All File Changes

v370_preview to v370_preview2 (2018-08-06 to 2018-08-13) v370

• src/hg/cirm/cdw/cdwServeTagStorm/cdwServeTagStorm.c
  • lines changed 38, context: html, text, full: html, text
    7d00a6555d2fd1a26fd0e218caebee856897a7a0 Mon Aug 6 14:37:03 2018 -0700
    fixes #21875. Does not allow users with no access to the meta.txt to click links showing the tagStorm in various text, csv, and tsv forms. cdwServeTagStorm now safely checks user has access. cdwWebBrowse also will now NOT display the meta links at all if the user does not have access.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 15, context: html, text, full: html, text
    7d00a6555d2fd1a26fd0e218caebee856897a7a0 Mon Aug 6 14:37:03 2018 -0700
    fixes #21875. Does not allow users with no access to the meta.txt to click links showing the tagStorm in various text, csv, and tsv forms. cdwServeTagStorm now safely checks user has access. cdwWebBrowse also will now NOT display the meta links at all if the user does not have access.
• src/hg/hgTables/filterFields.c
  • lines changed 3, context: html, text, full: html, text
    37dc37970d1c1e90981af07f61f50629d1292943 Tue Aug 7 10:46:57 2018 -0700
    fix #21878
• src/hg/hgTracks/interactTrack.c
  • lines changed 1, context: html, text, full: html, text
    6d394cb65b46140e8548f0e168928a16e54463b8 Tue Aug 7 18:34:58 2018 -0700
    Fix for problem when interact track is a subtrack. Still needs a little work when too many items to draw (need to adjust track height).
  • lines changed 7, context: html, text, full: html, text
    ef7e53bd098a62ded05b8c3a08afff08ff939063 Wed Aug 8 16:26:40 2018 -0700
    Minor changes to make it easier to see/mouseover/click on the interactions: 1) Darken color of grab box. 2) Make endpoint horizontals 2 pixels high (JK suggestion). refs #21109
  • lines changed 36, context: html, text, full: html, text
    f8d4a7651a5843d1c0bfa90cdb7da7582615c263 Thu Aug 9 13:47:29 2018 -0700
    Add filter to hide interactions lacking one or both ends in the window. Helpful for busy/noisy datasets. refs #21109
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 22, context: html, text, full: html, text
    464a0e810e09bbacdc65e4c764b9a7768a0e0d61 Fri Aug 10 14:20:52 2018 -0700
    Updating news on the Interact and bigInteract track features. ref#21615
  • lines changed 1, context: html, text, full: html, text
    ed50b0a6007094dc5a640e357fd137bd3cae4ed5 Fri Aug 10 14:27:04 2018 -0700
    Fixing announcement title. ref#21615
  • lines changed 1, context: html, text, full: html, text
    521457cbb0b27db566b7e8635d8a4bee6d295431 Fri Aug 10 15:10:28 2018 -0700
    Fixing credit line at the bottom of announcement
• src/hg/htdocs/images/GeneHancer_Example.png
  • lines changed 0, context: html, text, full: html, text
    d980e08ffba76861bdfdbcdc0dc320377d4e9915 Fri Aug 10 14:16:09 2018 -0700
    Uploading GeneHancer image for the release announcement Ref#21615
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    464a0e810e09bbacdc65e4c764b9a7768a0e0d61 Fri Aug 10 14:20:52 2018 -0700
    Updating news on the Interact and bigInteract track features. ref#21615
• src/hg/inc/interactUi.h
  • lines changed 6, context: html, text, full: html, text
    f8d4a7651a5843d1c0bfa90cdb7da7582615c263 Thu Aug 9 13:47:29 2018 -0700
    Add filter to hide interactions lacking one or both ends in the window. Helpful for busy/noisy datasets. refs #21109
• src/hg/inc/txAliDiff.h
  • lines changed 82, context: html, text, full: html, text
