All File Changes

v385_base to v386_preview (2019-07-22 to 2019-07-29) v386

• java/src/edu/ucsc/genome/qa/cgiCheck/canFam1.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• java/src/edu/ucsc/genome/qa/cgiCheck/ci1.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• java/src/edu/ucsc/genome/qa/cgiCheck/full.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• java/src/edu/ucsc/genome/qa/cgiCheck/hg17.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• java/src/edu/ucsc/genome/qa/cgiCheck/hgw1.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• java/src/edu/ucsc/genome/qa/cgiCheck/mm5.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• java/src/edu/ucsc/genome/qa/cgiCheck/quick.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• java/src/edu/ucsc/genome/qa/cgiCheck/quickAll.props
  • lines changed 1, context: html, text, full: html, text
    2efc079feaec773049b6d732ef27e90d017054c8 Mon Jul 22 13:43:52 2019 -0700
    Changing references of mysqlbeta to hgwbeta in props files regarding TrackCheck
• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    74597092e577172001a9662facf4ce09dd058db6 Wed Jul 24 15:12:57 2019 -0700
    incrementing blat version due to added ipv6 support
• src/blatz/server.c
  • lines changed 2, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/gfClient/gfClient.c
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/gfServer/gfServer.c
  • lines changed 14, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/gfServer/tests/testPcr
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/gfServer/tests/testProtNib
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/gfServer/tests/testProtTwoBit
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/gfServer/tests/testTransNib
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/gfServer/tests/testTransTwoBit
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 15, context: html, text, full: html, text
    2b01543b8fce9fa54413f639adae58bb1341b93b Wed Jul 24 09:54:55 2019 -0700
    Minor corrections and tweaks to links based on CR, #23798
• src/hg/cirm/gateway/htdocs/help/cirmFAQ.html
  • lines changed 105, context: html, text, full: html, text
    2a3dc37ea17f57616895c8ce3d559fa7696afa44 Wed Jul 24 09:57:08 2019 -0700
    Removing cirmFAQ stub. refs #23625
• src/hg/cirm/gateway/htdocs/index.html
  • lines changed 113, context: html, text, full: html, text
    21e023fc5b9b5f6831248fe46ed3c472fc5b3ef3 Tue Jul 23 14:04:31 2019 -0700
    Slight redesign of home page. Added section below menu bar that indicates what things people can do with the site. Added new commented out section for heart/brain of cells pages. no redmine
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 0, context: html, text, full: html, text
    990b1c20ef3c8c9f4ab55120421c99c1cc988a76 Tue Jul 23 14:18:36 2019 -0700
    Minor white space change to header on tools page, no redmine
• src/hg/geoIp/README.v4
  • lines changed 135, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/geoIpCountry.as
  • lines changed 8, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/geoIpCountry6.as
  • lines changed 8, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/geoIpNode.as
  • lines changed 8, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/geoIpNode6.as
  • lines changed 8, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/geoIpToCountryMaxMind.c
  • lines changed 189, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/geoIpToCountryMaxMind6.c
  • lines changed 277, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/makefile
  • lines changed 4, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/geoIp/save-old-for-compare
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/hgTables/hic.c
  • lines changed 1, context: html, text, full: html, text
    c7fe19c878fc68ef50674bbaa95a117499c27f56 Wed Jul 24 22:57:53 2019 -0700
    Fixing bad loop limit, which resulted in using a NULL pointer. refs #23853
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    96bb6d93227444de742fcf885bb700b91bd7dd31 Wed Jul 24 13:53:19 2019 -0700
    fix problem when setting visibilities of hub-based subtracks with undecorated names (without the hub_) #23872
• src/hg/hgTracks/hicTrack.c
  • lines changed 2, context: html, text, full: html, text
    de2d4b32bb2cf74eb931862533b7966acb4f2378 Wed Jul 24 22:52:56 2019 -0700
    Changes in response to code review, refs #23853
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    4b3fe214cfd89ea4ff51f009bcd7b914bbf54f74 Mon Jul 22 13:44:16 2019 -0700
    Change CGIs to use new omimGeneMap2 table
• src/hg/hgc/hgc.c
  • lines changed 36, context: html, text, full: html, text
    4b3fe214cfd89ea4ff51f009bcd7b914bbf54f74 Mon Jul 22 13:44:16 2019 -0700
    Change CGIs to use new omimGeneMap2 table
  • lines changed 1, context: html, text, full: html, text
