All File Changes

v363_preview to v363_preview2 (2018-03-12 to 2018-03-19) v363

• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 2, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/hg/hgCollection/hgCollection.c
  • lines changed 2, context: html, text, full: html, text
    50c1afeb6d02caceb8b68b0719f734ea57744944 Mon Mar 12 13:09:49 2018 -0700
    strip maxHeightPixels from trackDb's
  • lines changed 11, context: html, text, full: html, text
    216023c3cc8426beae32143f30f05bb0cfb09b40 Mon Mar 12 13:35:44 2018 -0700
    a little more tweaking on cleaning up a trackDb entry when putting them into a collection
  • lines changed 230, context: html, text, full: html, text
    80435e03cdc7e8d7a4cca8919985b94c40a5135d Tue Mar 13 17:00:20 2018 -0700
    eliminated duplicated code between the AJAX engine and the UI.
• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/hg/hgGene/domains.c
  • lines changed 1, context: html, text, full: html, text
    c38d3ab7815e03cf3d2235832e50c4bff288db12 Mon Mar 19 08:52:33 2018 -0700
    Fixing links to PDB images, fixes #21122
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 18, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/hg/hgTables/correlate.c
  • lines changed 1, context: html, text, full: html, text
    2af2aff96bc4532fa3b192c168952b6a11bd7357 Wed Mar 14 15:24:24 2018 -0700
    enable correlate function on mathWig
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    e4141d1ac618e15330fa41af60da0d02288b67e8 Fri Mar 16 15:52:42 2018 -0700
    made Multi-Region BED region warning more understandable and made display size of go-to region bigger
• src/hg/hgTracks/interactTrack.c
  • lines changed 18, context: html, text, full: html, text
    fc724a23c9a0ad34a6ff6e530eb93945fd94a5c5 Sun Mar 11 18:24:53 2018 -0700
    Add score filtering. refs #17512
  • lines changed 67, context: html, text, full: html, text
    d66e85de01cc0ad357015478051547eedfb5fa35 Mon Mar 12 15:52:44 2018 -0700
    Add click boxes to curves. Code still needs cleanup. refs #17512
  • lines changed 42, context: html, text, full: html, text
    3fd4131517e0d224eb271e312c9fda6419e1872d Tue Mar 13 15:51:59 2018 -0700
    1. Add support for spectrum setting. 2. Allow dot for empty field. 3. Show multiple items on details page if they overlap. 4. Some cleanup of map boxes. refs #17512
  • lines changed 3, context: html, text, full: html, text
    15f914c08ac9ec2b6eb6f2971596929909e2a815 Tue Mar 13 16:06:26 2018 -0700
    Add filter activated info to track label. refs #17512
• src/hg/hgTracks/wigTrack.c
  • lines changed 9, context: html, text, full: html, text
    9ffce6e1c30025e5dda5b736502ce8862bb9fe19 Mon Mar 12 10:44:00 2018 -0700
    make wiggle sorting give the same answer regardless of the type of graph
• src/hg/hgc/interactClick.c
  • lines changed 6, context: html, text, full: html, text
    fc724a23c9a0ad34a6ff6e530eb93945fd94a5c5 Sun Mar 11 18:24:53 2018 -0700
    Add score filtering. refs #17512
  • lines changed 48, context: html, text, full: html, text
    3fd4131517e0d224eb271e312c9fda6419e1872d Tue Mar 13 15:51:59 2018 -0700
    1. Add support for spectrum setting. 2. Allow dot for empty field. 3. Show multiple items on details page if they overlap. 4. Some cleanup of map boxes. refs #17512
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 7, context: html, text, full: html, text
    d1750706441ba7dc532813655529d118efd92526 Mon Mar 12 12:25:04 2018 -0700
    Adding a note about building search index in Ex3 of bigBed per code review, refs #21095
