File Changes for max

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

• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    f92a444ad6ba92b1190c76629b18d219e1809c7c Tue Feb 9 07:49:02 2021 -0800
    fixing a spurious linebreak in hgBlat that i introduced myself, refs #26918
  • lines changed 4, 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/hgTables/identifiers.c
  • lines changed 1, context: html, text, full: html, text
    56069e49520647ff3c5e9c7ba63d21a39d29352d Mon Feb 15 02:53:32 2021 -0800
    change after code review, refs #26951
• src/hg/makeDb/cadd/cadd.as
  • lines changed 15, 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/caddToBed.py
  • lines changed 36, 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/caddToWig.py
  • lines changed 63, 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/doc/hg19.txt
  • lines changed 14, 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/doc/hg38/cadd.txt
  • lines changed 14, 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/trackDb/human/cadd.html
  • lines changed 98, 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/virus/wuhCor1/strains.ra
  • lines changed 1, 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/trackDb.uniprot.ra
  • lines changed 8, 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/weizmanOrfs.ra
  • lines changed 1, context: html, text, full: html, text
    6b3051540d38f212e231b7cfb37bed56c38cdb58 Fri Feb 12 02:58:02 2021 -0800
    tweaking wuhCor1 Weizman a little
• src/product/README.building.source
  • lines changed 289, 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.cram
  • lines changed 54, 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.customTracks.dataBase
  • lines changed 230, 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.install
  • lines changed 229, 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.mysql.setup
  • lines changed 342, 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.proxy
  • lines changed 40, 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.requirements
  • lines changed 55, 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.trackDb
  • lines changed 150, 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.udc
  • lines changed 32, 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/mirrorManual.txt
  • lines changed 331, 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/utils/chromToUcsc/chromToUcsc
  • lines changed 21, context: html, text, full: html, text
    c5ade4059d7dd62cb99f0801773f0623c050fabb Tue Feb 9 07:02:15 2021 -0800
    adding GTF support for chromToUcsc, refs #26959
• src/utils/chromToUcsc/tests/expected/mm10.gtf
  • lines changed 10, context: html, text, full: html, text
    c5ade4059d7dd62cb99f0801773f0623c050fabb Tue Feb 9 07:02:15 2021 -0800
    adding GTF support for chromToUcsc, refs #26959
• src/utils/chromToUcsc/tests/in/grc38.100.gtf.gz
  • lines changed 0, context: html, text, full: html, text
    c5ade4059d7dd62cb99f0801773f0623c050fabb Tue Feb 9 07:02:15 2021 -0800
    adding GTF support for chromToUcsc, refs #26959
• src/utils/userApps/fetchChromSizes
  • lines changed 5, 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