    9ed6f979a8ec95ac934e5e8fef028d188b76a035 Mon Aug 6 14:38:57 2018 -0700
    pslMismatchGapToBed now outputs a single bed9+ instead of 5 different bed files, refs #21079
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    4561503c0972fa4871bff866833ea7a2ac44d7ef Wed Aug 8 14:19:14 2018 -0700
    code review: removing unnecessary re-test. refs #21870
• src/hg/lib/interactUi.c
  • lines changed 22, context: html, text, full: html, text
    f8d4a7651a5843d1c0bfa90cdb7da7582615c263 Thu Aug 9 13:47:29 2018 -0700
    Add filter to hide interactions lacking one or both ends in the window. Helpful for busy/noisy datasets. refs #21109
  • lines changed 1, context: html, text, full: html, text
    36643759e02d519eaa66ede1bc3298dea81c3df0 Thu Aug 9 16:01:14 2018 -0700
    Make setting a bit more flexible (anticipating another directional feature). refs #21109
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    2f0fcb2ddab64ea1f6386d68cfd7879267b7b99b Mon Aug 6 14:49:22 2018 -0700
    Woops forgot the makefile, refs #21079
• src/hg/lib/trackDbCustom.c
  • lines changed 4, context: html, text, full: html, text
    9ace9d69f447071f41281dd142bf667b25ee7da8 Wed Aug 8 11:03:54 2018 -0700
    don't errAbort if we see a release tag in a release tagged include file if the tag is the same.
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    ca4a954d98dfe214fe18d1d42fc7ff80c0813878 Mon Aug 13 16:54:45 2018 +0200
    improving track hub error a little, no redmine
• src/hg/lib/txAliDiff.as
  • lines changed 24, context: html, text, full: html, text
    9ed6f979a8ec95ac934e5e8fef028d188b76a035 Mon Aug 6 14:38:57 2018 -0700
    pslMismatchGapToBed now outputs a single bed9+ instead of 5 different bed files, refs #21079
• src/hg/lib/txAliDiff.c
  • lines changed 233, context: html, text, full: html, text
    9ed6f979a8ec95ac934e5e8fef028d188b76a035 Mon Aug 6 14:38:57 2018 -0700
    pslMismatchGapToBed now outputs a single bed9+ instead of 5 different bed files, refs #21079
• src/hg/lib/txAliDiff.sql
  • lines changed 30, context: html, text, full: html, text
    9ed6f979a8ec95ac934e5e8fef028d188b76a035 Mon Aug 6 14:38:57 2018 -0700
    pslMismatchGapToBed now outputs a single bed9+ instead of 5 different bed files, refs #21079
• src/hg/makeDb/doc/hg38/ncbiRefSeqGenomicDiff.txt
  • lines changed 99, context: html, text, full: html, text
    76bf2309472399482b007ffbf94d5de4c7eeb303 Tue Aug 7 10:34:35 2018 -0700
    RefSeq Genomic Diffs track QA ready, refs #21079
• src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    ae07cad8ebc406baee7428d3cd2eaad6a0131e0e Thu Aug 9 16:48:59 2018 -0700
    Moving the gap track to the second item in the 'Mapping and Sequencing' section of hgTracks, refs #20979
• src/hg/makeDb/trackDb/genscan.html
  • lines changed 1, context: html, text, full: html, text
    02101c0c9ea1e7830b260ce6c70b517d3c6541c7 Fri Aug 10 10:18:36 2018 -0700
    Making a help page link open in a new tab, refs #20979
  • lines changed 1, context: html, text, full: html, text
    072a7299c6689cb795ea1554aa6b72d545abd313 Fri Aug 10 10:24:25 2018 -0700
    Making another help page link open in a new tab, refs #20979
• src/hg/makeDb/trackDb/nestedRepeats.html
  • lines changed 1, context: html, text, full: html, text
    e3df0c5879ee68118db929ca0da156ef68d6c63d Fri Aug 10 12:51:27 2018 -0700
    Adding 'target=_blank' so help page links open in a new tab, refs #20979
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 12, context: html, text, full: html, text