  • lines changed 1, context: html, text, full: html, text
    89670b344009a48abf7c287b9b5452c54ca5a46c Mon Mar 12 12:34:09 2018 -0700
    Tweaking note about building search index in Ex3 of bigBed per code review, refs #21095
  • lines changed 10, context: html, text, full: html, text
    5934788e9f01d73b1dbb4b77e6e998ed98c8017f Mon Mar 12 16:19:41 2018 -0700
    Correcting search index details in bigBed example and trackDbLibrary, really about composites per code review, refs #21095
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 10, context: html, text, full: html, text
    58578cbd72e7002b2b56e075bcd9a830c9cc5e46 Fri Mar 16 15:55:47 2018 -0700
    added video to hgIntegrator help page
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 1, context: html, text, full: html, text
    5ae216d0eec6421d7c92fce09d6b1922e78f3517 Fri Mar 16 08:50:48 2018 -0700
    Adding BRCA1 A744C example in HGVS
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    5934788e9f01d73b1dbb4b77e6e998ed98c8017f Mon Mar 12 16:19:41 2018 -0700
    Correcting search index details in bigBed example and trackDbLibrary, really about composites per code review, refs #21095
• src/hg/htdocs/images/Castor_canadensis.jpg
  • lines changed 0, context: html, text, full: html, text
    b19e1aa670446a3f5e33e86b28251f0f232b1051 Fri Mar 16 15:07:48 2018 -0700
    photo from Colin Knowles, flickr refs #21116
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 8, context: html, text, full: html, text
    c204d68af71394eff95d6dc61795dc3fc6c47360 Mon Mar 12 11:17:23 2018 -0700
    add some tool tips for the discard changes button and the Add Collection button
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
  • lines changed 1, context: html, text, full: html, text
    a39e07718c771dcdf0caac731a07b4a4933df160 Mon Mar 12 10:49:40 2018 -0700
    Fixed minor typo in placeholder video for hgCollection, refs #11630
  • lines changed 98, context: html, text, full: html, text
    b22ed7dc4667ce67d270414121af32fc02c83861 Tue Mar 13 12:44:31 2018 -0700
    Minor hgCollect help doc changes via code review, refs #21098
  • lines changed 4, context: html, text, full: html, text
    b7ee3a8271a65637b307ca8484fec7db539bbfb5 Tue Mar 13 16:44:55 2018 -0700
    Removing placeholder url until our channel video is available
• src/hg/htdocs/training/index.html
  • lines changed 19, context: html, text, full: html, text
    ca42fb455f15585474a70cf47502e5ded6dcd6e2 Thu Mar 15 11:25:51 2018 -0700
    adding Leuven workshop
  • lines changed 1, context: html, text, full: html, text
    d5e78b4a216626b00a1d45aa10e25f57b3846b5a Thu Mar 15 12:00:23 2018 -0700
    spelling out April to match other month names
• src/hg/inc/hvGfx.h
  • lines changed 2, context: html, text, full: html, text
    ae53754392371fb4f12ce622b5ccaf79321d0556 Mon Mar 12 15:29:40 2018 -0700
    Curve function returns max y drawn (helps max box placement). refs #17512
• src/hg/inc/interactUi.h
  • lines changed 1, context: html, text, full: html, text
    3fd4131517e0d224eb271e312c9fda6419e1872d Tue Mar 13 15:51:59 2018 -0700
    1. Add support for spectrum setting. 2. Allow dot for empty field. 3. Show multiple items on details page if they overlap. 4. Some cleanup of map boxes. refs #17512
• src/hg/inc/seqWindow.h
  • lines changed 8, context: html, text, full: html, text
    6546198dd3ce4f12b81225c5093163f3a176b5e3 Tue Mar 13 14:17:15 2018 -0700
    Adding twoBitSeqWindow{New,Free} for seqWindow on 2bit files.
