Commits for hiram

v361_preview2 to v361_base (2018-02-05 to 2018-02-12) v361

3db7aaad0c425d624fcbf6d586039f1824699c76 Mon Feb 5 14:45:19 2018 -0800

• deliver pslSomeRecords with the user apps refs #20215
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text

ed9f39297a17ed41bd7043e138b10db491a78ca5 Mon Feb 5 15:45:47 2018 -0800

• deliver pslSomeRecords with the user apps refs #20215
  • src/userApps/fetchKentSource.sh - lines changed 1, context: html, text, full: html, text

753797baccc232c3ce0a1e91590839dbcc377bb1 Tue Feb 6 09:39:10 2018 -0800

• deliver pslSomeRecords with the user apps refs #20215
  • src/hg/pslSomeRecords/makefile - lines changed 14, context: html, text, full: html, text

5e52d1ec20a14f47c24836123e91966811d76914 Tue Feb 6 12:47:29 2018 -0800

• adding sacCer3 refs #20215
  • src/hg/utils/automation/dbAssemblyEquivalents.tab - lines changed 1, context: html, text, full: html, text

51e28851adb6118bf2046b53e6d128abaf2dbef8 Tue Feb 6 15:36:23 2018 -0800

• adding out links for SGD, RGD, ZFIN refs #20215
  • src/hg/utils/automation/gff3ToRefLink.pl - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl - lines changed 8, context: html, text, full: html, text

ac0402c703dc8d1fd914c14c4f59e49896e1baaa Wed Feb 7 11:09:33 2018 -0800

• adding ncbiRefSeq for rn6 ce11 sacCer3 danRer11 dm6 refs #20215
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 5, context: html, text, full: html, text

3d3c7589f5f4d3eb5849c6dfb32e1d5a8f5c6260 Thu Feb 8 06:45:06 2018 -0800

• adding ncbiRefSeq composite can not have overrides on refGene refs #20215
  • src/hg/makeDb/trackDb/rat/rn6/defaultPriority.ra - lines changed 4, context: html, text, full: html, text

6e75a4434cb410042b75fa3cc84acb4634d9a2e3 Thu Feb 8 14:36:01 2018 -0800

• adding XenBase BGD FlyBase and using externalId column refs #20215
  • src/hg/utils/automation/gff3ToRefLink.pl - lines changed 50, context: html, text, full: html, text
  • src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl - lines changed 4, context: html, text, full: html, text

2797186e7d69a8b79b92e30118bed55548f04caf Thu Feb 8 14:39:16 2018 -0800

• adding externalId column to ncbiRefSeqLink table refs #20215
  • src/hg/hgc/hgc.c - lines changed 41, context: html, text, full: html, text
  • src/hg/inc/ncbiRefSeqLink.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/ncbiRefSeqLink.as - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/ncbiRefSeqLink.c - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/ncbiRefSeqLink.sql - lines changed 1, context: html, text, full: html, text

9aa34beed680836d576d1a15a73d2fd513ab380d Thu Feb 8 14:44:05 2018 -0800

• now using dbPrefixUrls and dbPrefixLabels refs #20215
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text

55d77b0228ad39509c81008f511123a862caa25b Fri Feb 9 21:29:12 2018 -0800

• correct alpha,beta tags on the refSeqComposite vs. the refGene overrides refs #20215
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

81ecf226e4b100905ceb0935e388dce7dd498312 Fri Feb 9 21:32:39 2018 -0800

• refGene override moved to trackDb.refGene.ra refs #20215
  • src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra - lines changed 3, context: html, text, full: html, text

b5cdd1d92e39c13230a25b9896f1bce98dd2dfe8 Fri Feb 9 21:47:21 2018 -0800

• correct alpha tag on the refSeqComposite.ra refs #20215
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra - lines changed 1, context: html, text, full: html, text

f91fa0a6ea34c07d97b50867c1fe201a724ffbf5 Fri Feb 9 22:45:25 2018 -0800

• turning on refSeqComposite for make alpha refs #20215
  • src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu2/defaultPriority.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bonobo/panPan2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/defaultPriority.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro5/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chlorocebus/chlSab2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droPer1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gator/allMis1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/microbat/myoLuc2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhino/cerSim1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turkey/melGal5/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro7/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra - lines changed 2, context: html, text, full: html, text

f5c9f24f6b9af5e01ce858cba09f491ed4dfd2f2 Fri Feb 9 22:48:11 2018 -0800

• correct alpha beta public tags on refGene overrides refs #20215
  • src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

7f2c3954f5f2d47527f5fc91b9f874b5469c647e Fri Feb 9 22:51:09 2018 -0800

• adding refSeqComposite alpha and correct beta tags on refGene refs #20215
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

dd58dd23296c3ae3025880ef3b6a01952bd14b18 Fri Feb 9 22:53:04 2018 -0800

• adding refSeqComposite alpha and correct beta tags on refGene refs #20215
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

d5dc2901dd616116555fe196680097b6a0704eb1 Fri Feb 9 22:55:02 2018 -0800

• adding refSeqComposite alpha and correct beta tags on refGene refs #20215
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

6093c30a06d4fc075fad97207e07f2d7fffea225 Fri Feb 9 22:56:09 2018 -0800

• adding refSeqComposite alpha and correct beta tags on refGene refs #20215
  • src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

ba6a71dbe5422c7ea341c3cca2c375b6cd9fd562 Fri Feb 9 22:57:13 2018 -0800

• adding refSeqComposite alpha and correct beta tags on refGene refs #20215
  • src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bonobo/panPan1/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

06f12519cf05aef69d9fdeee7f241060db99ef59 Fri Feb 9 22:58:05 2018 -0800

• adding refSeqComposite alpha and correct beta tags on refGene refs #20215
  • src/hg/makeDb/trackDb/pig/susScr11/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr11/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

548c229eb797a61ea363c5f5437d87a7bce3d6ba Fri Feb 9 22:59:00 2018 -0800

• adding refSeqComposite alpha and correct beta tags on refGene refs #20215
  • src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr3/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text

93a41c2f6ec108052f1b0ff0721211e097fa15bd Fri Feb 9 23:05:22 2018 -0800

• adding refSeqComposite alpha refs #20215
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra - lines changed 2, context: html, text, full: html, text

e6d9c248e95c6de0099053752b60328f0fc0e92d Mon Feb 12 10:12:11 2018 -0800

• generic discussion of how to run up ucscToRefSeq track refs #20913
  • src/hg/makeDb/doc/ucscToRefSeq.txt - lines changed 106, context: html, text, full: html, text

c354a2511a0bfe8697e8e83e8b3d7745be920539 Mon Feb 12 10:18:37 2018 -0800

• v361 final build refs #20889
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

14f34a6c6cdc3691f0932bf2a5a77cd718f11ee4 Mon Feb 12 10:20:07 2018 -0800

• New version number v361
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text
  • src/inc/srcVersion.h - lines changed 1, context: html, text, full: html, text