All File Changes

v363_preview2 to v363_base (2018-03-19 to 2018-03-26) v363

• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 9, context: html, text, full: html, text
    00261a595c035c1bb559d924343b4e78a4942d86 Thu Mar 22 18:35:15 2018 -0700
    Trying to mitigate a race condition in cdwMakeValidFile
• src/hg/hgCollection/hgCollection.c
  • lines changed 11, context: html, text, full: html, text
    4272e1c7a2d10741a096eb7868c680bdb11e9895 Thu Mar 22 11:37:42 2018 -0700
    changes in response to code review #21090
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 11, context: html, text, full: html, text
    c3bb5a0e0757e2f66a06395b05fc78a7f2957e87 Fri Mar 23 11:34:33 2018 -0700
    manage dataVersion trackDb setting in conjuction with hgFixed.trackVersion table refs #20215
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 230, context: html, text, full: html, text
    29ee334981ae71d1c4caefcd64f0db3ec26f7547 Thu Mar 22 18:04:50 2018 -0700
    add support to using gencode gene id in all gencode track (rm21157)
  • lines changed 10, context: html, text, full: html, text
    c4f955645d376e77f358e545b36fbdefdc8ab8ce Thu Mar 22 18:19:49 2018 -0700
    make sure gencode label is set on first switch from old cart (rm21157)
• src/hg/hgTracks/interactTrack.c
  • lines changed 341, context: html, text, full: html, text
    69ed2f332551b505c78b081306d834224e70e5da Tue Mar 20 23:24:08 2018 -0700
    Code cleanup. Fix mouseover on curves. refs #17512
  • lines changed 4, context: html, text, full: html, text
    a367c929ac286f2c8868f59e63bb0de2331ec588 Wed Mar 21 00:15:18 2018 -0700
    Fix off-by-one. refs #17512
• src/hg/hgTracks/simpleTracks.c
  • lines changed 12, context: html, text, full: html, text
    c3bb5a0e0757e2f66a06395b05fc78a7f2957e87 Fri Mar 23 11:34:33 2018 -0700
    manage dataVersion trackDb setting in conjuction with hgFixed.trackVersion table refs #20215
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    4a555a4b6cf9a755a8fc9fc3635dbc7142306522 Wed Mar 21 12:15:58 2018 -0700
    Announcing petMar3 assembly release, refs #20819
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 6, context: html, text, full: html, text
    4a555a4b6cf9a755a8fc9fc3635dbc7142306522 Wed Mar 21 12:15:58 2018 -0700
    Announcing petMar3 assembly release, refs #20819
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    4a555a4b6cf9a755a8fc9fc3635dbc7142306522 Wed Mar 21 12:15:58 2018 -0700
    Announcing petMar3 assembly release, refs #20819
  • lines changed 4, context: html, text, full: html, text
    c94375512cf4deebb30a2180df975419f9e69f5b Wed Mar 21 14:05:23 2018 -0700
    Making a minor change to the announcement to remove redundancy, refs #20819
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    4a555a4b6cf9a755a8fc9fc3635dbc7142306522 Wed Mar 21 12:15:58 2018 -0700
    Announcing petMar3 assembly release, refs #20819
• src/hg/htdocs/staff.html
  • lines changed 3, context: html, text, full: html, text
    d4de9419f3e05874c533f50b6ebb3999e43e1ac4 Wed Mar 21 16:04:06 2018 -0700
    updating staff page, no rm
• src/hg/inc/encode/wgEncodeGencodeAttrs.h
  • lines changed 1, context: html, text, full: html, text
    29ee334981ae71d1c4caefcd64f0db3ec26f7547 Thu Mar 22 18:04:50 2018 -0700
    add support to using gencode gene id in all gencode track (rm21157)
• src/hg/inc/hgHgvs.h