    76bf2309472399482b007ffbf94d5de4c7eeb303 Tue Aug 7 10:34:35 2018 -0700
    RefSeq Genomic Diffs track QA ready, refs #21079
  • lines changed 2, context: html, text, full: html, text
    a2cd1aac8311b307dbed8be7bc32f7546da7bda0 Wed Aug 8 08:16:39 2018 -0700
    fixing ncbi refseq make beta build error, no refs
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 1, context: html, text, full: html, text
    e3df0c5879ee68118db929ca0da156ef68d6c63d Fri Aug 10 12:51:27 2018 -0700
    Adding 'target=_blank' so help page links open in a new tab, refs #20979
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 2, context: html, text, full: html, text
    b49e56c33ed3eb5a75f19ebc4bcc583e6fe5c6b3 Thu Aug 9 16:01:46 2018 -0700
    Reordering the RefSeq genes and Other RefSeq genes to the front of the 'Genes and Gene Predictions' section, refs #12746 and #20979
  • lines changed 2, context: html, text, full: html, text
    8bdc32bae7595f151acfe30f9fda8ae6e4d262cc Thu Aug 9 16:40:37 2018 -0700
    Reordering the 'mRNA and EST' section, refs #20979 and 12746
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fa4c544f5e9052a90d51c91d8dd4943e8022b9e0 Thu Aug 9 16:52:30 2018 -0700
    Moving the RepeatMasker track to the first item in the 'Variation and Repeats' section of hgTracks, refs #20979
• src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c
  • lines changed 206, context: html, text, full: html, text
    9ed6f979a8ec95ac934e5e8fef028d188b76a035 Mon Aug 6 14:38:57 2018 -0700
    pslMismatchGapToBed now outputs a single bed9+ instead of 5 different bed files, refs #21079
• src/inc/common.mk
  • lines changed 2, context: html, text, full: html, text
    bb7cd857b7dcb2214f1260455a2686f0665431e3 Mon Aug 13 08:06:02 2018 -0700
    fixing lib locations on new hgwdev, refs #21876
  • lines changed 2, context: html, text, full: html, text
    b3210d4c667f79214ceeec1b5248072b47a98065 Mon Aug 13 10:31:01 2018 -0700
    dynamic linking on libcrypto and libm refs #21876
  • lines changed 1, context: html, text, full: html, text
    e76c43019f385e694574c85b14c439e76f7db861 Mon Aug 13 10:38:37 2018 -0700
    also dynamic for libssl and libcrypto when building user app commands refs #21876
  • lines changed 2, context: html, text, full: html, text
    62934fae49d85ac9d7f53032bbbd0d7553f7a1c5 Mon Aug 13 10:57:55 2018 -0700
    ordering difficulties with libm refs #21876
• src/inc/common.mk.galt
  • lines changed 428, context: html, text, full: html, text
    c6e6631e7e05a58f07c54b2cd5cea7c97d83cf8e Mon Aug 13 10:02:17 2018 -0700
    temporary copy of my version of common.mk that compiles
• src/inc/vcf.h
  • lines changed 3, context: html, text, full: html, text
    6296e8a313306cb80b8fc78f1eee4980d0fe94f6 Fri Aug 10 15:26:29 2018 -0700
    allowing http links in VCF INFO fields, refs #21895
  • lines changed 1, context: html, text, full: html, text
    2ac935c8eb614926e850728cb41b36220dc04139 Fri Aug 10 15:38:25 2018 -0700
    oops, forget target _blank, refs #21895
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    971d468019c9e77103738f5d6e5b0c30a8930ae4 Mon Aug 13 11:45:11 2018 -0700
    v370 preview2, refs #21722
• src/utils/userApps/fetchChromSizes
  • lines changed 25, context: html, text, full: html, text
    ec633e36713743a8e810675f7f359e74d6625939 Mon Aug 6 15:46:50 2018 -0700
    fetchChromSizes: just try the curl, wget, etc commands instead of checking they exist first. We already were checking for the return code anyways, refs #21854

• lines changed: 1335
• files changed: 43