    3dc5333aee8dea626a021976a1d291360f348480 Thu Jul 25 10:34:12 2019 -0700
    Bring BLAT results (doUserPsl) in line with hgBlat and bigPsl BLAT custom track: sort by score instead of file order. refs #23865
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 3, context: html, text, full: html, text
    9abe26a72523c34f65aa05a4dde5a9535b408e23 Thu Jul 25 16:14:36 2019 -0700
    Clarifying psl output to replicate web results #23814
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    d2c9857e3683a637750c3c81d2d6d870495cac53 Tue Jul 23 11:18:17 2019 -0700
    Adding updates to docs for mysql to MariaDB changes, refs #23597
  • lines changed 21, context: html, text, full: html, text
    4aca7440dcd66b53fa9b917d6fd3eae971924031 Tue Jul 23 11:24:50 2019 -0700
    Making style changes for CR #23857
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 13, context: html, text, full: html, text
    9acffdf932d10e14764c201dd48455aa60b45a79 Mon Jul 22 13:17:59 2019 -0700
    Updating api.html with new /list/schema function #23777
  • lines changed 4, context: html, text, full: html, text
    f976a5aa9958ce375d3d213f5a4c593e5e02343d Tue Jul 23 13:59:56 2019 -0700
    Updating supported file formats #23777
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 0, context: html, text, full: html, text
    d2c9857e3683a637750c3c81d2d6d870495cac53 Tue Jul 23 11:18:17 2019 -0700
    Adding updates to docs for mysql to MariaDB changes, refs #23597
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    d2c9857e3683a637750c3c81d2d6d870495cac53 Tue Jul 23 11:18:17 2019 -0700
    Adding updates to docs for mysql to MariaDB changes, refs #23597
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 10, context: html, text, full: html, text
    d2c9857e3683a637750c3c81d2d6d870495cac53 Tue Jul 23 11:18:17 2019 -0700
    Adding updates to docs for mysql to MariaDB changes, refs #23597
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 4, context: html, text, full: html, text
    d2c9857e3683a637750c3c81d2d6d870495cac53 Tue Jul 23 11:18:17 2019 -0700
    Adding updates to docs for mysql to MariaDB changes, refs #23597
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    f5a5c79b96699bde35a84461ca36f120446b95f7 Fri Jul 19 16:04:15 2019 -0700
    Announcing the v31 All GENCODE tracks for hg38 and hg19, refs #23791 and #23790
• src/hg/htdocs/inc/gbFooter.html
  • lines changed 1, context: html, text, full: html, text
    cbdc37a80026690af9e6186232d3e0994364dd04 Wed Jul 24 12:56:04 2019 -0700
    Update link for Donate button. refs #23878
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    cbdc37a80026690af9e6186232d3e0994364dd04 Wed Jul 24 12:56:04 2019 -0700
    Update link for Donate button. refs #23878
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 1, context: html, text, full: html, text
    0aff23bab8d649c1d08109605e7dc898e44ca8d2 Wed Jul 24 14:49:00 2019 -0700
    MIssed one of the footers. refs #23878
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 1, context: html, text, full: html, text
    cbdc37a80026690af9e6186232d3e0994364dd04 Wed Jul 24 12:56:04 2019 -0700
    Update link for Donate button. refs #23878
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    cdb9a3f4ef701c7502b17b53d04d4bf3e7318a9e Wed Jul 24 08:45:49 2019 -0700
    Updating the Subscribe button to the redirected URL. Bob mentioned in an email that it was reported broken in a workshop, no Redmine.
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    f5a5c79b96699bde35a84461ca36f120446b95f7 Fri Jul 19 16:04:15 2019 -0700
    Announcing the v31 All GENCODE tracks for hg38 and hg19, refs #23791 and #23790
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    10ce0064723a30e5c00c5a0b2bb02c5b3db62c25 Tue Jul 23 11:53:40 2019 -0700
    Adding captial M to MariaDB in style/HGStyle.css, refs #23597
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    20b0ea5ab6b3e90e6e01940f777314368cecf18a Mon Jul 22 12:55:29 2019 -0700
    Fixing link per code review refs #23852
  • lines changed 24, context: html, text, full: html, text
    76a8fd6a749b8000954ae3c85d47dd83700637c4 Tue Jul 23 20:36:59 2019 -0700
    dropped completed JAX Lab workshop, moved ashg to top-four list
• src/hg/hubApi/tests/expected/err40.gz
  • lines changed 0, context: html, text, full: html, text
    96b647ceb7edf38ede9d998bead10ba08bd37386 Fri Jul 26 14:56:37 2019 -0700
    demonstrate bug in bigGenePred with no table type of track refs #23589
• src/hg/hubApi/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    96b647ceb7edf38ede9d998bead10ba08bd37386 Fri Jul 26 14:56:37 2019 -0700
    demonstrate bug in bigGenePred with no table type of track refs #23589
• src/hg/inc/geoMirror.h
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/inc/jksql.h
  • lines changed 5, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/lib/geoMirror.c