  • lines changed 3, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/inc/hui.h
  • lines changed 6, context: html, text, full: html, text
    1b1678cabcf7065d8c7e82da019cdcdd074570e8 Fri Mar 23 11:45:00 2018 -0700
    manage dataVersion trackDb setting in conjuction with hgFixed.trackVersion table refs #20215
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    a97dcf79cc86cb79231374f6250927a360b03645 Mon Mar 26 10:19:40 2018 -0700
    New version number v363
• src/hg/js/hgCollection.js
  • lines changed 2, context: html, text, full: html, text
    4272e1c7a2d10741a096eb7868c680bdb11e9895 Thu Mar 22 11:37:42 2018 -0700
    changes in response to code review #21090
• src/hg/lib/hgHgvs.c
  • lines changed 1, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/hui.c
  • lines changed 33, context: html, text, full: html, text
    29ee334981ae71d1c4caefcd64f0db3ec26f7547 Thu Mar 22 18:04:50 2018 -0700
    add support to using gencode gene id in all gencode track (rm21157)
  • lines changed 12, context: html, text, full: html, text
    c3bb5a0e0757e2f66a06395b05fc78a7f2957e87 Fri Mar 23 11:34:33 2018 -0700
    manage dataVersion trackDb setting in conjuction with hgFixed.trackVersion table refs #20215
• src/hg/lib/txAliDoubleGap.as
  • lines changed 15, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliMismatch.as
  • lines changed 14, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliQSkipped.as
  • lines changed 13, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliShiftyGap.as
  • lines changed 20, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/lib/txAliShortGap.as
  • lines changed 16, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/makeDb/doc/casCan1/initialBuild.txt
  • lines changed 269, context: html, text, full: html, text
    76b7570610850b5d46c0f620664aa78d969d2f96 Wed Mar 21 21:31:07 2018 -0700
    QA Ready refs #21116
• src/hg/makeDb/doc/criGriChoV2/initialBuild.txt
  • lines changed 30, context: html, text, full: html, text
    19333f51986cd07483a290b548d9624df0ccd4b6 Mon Mar 26 10:09:04 2018 -0700
    crispr build broken at last step refs #20540
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 15, context: html, text, full: html, text
    bfaf5bb6d1667d2d9faef2cc9d3fbbac012b730c Mon Mar 26 10:09:51 2018 -0700
    liftOver to felCat9 refs #21043
• src/hg/makeDb/doc/felCat8/initialBuild.txt
  • lines changed 14, context: html, text, full: html, text
    bfaf5bb6d1667d2d9faef2cc9d3fbbac012b730c Mon Mar 26 10:09:51 2018 -0700
    liftOver to felCat9 refs #21043
• src/hg/makeDb/doc/felCat9/initialBuild.txt
  • lines changed 367, context: html, text, full: html, text
    7f6db5b4eb9cf5e6e5b5fd41906b8a8de98fc9de Tue Mar 20 09:30:23 2018 -0700
    QA Ready refs #21043
• src/hg/makeDb/doc/ficAlb1/initialBuild.txt
  • lines changed 17, context: html, text, full: html, text
    038d205f7fdf28afaed7f5dc27b04f31628cf9a3 Mon Mar 26 10:10:58 2018 -0700
    attempting to run up tandemDups having much difficulty refs #9870
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 4, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 252, context: html, text, full: html, text
    69fa55e9782319bf001fa8c36ffbe390fced3205 Tue Mar 20 09:36:41 2018 -0700
    lastz chainNet for thaSir1 felCat9 and casCan1 refs #21043 #19883 #21116
  • lines changed 7, context: html, text, full: html, text