• src/hg/lib/cartJson.c
  • lines changed 23, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/hg/lib/genePred.c
  • lines changed 1, context: html, text, full: html, text
    baed67b5aa7f67279b04e4cf2e33cafd2268f10d Mon Mar 12 15:46:09 2018 -0700
    Adding obscure util pslFixCdsJoinGap, to correct the output of genePredToFakePsl for transcripts with +1 ribosomal frameshift. genePred exons skip over a base to maintain frame; genePredToFakePsl sees a 1-base gap on target, 0-base gap on query. However, the query base is skipped as described in Genbank CDS strings such as "join(168..260,262..741)". Use CDS strings to recognize these cases, and if the PSL has a 1-sided gap on target at the exact position of the skipped base then make the gap 2-sided to avoid making the alignment off-by-1 after that point and becoming a swamp of mismatches. The ideal solution would be to remove the gap and properly interpret join CDS in the rest of our software, but this will at least prevent totally incorrect genePred-derived PSL for transcripts with +1 ribosomal frameshift for now. refs #21048
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    4f80b3af4cb02e10216ba047ea8de0378c4abe3d Mon Mar 19 09:58:16 2018 -0700
    hListGencodeTables' version comparison didn't account for the 'VM' mouse version strings; if there's a letter following the V, skip it. Thanks Cath! refs #21076
• src/hg/lib/hgHgvs.c
  • lines changed 3, context: html, text, full: html, text
    a0d13c768fa16b3baf5f6c50babff087f13b1421 Wed Mar 14 17:06:27 2018 -0700
    Use wgEncodeGencodeCompV* for ENS* searches, not just the Basic subset. refs #21076
• src/hg/lib/hvGfx.c
  • lines changed 33, context: html, text, full: html, text
    ae53754392371fb4f12ce622b5ccaf79321d0556 Mon Mar 12 15:29:40 2018 -0700
    Curve function returns max y drawn (helps max box placement). refs #17512
• src/hg/lib/interactUi.c
  • lines changed 44, context: html, text, full: html, text
    fc724a23c9a0ad34a6ff6e530eb93945fd94a5c5 Sun Mar 11 18:24:53 2018 -0700
    Add score filtering. refs #17512
  • lines changed 11, context: html, text, full: html, text
    19a4f092a245f0dc66faafeaef874a53baa4ab81 Tue Mar 13 16:25:34 2018 -0700
    Unrequire the directionality setting (default to false). refs #17512
• src/hg/lib/seqWindow.c
  • lines changed 72, context: html, text, full: html, text
    6546198dd3ce4f12b81225c5093163f3a176b5e3 Tue Mar 13 14:17:15 2018 -0700
    Adding twoBitSeqWindow{New,Free} for seqWindow on 2bit files.
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    19a4f092a245f0dc66faafeaef874a53baa4ab81 Tue Mar 13 16:25:34 2018 -0700
    Unrequire the directionality setting (default to false). refs #17512
• src/hg/makeDb/doc/casCan1/initialBuild.txt
  • lines changed 875, context: html, text, full: html, text
    8345d6fd09956174344d777fc32c3d1cb251cbc3 Sat Mar 17 16:21:06 2018 -0700
    running up repeat masker, trying new version refs #21116
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    42affb99027a59b46497e56640af8c5f575b50b2 Mon Mar 12 14:28:14 2018 -0700
    adding felCat9 to the update alignments refs #21043
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    0231207f092bfd75637b84345f914a51edf35463 Tue Mar 13 10:24:42 2018 -0700
    adding thaSir1 to the update alignments refs #16028
  • lines changed 1, context: html, text, full: html, text
    9ed002e372d24c0b841043e05114b69fb17e1bbe Mon Mar 19 10:04:49 2018 -0700
    Added casCan1/Castor canadensis/American beaver; refs #21116
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 24, context: html, text, full: html, text
    833ef635c5d7fe764c01f9ce03ce04e25450dbb1 Tue Mar 13 10:23:28 2018 -0700
    adding thaSir1 - Thamnophis sirtalis/Garter snake refs #16028
  • lines changed 1, context: html, text, full: html, text
    8fcc159bc6ae014eca0d43f6436171f74c4b573a Sat Mar 17 08:46:40 2018 -0700
    fix a typo in thaSir1
