Commits for hiram

v348_preview2 to v348_base (2017-04-17 to 2017-04-24) v348

32522a28f00d0358694a9faad29efb63bf8374d7 Fri Apr 14 15:06:19 2017 -0700

• correctly avoid running on empty results refs #19338
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 16, context: html, text, full: html, text

314097b00bbc24f15f594c0154215bf0d10c0972 Tue Apr 18 12:08:11 2017 -0700

• lastz chainNet refs #19228
  • src/hg/makeDb/doc/mm10.txt - lines changed 58, context: html, text, full: html, text

69dfe94a49d2985183f5a63148b03fb626e940c1 Tue Apr 18 12:09:36 2017 -0700

• add databaseExists and constructing bigBed gapOverlap result refs #19338
  • src/hg/utils/automation/HgAutomate.pm - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 39, context: html, text, full: html, text

e3d377d9bad0ac103c113d7be88f994938852334 Wed Apr 19 10:26:03 2017 -0700

• lastz chainNet to criGriChoV1 refs #19228
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 63, context: html, text, full: html, text

261cc77bd958e5910320428eabb7e1cc265053e2 Wed Apr 19 10:44:26 2017 -0700

• adding criGriChoV1 rules refs #19228
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

f6927d332aef2c506c4ee88c47f3884754813bd8 Wed Apr 19 10:46:51 2017 -0700

• loading genbank run and liftOver to criGri1 refs #19228
  • src/hg/makeDb/doc/criGriChoV1/initialBuild.txt - lines changed 66, context: html, text, full: html, text

ad5c9b269dfadd165133d9cc6f702d77b9dd0aa5 Wed Apr 19 10:52:44 2017 -0700

• adding criGriChoV1 to the update alignments refs #19228
  • 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

23728dc5266886aa0cb32bf22b1738cb1d2ea220 Wed Apr 19 11:42:27 2017 -0700

• add liftOvers between criGri1 and criGriChoV1 refs #19228
  • src/hg/makeDb/doc/criGri1.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/criGriChoV1/initialBuild.txt - lines changed 43, context: html, text, full: html, text

7a5b72bdf0df6ce3c51506b9f591ae694393754e Wed Apr 19 14:41:05 2017 -0700

• updated contigOverlap.html and renamed refs #19228
  • src/hg/makeDb/trackDb/gapOverlap.html - lines changed 37, context: html, text, full: html, text

38860c459386ca6ce8c7f28185c173d9416578d9 Wed Apr 19 15:03:07 2017 -0700

• catching up Mus caroli assembly refs #13553
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.allGaps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.build.stats.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.cpgIslands.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.description.html - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.names.tab - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.repeatMasker.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.windowMasker.html - lines changed 38, context: html, text, full: html, text

c24f15c92ce6b6562d2f77d14be171e5547ccb24 Wed Apr 19 15:03:52 2017 -0700

• catching up Mus pahari assembly refs #13553
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.allGaps.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.cpgIslands.html - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.description.html - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.names.tab - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.repeatMasker.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.windowMasker.html - lines changed 38, context: html, text, full: html, text

ccd6e5c59b8e649a2a599ffb20c42b505816d424 Wed Apr 19 15:04:45 2017 -0700

• catching up trackDb to add gapOverlap track refs #13553
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/GCA_001624535.1_FVB_NJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/GCA_001624745.1_NZO_HlLtJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/GCA_001624775.1_PWK_PhJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/GCA_001624835.1_WSB_EiJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1_C57BL_6NJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.trackDb.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/GCA_900094665.1_CAROLI_EIJ_v1.trackDb.txt - lines changed 224, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt - lines changed 229, context: html, text, full: html, text

50827e9e55e77dec673bf470d9be76be34137c00 Wed Apr 19 15:10:26 2017 -0700

• correct trackDb for pahari refs #13553
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt - lines changed 229, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/GCA_900095145.1_PAHARI_EIJ_v1.trackDb.txt - lines changed 224, context: html, text, full: html, text