    008c37f0b59188a483222edcb7c514e0bd8689fa Wed Mar 21 13:46:22 2018 -0700
    completed chainNet lastz runs to beaver/casCan1 refs #2116
  • lines changed 10, context: html, text, full: html, text
    e3dec7ffbb0614d2796e0706b2313f7ea7849e3e Thu Mar 22 14:34:53 2018 -0700
    completed neoSch1 QA Ready refs #19883
  • lines changed 86, context: html, text, full: html, text
    611e96cad657e7efb518aab3ac07c7d514d9e3dc Sun Mar 25 14:45:22 2018 -0700
    lastz chaiNet done to mm10 and hg38 refs #20979
• src/hg/makeDb/doc/mm10.txt
  • lines changed 5, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
  • lines changed 215, context: html, text, full: html, text
    4966d743257e8792a1c00561c286ec77c8ccdd6d Tue Mar 20 09:34:36 2018 -0700
    lastz chainNet for thaSir1 felCat9 and casCan1 refs #21043 #19883 #21116
  • lines changed 7, context: html, text, full: html, text
    008c37f0b59188a483222edcb7c514e0bd8689fa Wed Mar 21 13:46:22 2018 -0700
    completed chainNet lastz runs to beaver/casCan1 refs #2116
  • lines changed 6, context: html, text, full: html, text
    e3dec7ffbb0614d2796e0706b2313f7ea7849e3e Thu Mar 22 14:34:53 2018 -0700
    completed neoSch1 QA Ready refs #19883
  • lines changed 68, context: html, text, full: html, text
    611e96cad657e7efb518aab3ac07c7d514d9e3dc Sun Mar 25 14:45:22 2018 -0700
    lastz chaiNet done to mm10 and hg38 refs #20979
• src/hg/makeDb/doc/neoSch1/initialBuild.txt
  • lines changed 124, context: html, text, full: html, text
    e3dec7ffbb0614d2796e0706b2313f7ea7849e3e Thu Mar 22 14:34:53 2018 -0700
    completed neoSch1 QA Ready refs #19883
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 1365, context: html, text, full: html, text
    1e2f999205030c61a3b9999fab726875af577546 Mon Mar 26 10:12:13 2018 -0700
    running up a 3-way multiple alignment no redmine
• src/hg/makeDb/doc/panTro5/initialBuild.txt
  • lines changed 13, context: html, text, full: html, text
    a8ef7d52b32a22999c95967270a8fb4eda3b321e Mon Mar 26 10:12:53 2018 -0700
    liftOver to panTro6 refs #20979
• src/hg/makeDb/doc/panTro6/initialBuild.txt
  • lines changed 968, context: html, text, full: html, text
    3e7d2e3f6fc6b0e8c12a0b5daf10d4cdc7f73b21 Sat Mar 24 22:06:03 2018 -0700
    running up lastz chainNet to mm10 and hg38 refs #20979
  • lines changed 200, context: html, text, full: html, text
    611e96cad657e7efb518aab3ac07c7d514d9e3dc Sun Mar 25 14:45:22 2018 -0700
    lastz chaiNet done to mm10 and hg38 refs #20979
• src/hg/makeDb/doc/ponAbe3/initialBuild.txt
  • lines changed 1006, context: html, text, full: html, text
    987435c6cae84cc8cfbda95139d31f645fb7ca43 Mon Mar 26 10:06:31 2018 -0700
    running repeatMasker windowMasker refs #20980
• src/hg/makeDb/doc/thaSir1/initialBuild.txt
  • lines changed 835, context: html, text, full: html, text
    6907e96ac2f83570458d8d4602f9a50bc4980db9 Tue Mar 20 12:15:22 2018 -0700
    QA Ready refs #16028
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    6a70196500cdf94ac6218c9ee739511b65e6d657 Sun Mar 25 14:35:27 2018 -0700
    adding panTro6 to the system refs #20979
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    c85c2c2d8baabfdf5df628a26bfe9043c5f82682 Mon Mar 19 10:37:41 2018 -0700
    make the change to use genbank instead of hgwdev as build server. This has been happening for a while now, but I didn't make the change in the source tree.
