Commits for max

v410_base to v411_preview (2021-02-08 to 2021-02-15) v411

c5ade4059d7dd62cb99f0801773f0623c050fabb Tue Feb 9 07:02:15 2021 -0800

• adding GTF support for chromToUcsc, refs #26959
  • src/utils/chromToUcsc/chromToUcsc - lines changed 21, context: html, text, full: html, text
  • src/utils/chromToUcsc/tests/expected/mm10.gtf - lines changed 10, context: html, text, full: html, text
  • src/utils/chromToUcsc/tests/in/grc38.100.gtf.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

f92a444ad6ba92b1190c76629b18d219e1809c7c Tue Feb 9 07:49:02 2021 -0800

• fixing a spurious linebreak in hgBlat that i introduced myself, refs #26918
  • src/hg/hgBlat/hgBlat.c - lines changed 1, context: html, text, full: html, text

50d8ee9d40c249470a706bfa94dccfca19364707 Tue Feb 9 09:07:22 2021 -0800

• adding docs page for CADD track, refs #18492
  • src/hg/makeDb/trackDb/human/cadd.html - lines changed 98, context: html, text, full: html, text

2fa2ae0051bcf6ed6c3ca627ec5b700c828e9d04 Wed Feb 10 04:59:15 2021 -0800

• fixing links in new alt/fix notes in hgBlat, found by Gerardo, refs #26918
  • src/hg/hgBlat/hgBlat.c - lines changed 4, context: html, text, full: html, text

0e016ca51069bf70ea5c9e08d7ef2fa4dd81a838 Wed Feb 10 06:11:16 2021 -0800

• adding makedoc for cadd track, refs #18492
  • src/hg/makeDb/cadd/cadd.as - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/cadd/caddToBed.py - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/cadd/caddToWig.py - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/cadd.txt - lines changed 14, context: html, text, full: html, text

3f9969b5073ecebea3f0474a1302ac6dc3ad7688 Thu Feb 11 05:23:16 2021 -0800

• changing default tracks for wuhCor1, email from Kate
  • src/hg/makeDb/trackDb/virus/wuhCor1/strains.ra - lines changed 1, context: html, text, full: html, text

c3431e6dc17aa3c520229701ae73af03786d3ed7 Fri Feb 12 02:52:11 2021 -0800

• hiding wuhCor1 protease tracks, email from Kate, no redmine
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra - lines changed 8, context: html, text, full: html, text

6b3051540d38f212e231b7cfb37bed56c38cdb58 Fri Feb 12 02:58:02 2021 -0800

• tweaking wuhCor1 Weizman a little
  • src/hg/makeDb/trackDb/virus/wuhCor1/weizmanOrfs.ra - lines changed 1, context: html, text, full: html, text

295b9dbab341deac96c7f6166bea56f0fc7fa770 Fri Feb 12 05:38:32 2021 -0800

• changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart)
  • src/product/README.building.source - lines changed 289, context: html, text, full: html, text
  • src/product/README.cram - lines changed 54, context: html, text, full: html, text
  • src/product/README.customTracks.dataBase - lines changed 230, context: html, text, full: html, text
  • src/product/README.install - lines changed 229, context: html, text, full: html, text
  • src/product/README.mysql.setup - lines changed 342, context: html, text, full: html, text
  • src/product/README.proxy - lines changed 40, context: html, text, full: html, text
  • src/product/README.requirements - lines changed 55, context: html, text, full: html, text
  • src/product/README.trackDb - lines changed 150, context: html, text, full: html, text
  • src/product/README.udc - lines changed 32, context: html, text, full: html, text
  • src/product/mirrorManual.txt - lines changed 331, context: html, text, full: html, text

69485aeccc760b6d9db9e6ed6be817272f279635 Sat Feb 13 03:23:32 2021 -0800

• fixing fetchChromSizes for hg19-hg38 patch levels, no redmine, email from Beagon/Ana
  • src/utils/userApps/fetchChromSizes - lines changed 5, context: html, text, full: html, text

56069e49520647ff3c5e9c7ba63d21a39d29352d Mon Feb 15 02:53:32 2021 -0800

• change after code review, refs #26951
  • src/hg/hgTables/identifiers.c - lines changed 1, context: html, text, full: html, text