3f3872bdc25b12cda856dacf66679dcf9c8f283d Wed Apr 19 15:49:21 2017 -0700

• no need to deliver gitTools scripts in userApps, good enough to deliver only in-house no redmine
  • src/utils/makefile - lines changed 2, context: html, text, full: html, text

e0ab9fcd4c7cca38b22e3a43a918b27d2b3c7585 Wed Apr 19 16:13:25 2017 -0700

• adding gapOverlap.html refs #13553
  • src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/html/GCA_001624505.1_DBA_2J_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/html/GCA_001624535.1_FVB_NJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/html/GCA_001624675.1_NOD_ShiLtJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/html/GCA_001624745.1_NZO_HlLtJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/html/GCA_001624775.1_PWK_PhJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/html/GCA_001624835.1_WSB_EiJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/html/GCA_001624865.1_SPRET_EiJ_v1.gapOverlap.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/html/GCA_001632525.1_BALB_cJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/html/GCA_001632555.1_C57BL_6NJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/html/GCA_001632575.1_C3H_HeJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/html/GCA_001632615.1_LP_J_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.gapOverlap.html - lines changed 44, context: html, text, full: html, text

ea9e468626d6e477199416b03cf880e3fd57ddaf Wed Apr 19 22:52:28 2017 -0700

• do not load empty files refs #19228
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 3, context: html, text, full: html, text

84b4480b58ebaa582a06f4111e18dc5251cdcbd3 Thu Apr 20 11:31:34 2017 -0700

• 4-way alignment on galVar1 for Juergen Schmotz no redmine
  • src/hg/htdocs/images/phylo/galVar1.4way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

08071178d0f2a2be1ef71bdfe627c1afad60444b Thu Apr 20 12:16:43 2017 -0700

• remove template comment block refs #19247
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 7, context: html, text, full: html, text

c1a6825d1818e050b30ffa0bf91a9abed26b613d Thu Apr 20 12:17:31 2017 -0700

• remove out of date file refs #19247
  • src/hg/makeDb/trackDb/contigOverlaps.html - lines changed 36, context: html, text, full: html, text

b056b2cca67fa4e8a5943a90fea6061c3b2ed380 Thu Apr 20 14:11:48 2017 -0700

• 4-way alignment for Juergen Schmitz no redmine
  • src/hg/htdocs/images/phylo/galVar1.4way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/phylo/galVar1_4way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/phylo/hg38_4way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

1b6ada65366179f9b4feeaa10963f51f8476c429 Thu Apr 20 14:48:13 2017 -0700

• 4-way alignment for Juergen Schmitz no redmin
  • src/hg/htdocs/images/phylo/mm10_4way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

9fdca34a204e7c3151bf55ccf05b8f2b06095a0c Fri Apr 21 16:46:49 2017 -0700

• 4-way with tupChi1 for Juergen Schmitz no redmine
  • src/hg/makeDb/doc/hg38/multiz4way.txt - lines changed 1436, context: html, text, full: html, text

3af0d99192a1e3c83c102f023c4e0c9a9e9c66f5 Fri Apr 21 17:33:00 2017 -0700

• adding 4-way with tupChi1 in place of tupBel1 for Juergen Schmitz no redmine
  • src/hg/makeDb/trackDb/galVar/galVar1/cons4way.html - lines changed 417, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.4way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.5way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra - lines changed 2, context: html, text, full: html, text

0fe12971325f08fdf4960957f37ec035b4b577bc Fri Apr 21 17:52:51 2017 -0700

• adding 4-way alignment with tupChi1 for Juergen Schmitz no redmine
  • src/hg/makeDb/trackDb/human/hg38/cons4way.html - lines changed 417, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.4way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

fa50cd18cfd29029efd24065994ea588cb529612 Fri Apr 21 21:34:36 2017 -0700

• adding 4-way alignment with tupChi1 for Juergen Schmitz no redmine
  • src/hg/makeDb/doc/mm10.txt - lines changed 1422, context: html, text, full: html, text

51fa7206d8387f05056d52344637438aff75e357 Fri Apr 21 21:37:20 2017 -0700

• adding mm10 4-way alignment with tupChi1 for Juergen Schmitz no redmine
  • src/hg/makeDb/trackDb/mouse/mm10/cons4way.html - lines changed 417, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.4way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text

5fa39cc02a7c82ba345708b439913698647bcd46 Fri Apr 21 22:53:23 2017 -0700

• adding 4-way alignment with tupChi1 for Juergen Schmitz no redmine
  • src/hg/makeDb/doc/galVar1/multiz4way.txt - lines changed 1427, context: html, text, full: html, text

1df4bd81ec254ef18855c4f0854072cb04d22c9f Fri Apr 21 23:26:02 2017 -0700

• correct name on phyloP track no redmine
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.4way.ra - lines changed 1, context: html, text, full: html, text

c094b650e99784b7311d20975a26bfbdd3af45c8 Mon Apr 24 10:29:38 2017 -0700

• v348 final build refs #19231
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

4558738b4fb6ac1522a042b40509772845825f99 Mon Apr 24 10:35:34 2017 -0700

• New version number v348
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text