  • lines changed 24, context: html, text, full: html, text
    6a70196500cdf94ac6218c9ee739511b65e6d657 Sun Mar 25 14:35:27 2018 -0700
    adding panTro6 to the system refs #20979
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    6a70196500cdf94ac6218c9ee739511b65e6d657 Sun Mar 25 14:35:27 2018 -0700
    adding panTro6 to the system refs #20979
• src/hg/makeDb/genbank/makefile
  • lines changed 3, context: html, text, full: html, text
    2c78bc43eb28c26ba2db8030ea2a2fcadd8dcfe8 Mon Mar 19 12:56:37 2018 -0700
    copy server files over to genbank-101
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 9, context: html, text, full: html, text
    3753975cb92612394220ce12cdd30ad429736938 Mon Mar 26 10:14:09 2018 -0700
    some extra verbose(3) for debugging no redmine
• src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
  • lines changed 964, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    afeecd22e96af200aa243b4334550a61570ac226 Wed Mar 21 17:03:48 2018 -0700
    adding casCan1 definitions refs #21116
  • lines changed 9, context: html, text, full: html, text
    672c01f6a8c31818c4e5dd061161b511068305f9 Sat Mar 24 22:09:16 2018 -0700
    adding panTro6 rules refs #20979
• src/hg/makeDb/trackDb/chimp/panTro6/description.html
  • lines changed 64, context: html, text, full: html, text
    9d07cef01b2d3acd8c1d030faf43f7f10604db8e Sat Mar 24 08:24:59 2018 -0700
    adding panTro6 to the browser refs #20979
• src/hg/makeDb/trackDb/chimp/panTro6/gap.html
  • lines changed 32, context: html, text, full: html, text
    9d07cef01b2d3acd8c1d030faf43f7f10604db8e Sat Mar 24 08:24:59 2018 -0700
    adding panTro6 to the browser refs #20979
• src/hg/makeDb/trackDb/chimp/panTro6/gold.html
  • lines changed 36, context: html, text, full: html, text
    9d07cef01b2d3acd8c1d030faf43f7f10604db8e Sat Mar 24 08:24:59 2018 -0700
    adding panTro6 to the browser refs #20979
• src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    9d07cef01b2d3acd8c1d030faf43f7f10604db8e Sat Mar 24 08:24:59 2018 -0700
    adding panTro6 to the browser refs #20979
  • lines changed 7, context: html, text, full: html, text
    8a5fa10564b53cc6f586b5506a5956b1ddd559aa Sat Mar 24 08:35:15 2018 -0700
    add gold/assembly search rule and include NCBI RefSeq composite refs #20979
• src/hg/makeDb/trackDb/cow/snp148.shared.html
  • lines changed 32, context: html, text, full: html, text
    cd12869d1f0a3d9de1e8e1997b6d6ed29f75c1a9 Thu Mar 22 08:49:07 2018 -0700
    Fixing broken links for bosTau8, no Redmine.
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 2, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/genomicSuperDups.html
  • lines changed 1, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/gorilla/gorGor5/gap.html
  • lines changed 2, context: html, text, full: html, text
    3422cabdba92a8cdd867839e6dea98f32456bad8 Wed Mar 21 08:41:32 2018 -0700
    Fixing broken links for gorGor5, no Redmine.
• src/hg/makeDb/trackDb/gorilla/gorGor5/gold.html
  • lines changed 2, context: html, text, full: html, text
    3422cabdba92a8cdd867839e6dea98f32456bad8 Wed Mar 21 08:41:32 2018 -0700
    Fixing broken links for gorGor5, no Redmine.
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 21, context: html, text, full: html, text
    10f796c6c24568a19fd7dc445a9ea87e8b0ade80 Wed Mar 21 14:25:23 2018 -0700
    adding Beaver casCan1 chainNet definitions refs #21116
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 17, context: html, text, full: html, text
    a4e273160689f332baa2138d7cb06419af9c0550 Sat Mar 24 22:04:42 2018 -0700
    adding panTro6 chainNet definitions refs #20979
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
  • lines changed 18, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV27.html
  • lines changed 0, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV27.ra
  • lines changed 35, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    9d07cef01b2d3acd8c1d030faf43f7f10604db8e Sat Mar 24 08:24:59 2018 -0700
    adding panTro6 to the browser refs #20979
  • lines changed 1, context: html, text, full: html, text
    dcb5f4e014a749344101c180eb667341effd4432 Sun Mar 25 23:28:27 2018 -0700
    adding ponAbe3 browser refs #20980
• src/hg/makeDb/trackDb/mammal/casCan1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    4a7c04670850782c51fd8edeacde940cf4f6a21e Wed Mar 21 19:02:07 2018 -0700
    adding NCBI RefSeq and gold/assembly search rule refs #21116
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 10, context: html, text, full: html, text
    72b9305613ecc966402bd63d7f83292a3810f895 Wed Mar 21 08:50:05 2018 -0700
    Fixing broken links for calJac1, no Redmine.
• src/hg/makeDb/trackDb/marmoset/calJac1/nscanGene.html
  • lines changed 4, context: html, text, full: html, text
    72b9305613ecc966402bd63d7f83292a3810f895 Wed Mar 21 08:50:05 2018 -0700
    Fixing broken links for calJac1, no Redmine.