  • lines changed 26, context: html, text, full: html, text
    9ed002e372d24c0b841043e05114b69fb17e1bbe Mon Mar 19 10:04:49 2018 -0700
    Added casCan1/Castor canadensis/American beaver; refs #21116
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    1e6dadeefac29cf8bc030aa6fc04d1c8ee883b60 Thu Mar 15 15:30:28 2018 -0700
    Turning on Genbank updates for petMar2 on hgwbeta, refs #20819
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    42affb99027a59b46497e56640af8c5f575b50b2 Mon Mar 12 14:28:14 2018 -0700
    adding felCat9 to the update alignments refs #21043
  • lines changed 1, context: html, text, full: html, text
    0231207f092bfd75637b84345f914a51edf35463 Tue Mar 13 10:24:42 2018 -0700
    adding thaSir1 to the update alignments refs #16028
  • lines changed 1, context: html, text, full: html, text
    9ed002e372d24c0b841043e05114b69fb17e1bbe Mon Mar 19 10:04:49 2018 -0700
    Added casCan1/Castor canadensis/American beaver; refs #21116
• src/hg/makeDb/genbank/etc/mkdownload
  • lines changed 1, context: html, text, full: html, text
    953e9a60b80f0a6d93f04a937804c3cf6beff56f Tue Mar 13 12:35:35 2018 -0700
    moving back to using /cluster/data/ instead of /data
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    7b5abb416f90bae7acbb0c36932c34342cdc1f8a Fri Mar 16 14:13:17 2018 -0700
    Turning on GenBank updates on the RR for petMar3, refs #20819
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    145ad3e0fbd252c057325523aaa4e79a45125d85 Tue Mar 13 09:35:09 2018 -0700
    Added thaSir1/Thamnophis sirtalis/Garter snake; refs #16028
  • lines changed 2, context: html, text, full: html, text
    9ed002e372d24c0b841043e05114b69fb17e1bbe Mon Mar 19 10:04:49 2018 -0700
    Added casCan1/Castor canadensis/American beaver; refs #21116
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    50d47c0d1ffc7585bcb00d91561bff75c1196d27 Tue Mar 13 14:28:11 2018 -0700
    adding neoSch1 exclude to ensemblTranscriptId refs #19883
  • lines changed 9, context: html, text, full: html, text
    a605723b58bb8ffd7d8266266fc8cb90fe02df15 Tue Mar 13 14:32:25 2018 -0700
    adding rules for felCat9 refs #21043
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    3dda4a265fb7dab115555d35d972884709ad0737 Wed Mar 14 13:40:31 2018 -0700
    add rules for thaSir1 refs #16028
• src/hg/makeDb/trackDb/cat/felCat9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9b2f4235d4cea9e6564db21391acf742ba77dd2a Thu Mar 15 11:09:26 2018 -0700
    using NCBI RefSeq composite refs #21043 #16028
• src/hg/makeDb/trackDb/dog/canFam1/description.html
  • lines changed 3, context: html, text, full: html, text
    ca42fb455f15585474a70cf47502e5ded6dcd6e2 Thu Mar 15 11:25:51 2018 -0700
    adding Leuven workshop
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • lines changed 3, context: html, text, full: html, text
    ca42fb455f15585474a70cf47502e5ded6dcd6e2 Thu Mar 15 11:25:51 2018 -0700
    adding Leuven workshop
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 1, context: html, text, full: html, text
    ca42fb455f15585474a70cf47502e5ded6dcd6e2 Thu Mar 15 11:25:51 2018 -0700
    adding Leuven workshop
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 17, context: html, text, full: html, text
    1e412cddaaa2b51940c0d061c16525c717fa3a76 Wed Mar 14 14:22:28 2018 -0700
    adding felCat9 chainNet refs #21043
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 35, context: html, text, full: html, text
    d5bf3fd17e8249fc1ac8f859ac4f78ac263a7072 Fri Mar 16 11:04:36 2018 -0700
    adding petMar3 and thaSir1 definitions refs #20819 #16028
• src/hg/makeDb/trackDb/lamprey/petMar3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    15f445ca4ee2c1bfd2896fd0470c2acd1bef6114 Fri Mar 16 12:28:09 2018 -0700
    Fixing the matrix and chain lines between petMar3 and hg38. refs #20819