  • lines changed 85, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/lib/hgFind.c
  • lines changed 3, context: html, text, full: html, text
    b7c6d6156dde49066ac21e4d0288b80faf85ae16 Mon Jul 22 14:45:14 2019 -0700
    don't crash if a requested mrna from search isn't aligned
• src/hg/lib/hic.c
  • lines changed 78, context: html, text, full: html, text
    de2d4b32bb2cf74eb931862533b7966acb4f2378 Wed Jul 24 22:52:56 2019 -0700
    Changes in response to code review, refs #23853
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    de2d4b32bb2cf74eb931862533b7966acb4f2378 Wed Jul 24 22:52:56 2019 -0700
    Changes in response to code review, refs #23853
• src/hg/lib/jksql.c
  • lines changed 10, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/makeDb/doc/hg38/mane.txt
  • lines changed 8, context: html, text, full: html, text
    fa3428629bcae3d0b2d76fa11d634c5a8570bae3 Tue Jul 23 14:37:41 2019 -0700
    upgrade MANE track to 0.6
• src/hg/makeDb/doc/hg38/patchUpdate.12.txt
  • lines changed 13, context: html, text, full: html, text
    b80a59e82af6a5a67934e199bf4113950f9c4706 Wed Jul 24 15:58:57 2019 -0700
    Updating hgdownload-test link for hg38/bigZips/hg38.chrom.sizes and adding hg38*.chrom.sizes links to subdirectories.
• src/hg/makeDb/schema/all.joiner
  • lines changed 5, context: html, text, full: html, text
    5c903d730ffe0f61eee22a328942eb807d543239 Wed Jul 24 09:57:06 2019 -0700
    Adding all.joiner rules for omimGeneMap2, refs #23863
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    2c90609c76514bf1c0990ad4518dd92f41a9097a Fri Jul 19 16:09:40 2019 -0700
    Adding pennantIcons for the All GENCODE V31 tracks for hg19 and hg38, refs #23791 and #23790
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
  • lines changed 17, context: html, text, full: html, text
    6d894f61de4165c38db14f51f682cb522bd790d7 Fri Jul 26 12:46:14 2019 -0700
    oops... new MANE track slipped out. D'oh! Make alpha and beta,public versions
• src/hg/makeDb/trackDb/human/hg38/mane.html
  • lines changed 4, context: html, text, full: html, text
    fa3428629bcae3d0b2d76fa11d634c5a8570bae3 Tue Jul 23 14:37:41 2019 -0700
    upgrade MANE track to 0.6
  • lines changed 2, context: html, text, full: html, text
    1b47ebf80b0616f3b9290aeb811f064aa1d2dcb7 Fri Jul 26 16:08:46 2019 -0700
    fixing broken download link in mane.html #23873
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 5, context: html, text, full: html, text
    fa3428629bcae3d0b2d76fa11d634c5a8570bae3 Tue Jul 23 14:37:41 2019 -0700
    upgrade MANE track to 0.6
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    6d894f61de4165c38db14f51f682cb522bd790d7 Fri Jul 26 12:46:14 2019 -0700
    oops... new MANE track slipped out. D'oh! Make alpha and beta,public versions
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    2c90609c76514bf1c0990ad4518dd92f41a9097a Fri Jul 19 16:09:40 2019 -0700
    Adding pennantIcons for the All GENCODE V31 tracks for hg19 and hg38, refs #23791 and #23790
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    6d894f61de4165c38db14f51f682cb522bd790d7 Fri Jul 26 12:46:14 2019 -0700
    oops... new MANE track slipped out. D'oh! Make alpha and beta,public versions
• src/hg/makeDb/trackDb/human/trackDb.ra
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    5fe94335dd93caac080aa83e086c39539df504dc Wed Jul 24 08:57:36 2019 -0700
    Adding omimGeneMap2 to list of table browser restricted tables, refs #23863
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenChromHmm.html
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    4414a5143fa69641171e89d48a260d466739e113 Tue Jul 23 16:52:35 2019 -0700
    Second pass track descriptions for Mouse ENCODE tracks, after input from David Gorkin, Ren Lab. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenHistone.html
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    4414a5143fa69641171e89d48a260d466739e113 Tue Jul 23 16:52:35 2019 -0700
    Second pass track descriptions for Mouse ENCODE tracks, after input from David Gorkin, Ren Lab. refs #23693
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.histones.ra
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    77a5e88408d81b88d20c31e13e2535e2b941846a Tue Jul 23 18:17:53 2019 -0700
    Fix up subtrack labels. refs #23693
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    83b858b4e01baddd0db58d85c11cfd23016d0743 Wed Jul 24 08:24:33 2019 -0700
    cosmetics
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    d224ff5e0c5a7bdefe7ef48eefe18b39ad1658ad Wed Jul 24 08:36:05 2019 -0700
    Add subtrack colors to UI. refs #23693
• src/hg/makeDb/trackDb/opossum/multiz5way.html
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    55a7d0bdb8cb52deaf829c50d9b5db7c95018f79 Mon Jul 29 08:40:19 2019 -0700
    Updating http to https for monDom1, uiLinks cronjob.