• src/hg/makeDb/trackDb/marmoset/calJac1/phastConsElements9way.html
  • lines changed 6, context: html, text, full: html, text
    72b9305613ecc966402bd63d7f83292a3810f895 Wed Mar 21 08:50:05 2018 -0700
    Fixing broken links for calJac1, no Redmine.
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 4, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 19, context: html, text, full: html, text
    a4e273160689f332baa2138d7cb06419af9c0550 Sat Mar 24 22:04:42 2018 -0700
    adding panTro6 chainNet definitions refs #20979
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    10f796c6c24568a19fd7dc445a9ea87e8b0ade80 Wed Mar 21 14:25:23 2018 -0700
    adding Beaver casCan1 chainNet definitions refs #21116
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    a208b6494eb8e9dfde4d24e3ab8364931fce6bab Thu Mar 22 09:55:14 2018 -0700
    adding neoSch1 Monk seal chainNet definitions refs #19883
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM16.html
  • lines changed 0, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM16.ra
  • lines changed 32, context: html, text, full: html, text
    6b82df9c93a5eeb2447321098de0f570673ededd Mon Mar 19 21:12:42 2018 -0700
    Added search for gencode proteinId. This was done by updating the program that generates the gencode trackDb ra and html files. The way the contitional text generation was done had gotten error prone, so it was restructed. The change isn't as drastic as it looks. The results were compared to the old ra files to make sure there changes were what was expected. RM21077
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    10f796c6c24568a19fd7dc445a9ea87e8b0ade80 Wed Mar 21 14:25:23 2018 -0700
    adding Beaver casCan1 chainNet definitions refs #21116
• src/hg/makeDb/trackDb/nscanGene.html
  • lines changed 1, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/orangutan/ponAbe3/description.html
  • lines changed 64, context: html, text, full: html, text
    dcb5f4e014a749344101c180eb667341effd4432 Sun Mar 25 23:28:27 2018 -0700
    adding ponAbe3 browser refs #20980
• src/hg/makeDb/trackDb/orangutan/ponAbe3/gap.html
  • lines changed 31, context: html, text, full: html, text
    dcb5f4e014a749344101c180eb667341effd4432 Sun Mar 25 23:28:27 2018 -0700
    adding ponAbe3 browser refs #20980
• src/hg/makeDb/trackDb/orangutan/ponAbe3/gold.html
  • lines changed 34, context: html, text, full: html, text
    dcb5f4e014a749344101c180eb667341effd4432 Sun Mar 25 23:28:27 2018 -0700
    adding ponAbe3 browser refs #20980
• src/hg/makeDb/trackDb/orangutan/ponAbe3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    dcb5f4e014a749344101c180eb667341effd4432 Sun Mar 25 23:28:27 2018 -0700
    adding ponAbe3 browser refs #20980
• src/hg/makeDb/trackDb/rat/recombRateRat.html
  • lines changed 1, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rat/rn3/ECgene.html
  • lines changed 1, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rat/rn3/ecoresFr1.html
  • lines changed 3, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rat/rn3/ecoresTetraodon.html
  • lines changed 3, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rat/rn3/knownGene.html
  • lines changed 3, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rgdEst.html
  • lines changed 3, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rgdGene.html
  • lines changed 3, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rgdQtl.html
  • lines changed 1, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/rgdSslp.html
  • lines changed 3, context: html, text, full: html, text
    0879850ae875fb7af3ceab7594beb58d460da1f7 Wed Mar 21 09:43:09 2018 -0700
    Fixing broken links for rn3, no Redmine.
• src/hg/makeDb/trackDb/seal/neoSch1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    6bfc2469cc844e0e9674a1b42f03fb9080bdd463 Thu Mar 22 12:44:45 2018 -0700
    adding NCBI RefSeq composite include refs #19883
• src/hg/makeDb/trackDb/squirt/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    870185a08110ef308cba1ef387ad8ea9fa186775 Mon Mar 26 10:06:19 2018 -0700
    Fixing broken links for ci3, no Redmine.
• src/hg/makeDb/trackDb/squirt/refGene.html
  • lines changed 1, context: html, text, full: html, text
    870185a08110ef308cba1ef387ad8ea9fa186775 Mon Mar 26 10:06:19 2018 -0700
    Fixing broken links for ci3, no Redmine.