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    e22c7873bd6ed887c64d91410d58d7940aaf0b20 Sat Mar 17 16:04:02 2018 -0700
    adding casCan1 to the build refs #21116
• src/hg/makeDb/trackDb/mammal/casCan1/description.html
  • lines changed 64, context: html, text, full: html, text
    e22c7873bd6ed887c64d91410d58d7940aaf0b20 Sat Mar 17 16:04:02 2018 -0700
    adding casCan1 to the build refs #21116
• src/hg/makeDb/trackDb/mammal/casCan1/gap.html
  • lines changed 30, context: html, text, full: html, text
    e22c7873bd6ed887c64d91410d58d7940aaf0b20 Sat Mar 17 16:04:02 2018 -0700
    adding casCan1 to the build refs #21116
• src/hg/makeDb/trackDb/mammal/casCan1/gold.html
  • lines changed 33, context: html, text, full: html, text
    e22c7873bd6ed887c64d91410d58d7940aaf0b20 Sat Mar 17 16:04:02 2018 -0700
    adding casCan1 to the build refs #21116
• src/hg/makeDb/trackDb/mammal/casCan1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    e22c7873bd6ed887c64d91410d58d7940aaf0b20 Sat Mar 17 16:04:02 2018 -0700
    adding casCan1 to the build refs #21116
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    1d2358ba3452b4064e5b07acef93babd8361d998 Fri Mar 16 11:35:05 2018 -0700
    Adding the petMar3 chain/net tracks and turning off the petMar2 net by default. refs #20819
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 5, context: html, text, full: html, text
    96ae63d25a33ef608903eeb39086ae5734738f52 Wed Mar 14 08:44:20 2018 -0700
    Fixing broken links for monDom4, no Redmine.
• src/hg/makeDb/trackDb/opossum/monDom4/phastConsElements7way.html
  • lines changed 5, context: html, text, full: html, text
    96ae63d25a33ef608903eeb39086ae5734738f52 Wed Mar 14 08:44:20 2018 -0700
    Fixing broken links for monDom4, no Redmine.
• src/hg/makeDb/trackDb/reptiles/thaSir1/gap.html
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    cdf91c81db9caed7ed685f0cfdd8fa1bb2eb6d38 Mon Mar 12 11:37:14 2018 -0700
    updated with refseq release refs #16028;
• src/hg/makeDb/trackDb/reptiles/thaSir1/gold.html
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    cdf91c81db9caed7ed685f0cfdd8fa1bb2eb6d38 Mon Mar 12 11:37:14 2018 -0700
    updated with refseq release refs #16028;
• src/hg/makeDb/trackDb/reptiles/thaSir1/trackDb.ra
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    ca878b30bf9a36fbce8c84a6f152304ed1a6ce06 Mon Mar 12 12:14:15 2018 -0700
    add gold table assembly track search rule refs #16028
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    9b2f4235d4cea9e6564db21391acf742ba77dd2a Thu Mar 15 11:09:26 2018 -0700
    using NCBI RefSeq composite refs #21043 #16028
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    1e412cddaaa2b51940c0d061c16525c717fa3a76 Wed Mar 14 14:22:28 2018 -0700
    adding felCat9 chainNet refs #21043
• src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra
  • lines changed 54, context: html, text, full: html, text
    2e7ad11191e60b2322245f490687a533c28b3922 Wed Mar 14 13:57:54 2018 -0700
    adding thaSir1 chainNet refs #16028
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
  • lines changed 1, context: html, text, full: html, text
    0f0a32f6dd3bb2e36cd6da6b9d7b3cbaf7317291 Mon Mar 19 09:02:55 2018 -0700
    Uncommenting dataVersion line for uniprot track, woops, refs #21121
• src/hg/utils/automation/doGapOverlap.pl
  • lines changed 10, context: html, text, full: html, text
    1e89a2d72b3c0465f0142798bc9c8fa32395bb94 Mon Mar 12 12:02:30 2018 -0700
    adding an endSize argument refs #16028
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 2, context: html, text, full: html, text
    dfd0e37b8be3b2b516728de719e9a7d5345ec295 Fri Mar 9 10:23:05 2018 -0800
    Use Mark's awesome new -refseqHacks option for gff3ToGenePred; it automatically turns on -useName, -allowMinimalGenes and processAllGeneChildren, and handles genes whose children are CDS (no transcript-level record). refs #20215