• src/hg/makeDb/trackDb/trackDb.ra
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    5e0ea5d6cc41e80ef726e531abc93d57737af1b1 Mon Jul 22 12:47:48 2019 -0700
    Adding crispr10K track back to hg38 no RM
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/transcriptome.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/nucleosome.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/nucleosomeAdjustedCoverage.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/nucleosomeControlCoverage.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/nucleosomeDensity.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/nucleosomeStringency.html
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    9babbff6237fa5d4e9992373eee2d7e5c9cbb0ea Thu Jul 25 09:49:55 2019 -0700
    Updating http to https for ce4, uiLinks cronjob.
• src/hg/makefile
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
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    24df7c63a1f95a59e027efd0c4d0262955e62b88 Mon Jul 22 11:57:26 2019 -0700
    oops. not needed.
• src/hg/utils/automation/asmHubTrackDb.sh
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    88603b198e1787fb26de0479d1782532fbb71b67 Tue Jul 23 10:14:37 2019 -0700
    added cytoBand navigation refs #23734
• src/hg/utils/automation/doAssemblyHub.pl
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    88603b198e1787fb26de0479d1782532fbb71b67 Tue Jul 23 10:14:37 2019 -0700
    added cytoBand navigation refs #23734
• src/hg/utils/automation/doRepeatMasker.pl
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    463df2eb31411fdb0a5462ff1ac4c7bc7c834ade Thu Jul 25 21:42:06 2019 -0700
    manage long sequence names going into RM and work around nested repeats errors refs #23734
• src/hg/utils/automation/gpToIx.pl
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    05219e2ffe569b3403687b96701006e2ff16116d Tue Jul 23 13:13:17 2019 -0700
    creating index from genePred file for assembly ncbiGene track searching refs #23734
• src/hg/utils/geoMirrorNode/geoMirrorNode.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/hg/utils/hubClone/hubClone.c
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    a04b6192ec6869a40993a00985403da5ce1c2c21 Wed Jul 24 16:43:00 2019 -0700
    Fixing bug in hubClone found by Braney, refs #23850
• src/htslib/knetfile.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/inc/genoFind.h
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    74597092e577172001a9662facf4ce09dd058db6 Wed Jul 24 15:12:57 2019 -0700
    incrementing blat version due to added ipv6 support
• src/inc/internet.h
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/inc/net.h
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/inc/rudp.h
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/lib/common.c
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    2398713f34d6992ef64995a9737b724631771b35 Fri Jul 26 15:45:20 2019 -0700
    let umask decide what modes should be set on created files
• src/lib/https.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/lib/internet.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
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    59e838db401f7d00cab3dc0b741beb6c4853bb31 Mon Jul 22 15:22:54 2019 -0700
    improved subnet error
• src/lib/net.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/lib/rudp.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/inc/paraLib.h
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/inc/paraMessage.h
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/inc/paraVersion.h
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/lib/paraLib.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/lib/paraMessage.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraHub/paraHub.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraHub/paraHub.h
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraHub/sockSuck.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraHub/spoke.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraHubStop/paraHubStop.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraNode/paraNode.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraNodeStatus/paraNodeStatus.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/paraNodeStop/paraNodeStop.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/parasol/parasol.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/parasol/version.doc
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/utils/bedToBigBed/bedToBigBed.c
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    32caec3dbd6130357867cf65a101ee4757f7c259 Wed Jul 24 16:04:17 2019 -0700
    Adding a note about how to find the most up-to-date chrom.sizes file for an assembly with patch sequences, no Redmine.
• src/utils/dnsInfo/dnsInfo.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/utils/dnsInfo/makefile
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.
• src/utils/qa/weeklybld/buildEnv.csh
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    37c5f50c32c6088b1b8637759e4daef5f8107571 Mon Jul 29 10:16:52 2019 -0700
    v386 preview1
• src/weblet/bottleneck/bottleneck.c
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    5359edc160de518d8e43fdd3448365c15b912c3c Mon Jul 22 11:48:10 2019 -0700
    Added ipv6 support. Listening processes us hybrid dual stack feature of OS to simplify implementation and use a single listening socket. Works with both TCP and UDP. Parasol working. geoIp also updated and ready for IPv6. Should be invisible to most users, while providing connections via ipv6 where available. Supports both ipv4 and ipv6.

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• files changed: 131