• src/hg/makeDb/trackDb/squirt/rmsk.html
  • lines changed 1, context: html, text, full: html, text
    870185a08110ef308cba1ef387ad8ea9fa186775 Mon Mar 26 10:06:19 2018 -0700
    Fixing broken links for ci3, no Redmine.
• src/hg/makeDb/trackDb/squirt/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    870185a08110ef308cba1ef387ad8ea9fa186775 Mon Mar 26 10:06:19 2018 -0700
    Fixing broken links for ci3, no Redmine.
• src/hg/makeDb/trackDb/tantan.html
  • lines changed 16, context: html, text, full: html, text
    22c0beb9c98122cfc85aed0b561fab682a26d8c4 Mon Mar 26 10:14:48 2018 -0700
    adding tantan repeat track experiment no redmine
• src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra
  • lines changed 53, context: html, text, full: html, text
    10f796c6c24568a19fd7dc445a9ea87e8b0ade80 Wed Mar 21 14:25:23 2018 -0700
    adding Beaver casCan1 chainNet definitions refs #21116
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
  • lines changed 55, context: html, text, full: html, text
    a208b6494eb8e9dfde4d24e3ab8364931fce6bab Thu Mar 22 09:55:14 2018 -0700
    adding neoSch1 Monk seal chainNet definitions refs #19883
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
  • lines changed 53, context: html, text, full: html, text
    a4e273160689f332baa2138d7cb06419af9c0550 Sat Mar 24 22:04:42 2018 -0700
    adding panTro6 chainNet definitions refs #20979
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    22c0beb9c98122cfc85aed0b561fab682a26d8c4 Mon Mar 26 10:14:48 2018 -0700
    adding tantan repeat track experiment no redmine
• src/hg/makeDb/trackDb/transMapTailer.html
  • lines changed 1, context: html, text, full: html, text
    cd12869d1f0a3d9de1e8e1997b6d6ed29f75c1a9 Thu Mar 22 08:49:07 2018 -0700
    Fixing broken links for bosTau8, no Redmine.
• src/hg/mouseStuff/axtChain/axtChain.c
  • lines changed 4, context: html, text, full: html, text
    b8303f22da89371b05a46134dfddbb3e9515c408 Fri Mar 23 10:27:55 2018 -0700
    better error message from axtChain when 2bit or nib arguments do not exist refs #20928
• src/hg/utils/automation/makePushQSql.pl
  • lines changed 34, context: html, text, full: html, text
    e87f79b092f5e36115fd288fad5cea22646b4646 Tue Mar 20 10:13:02 2018 -0700
    some genbank tables are no longer required items refs #16028
  • lines changed 14, context: html, text, full: html, text
    04304727abc7186de4c1f5491a856d78398d4b0a Thu Mar 22 14:20:09 2018 -0700
    recognize tables in a track type psl refs #19883
• src/hg/utils/automation/verifyBrowser.pl
  • lines changed 19, context: html, text, full: html, text
    26322399c9941a152481478073184d343637bcaf Mon Mar 19 18:37:45 2018 -0700
    add check for to/from previous version liftOvers when version > 1 no redmine
  • lines changed 26, context: html, text, full: html, text
    d2c809ae4d4554bed631c747bce60636cb27ef0a Tue Mar 20 09:45:17 2018 -0700
    Ensembl genes can be optional, show count of tables in optional categories refs #16028
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    104d5620c3a548f3f65b7b9e81e101c461bcbd77 Tue Mar 20 12:18:21 2018 -0700
    add blatServer check refs #16028
  • lines changed 29, context: html, text, full: html, text
    1053ac3a46b6a3064a2cf6671627a25ff2e1e385 Wed Mar 21 18:49:08 2018 -0700
    check for chainNet on hg38 and mm10 to target db and gold search rule and all.joiner entry refs #21116
  • lines changed 40, context: html, text, full: html, text
    2396e45154fb57b93e7988d5f00efc2d64bbbcb9 Thu Mar 22 12:49:25 2018 -0700
    move the RBest and Syntenic chainNets to optional list and avoid hg38 and mm10 self checks refs #19883
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    b7539ba8ad8a6148ebd8232baeaab4d6730898f6 Mon Mar 26 10:07:38 2018 -0700
    table exists if 1 or more columns and make the RBest and Syntenic tracks optional on mm10 and hg38 refs #21128
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 1, context: html, text, full: html, text
    eb5731dbdd76cdea9fbd164142cfe61d5c9ea3e5 Mon Mar 26 08:54:13 2018 -0700