  • lines changed 12, context: html, text, full: html, text
    ec41c945d901177092a81b1a7fbd8b51aa789685 Mon Mar 12 11:45:32 2018 -0700
    add the warnOnly option refs #20215
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    a7a1e38478582671487e3e3da3a3994a6c85d0fa Mon Mar 12 18:33:57 2018 -0700
    add Angie.s pslFixCdsJoinGap to the fake.psl construction refs #21048
• src/hg/utils/automation/nBedToEnds.pl
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    bdf12f0280bcc80caaef1b11084d7990f9c4f939 Mon Mar 12 12:02:53 2018 -0700
    adding an endSize argument refs #16028
• src/hg/utils/automation/verifyBrowser.pl
  • lines changed 149, context: html, text, full: html, text
    b2deb4896d7748bc6103f63049a3b108078f8aea Thu Mar 15 16:31:43 2018 -0700
    checking browser for required tables to completion no redmine
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    ff73ff3e67ccd5bf94ca8d9993ba945aa584cdb2 Fri Mar 16 08:32:57 2018 -0700
    work in progress no redmine
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    c810fea4c95e63f3e88c9d42c2c6336445108f42 Fri Mar 16 10:56:25 2018 -0700
    tool to verify tables present in a completed browser build no redmine
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    0e907c765b761a338cf93f63419790e4311f1434 Fri Mar 16 11:25:09 2018 -0700
    avoid chain/net self no redmine
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    0e44733bd33b3ed5ed905e114d2027f9259b5f7a Mon Mar 19 10:08:19 2018 -0700
    expand optional list to include Ensembl gene tables no redmine
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    baed67b5aa7f67279b04e4cf2e33cafd2268f10d Mon Mar 12 15:46:09 2018 -0700
    Adding obscure util pslFixCdsJoinGap, to correct the output of genePredToFakePsl for transcripts with +1 ribosomal frameshift. genePred exons skip over a base to maintain frame; genePredToFakePsl sees a 1-base gap on target, 0-base gap on query. However, the query base is skipped as described in Genbank CDS strings such as "join(168..260,262..741)". Use CDS strings to recognize these cases, and if the PSL has a 1-sided gap on target at the exact position of the skipped base then make the gap 2-sided to avoid making the alignment off-by-1 after that point and becoming a swamp of mismatches. The ideal solution would be to remove the gap and properly interpret join CDS in the rest of our software, but this will at least prevent totally incorrect genePred-derived PSL for transcripts with +1 ribosomal frameshift for now. refs #21048
• src/hg/utils/phyloTrees/219.nh
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    e5a07ad4b344498ffcfe31363420979b3a5f2692 Mon Mar 19 09:53:15 2018 -0700
    adding casCan1 beaver taxId 51338 refs #21116
• src/hg/utils/pslFixCdsJoinGap/makefile
  • lines changed 3, context: html, text, full: html, text
    baed67b5aa7f67279b04e4cf2e33cafd2268f10d Mon Mar 12 15:46:09 2018 -0700
    Adding obscure util pslFixCdsJoinGap, to correct the output of genePredToFakePsl for transcripts with +1 ribosomal frameshift. genePred exons skip over a base to maintain frame; genePredToFakePsl sees a 1-base gap on target, 0-base gap on query. However, the query base is skipped as described in Genbank CDS strings such as "join(168..260,262..741)". Use CDS strings to recognize these cases, and if the PSL has a 1-sided gap on target at the exact position of the skipped base then make the gap 2-sided to avoid making the alignment off-by-1 after that point and becoming a swamp of mismatches. The ideal solution would be to remove the gap and properly interpret join CDS in the rest of our software, but this will at least prevent totally incorrect genePred-derived PSL for transcripts with +1 ribosomal frameshift for now. refs #21048
• src/hg/utils/pslFixCdsJoinGap/pslFixCdsJoinGap.c
  • lines changed 138, context: html, text, full: html, text
    baed67b5aa7f67279b04e4cf2e33cafd2268f10d Mon Mar 12 15:46:09 2018 -0700
