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra - lines changed 2, context: html, text, full: html, text

a3a57469a0979a5bf4a473460a49123ab20f5858 Fri Feb 10 13:53:43 2017 -0800

• fixup bogus chicken references in make doc refs #18756
  • src/hg/makeDb/doc/melGal5/lastzRuns.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/micOch1/initialBuild.txt - lines changed 2, context: html, text, full: html, text

fecfe9645ba4413fc5998afe0b437fa514ad4a19 Fri Feb 10 14:04:52 2017 -0800

• adding taxonomy and common name lists as extracted from RefSeq assembly_summary file and eutils entrez scanning refs #18785
  • src/hg/utils/phyloTrees/refSeq/README.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/refSeq/Vertebrata.commonNames.tsv - lines changed 212, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/refSeq/Vertebrata.taxonomy.tsv - lines changed 212, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/refSeq/commonNames.pl - lines changed 87, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/refSeq/taxId.commonName.vertebrates.tsv - lines changed 192, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/refSeq/taxonomyNames.pl - lines changed 72, context: html, text, full: html, text