    Correcting minor spelling error in usage message: metadaa -> metadata, no redmine
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/utils/phyloTrees/placentals.txt
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    7f9a26caa49ff5bea1f9791e8513b94c6587d3e6 Mon Mar 26 10:15:57 2018 -0700
    adding American beaver Castor canadensis refs #21116
• src/hg/utils/pslMismatchGapToBed/makefile
  • lines changed 3, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
• src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c
  • lines changed 518, context: html, text, full: html, text
    b91a917e39c8d58d0de5e6325606f098ef0fb60b Wed Mar 21 09:22:21 2018 -0700
    New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts. Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed. This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track. refs #21079
  • lines changed 5, context: html, text, full: html, text
    65a5a83fd4a3921e2a725241e24be49054c1ae40 Wed Mar 21 15:25:56 2018 -0700
    Oops, ignoreQNamePrefix needs to be applied before we call checkTranscript. refs #21079
• src/inc/common.h
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    15077d5121318029606a3282c3ffa73e6f8a53a2 Wed Mar 21 15:49:49 2018 -0700
    Updating a comment on case sensitivity on slNameInList.
• src/inc/portable.h
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    b8303f22da89371b05a46134dfddbb3e9515c408 Fri Mar 23 10:27:55 2018 -0700
    better error message from axtChain when 2bit or nib arguments do not exist refs #20928
• src/inc/srcVersion.h
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    a97dcf79cc86cb79231374f6250927a360b03645 Mon Mar 26 10:19:40 2018 -0700
    New version number v363
• src/lib/common.c
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    15077d5121318029606a3282c3ffa73e6f8a53a2 Wed Mar 21 15:49:49 2018 -0700
    Updating a comment on case sensitivity on slNameInList.
• src/lib/osunix.c
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    b8303f22da89371b05a46134dfddbb3e9515c408 Fri Mar 23 10:27:55 2018 -0700
    better error message from axtChain when 2bit or nib arguments do not exist refs #20928
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
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    1ec4e5a8d2d2a48f66326c6a4131c42bdf2348d5 Wed Mar 21 15:41:36 2018 -0700
    Fixing case sensitivity/insensitivity that was tripping up Will's merge of the Loring lab new data set with out.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, context: html, text, full: html, text
    2b9e72f7cb3c431864f468e03d5ff5910ee165bc Wed Mar 21 15:21:30 2018 -0700
    Fixing an odd corner case in bedToBigBed: multiple insertions at the end of a sequence. Tangentially refs #21079
• src/utils/bedToBigBed/tests/input/multiInsAtEnd.bed
  • lines changed 2, context: html, text, full: html, text
    2b9e72f7cb3c431864f468e03d5ff5910ee165bc Wed Mar 21 15:21:30 2018 -0700
    Fixing an odd corner case in bedToBigBed: multiple insertions at the end of a sequence. Tangentially refs #21079
• src/utils/bedToBigBed/tests/makefile
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    2b9e72f7cb3c431864f468e03d5ff5910ee165bc Wed Mar 21 15:21:30 2018 -0700
    Fixing an odd corner case in bedToBigBed: multiple insertions at the end of a sequence. Tangentially refs #21079
• src/utils/faLowerToN/faLowerToN.c
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    7dc72516c18322453473dc52a2eab5de480e297a Mon Mar 26 10:17:05 2018 -0700
    add static to lowerToN() function to avoid conflict with same named function in library noticed by Encode DCC user no redmine
• src/utils/qa/sessionStats.csh
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    f7ecd5e41d6f499eac67a80c32d3ab5944f4cc6f Fri Mar 23 17:34:42 2018 -0700
    added detection of lastUse values for last two months
• src/utils/qa/weeklybld/buildEnv.csh
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    7e09c0dfe844a7e624aa2a1c6e4ab0dbb498f2bd Mon Mar 26 10:03:59 2018 -0700
    v363 final build refs #21106

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• files changed: 140