    Adding obscure util pslFixCdsJoinGap, to correct the output of genePredToFakePsl for transcripts with +1 ribosomal frameshift. genePred exons skip over a base to maintain frame; genePredToFakePsl sees a 1-base gap on target, 0-base gap on query. However, the query base is skipped as described in Genbank CDS strings such as "join(168..260,262..741)". Use CDS strings to recognize these cases, and if the PSL has a 1-sided gap on target at the exact position of the skipped base then make the gap 2-sided to avoid making the alignment off-by-1 after that point and becoming a swamp of mismatches. The ideal solution would be to remove the gap and properly interpret join CDS in the rest of our software, but this will at least prevent totally incorrect genePred-derived PSL for transcripts with +1 ribosomal frameshift for now. refs #21048
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    454e33bd121d0b0d5c8a714b793b6b1d060a1e56 Tue Mar 13 09:18:45 2018 -0700
    Oops, forgot to update qNumInsert and qBaseInsert columns when adding the q gap. Thanks Chris L! refs #20215 #21048
• src/inc/common.h
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    3fd4131517e0d224eb271e312c9fda6419e1872d Tue Mar 13 15:51:59 2018 -0700
    1. Add support for spectrum setting. 2. Allow dot for empty field. 3. Show multiple items on details page if they overlap. 4. Some cleanup of map boxes. refs #17512
• src/inc/jsonParse.h
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    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/inc/jsonWrite.h
  • lines changed 2, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/lib/common.c
  • lines changed 6, context: html, text, full: html, text
    3fd4131517e0d224eb271e312c9fda6419e1872d Tue Mar 13 15:51:59 2018 -0700
    1. Add support for spectrum setting. 2. Allow dot for empty field. 3. Show multiple items on details page if they overlap. 4. Some cleanup of map boxes. refs #17512
• src/lib/jsonParse.c
  • lines changed 40, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/lib/jsonWrite.c
  • lines changed 13, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/tagStorm/tagSchemaToJson/tagSchemaToJson.c
  • lines changed 1, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/tagStorm/tagStormToJson/tagStormToJson.c
  • lines changed 1, context: html, text, full: html, text
    1ee99ce653ae839e4774120c3f3923dc129c8533 Fri Mar 16 14:41:14 2018 -0700
    Moved jsonStringEscape inside jsonWriteString because it's silly to have to remember to call it first every time. tagStorm programs were doing their own limited escaping (double-quotes only); now they get the same escaping as everywhere else. refs MLQ #21113
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    d0a925fb48864a96943414f9014e3199ee2d74e1 Mon Mar 19 10:11:40 2018 -0700
    v363 preview2 refs #21106
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    1def790bb3c8df0ac48cf465da1ccec2874fcd17 Tue Mar 13 19:52:52 2018 -0700
    adding genome-euro to the push commands for hgdownload pushes refs #20999
• src/utils/qa/weeklybld/doZip.csh
  • lines changed 3, context: html, text, full: html, text
    1def790bb3c8df0ac48cf465da1ccec2874fcd17 Tue Mar 13 19:52:52 2018 -0700
    adding genome-euro to the push commands for hgdownload pushes refs #20999
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 5, context: html, text, full: html, text
    1def790bb3c8df0ac48cf465da1ccec2874fcd17 Tue Mar 13 19:52:52 2018 -0700
    adding genome-euro to the push commands for hgdownload pushes refs #20999
• src/utils/qa/weeklybld/userApps.sh
  • lines changed 11, context: html, text, full: html, text
    1def790bb3c8df0ac48cf465da1ccec2874fcd17 Tue Mar 13 19:52:52 2018 -0700
    adding genome-euro to the push commands for hgdownload pushes refs #20999

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• files changed: 109