All File Changes

v360_base to v361_preview (2018-01-22 to 2018-01-29) v361

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1b4e4c4e1ae303ef3ed233746fd153a30c9f896a Sun Jan 28 01:11:34 2018 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1b4e4c4e1ae303ef3ed233746fd153a30c9f896a Sun Jan 28 01:11:34 2018 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    1b4e4c4e1ae303ef3ed233746fd153a30c9f896a Sun Jan 28 01:11:34 2018 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/autoSql/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/autoSql/tests/testSymCols.c
  • lines changed 1, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/bioImage/bioImageLoad/bioImageLoad.c
  • lines changed 26, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 3, context: html, text, full: html, text
    adc1d88ffc7851fd45b13c2fe8f78ac091634a87 Mon Jan 29 02:22:42 2018 -0800
    Cleaning up sql for safer usage to avoid injection.
• src/hg/cirm/cdw/cdwRunOnIds/cdwRunOnIds.c
  • lines changed 2, context: html, text, full: html, text
    adc1d88ffc7851fd45b13c2fe8f78ac091634a87 Mon Jan 29 02:22:42 2018 -0800
    Cleaning up sql for safer usage to avoid injection.
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 6, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
  • lines changed 3, context: html, text, full: html, text
    adc1d88ffc7851fd45b13c2fe8f78ac091634a87 Mon Jan 29 02:22:42 2018 -0800
    Cleaning up sql for safer usage to avoid injection.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 11, context: html, text, full: html, text
    adc1d88ffc7851fd45b13c2fe8f78ac091634a87 Mon Jan 29 02:22:42 2018 -0800
    Cleaning up sql for safer usage to avoid injection.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 26, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 3, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 26, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/gisaid/gisaidTable/gisaidSubjInfo.c
  • lines changed 9, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/gisaid/gisaidTable/gisaidTable.c
  • lines changed 5, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/gsid/gsidMember/gsidMember.c
  • lines changed 1, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/gsid/gsidTable/gsidSubjInfo.c
  • lines changed 9, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/hgCollection/hgCollection.c
  • lines changed 77, context: html, text, full: html, text
    4b8ba2cfec3666d658121a82d297c1e07fcf629b Tue Jan 23 15:11:36 2018 -0800
    ongoing work on hgCollection
  • lines changed 22, context: html, text, full: html, text
    106e8022559428926af59dde22e697ca3d96ddce Sat Jan 27 09:41:18 2018 -0800
    ongoing work on hgCollection
• src/hg/hgLogin/hgLogin.c
  • lines changed 49, context: html, text, full: html, text
    3002a680b61eb4446e965da8e6f09a530ea9e3d6 Fri Jan 26 16:20:56 2018 -0800
    allow a second (recovery) email address on hgLogin, refs #20888
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    4b8ba2cfec3666d658121a82d297c1e07fcf629b Tue Jan 23 15:11:36 2018 -0800
    ongoing work on hgCollection
• src/hg/hgVai/hgVai.c
  • lines changed 5, context: html, text, full: html, text
    f0aa2132b515869f610cef5a880789875eb2c3e0 Sat Jan 27 10:36:42 2018 -0800
    Minor inefficiency when generating VCF from dbSNP IDs: refAl is trimmed from "-" to "", so when altAl "-" was compared to refAl it differed, causing the reference allele to appear redundantly in the alt alleles column. So trim altAl "-" to "" before comparing for consistency.
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/htdocs/goldenPath/help/hgCollectionHelp.html
  • lines changed 43, context: html, text, full: html, text
    59e4d559d079e8b3a1ea23b8dd864193906ce3a6 Sun Jan 28 15:16:15 2018 -0800
    some hgCollection doc that is more accurate
  • lines changed 5, context: html, text, full: html, text
    2691eecdd8bcd7819218ce0f1c62ecc7c4ef4612 Sun Jan 28 17:30:40 2018 -0800
    hgCollection tweaks
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 1, context: html, text, full: html, text
    855bc8c629b424f92a9aa271e716a800aa2ffccf Tue Jan 23 15:04:24 2018 -0800
    documenting uuid dependency, now also comitting the html version of mirrorManual.txt
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 3, context: html, text, full: html, text
    855bc8c629b424f92a9aa271e716a800aa2ffccf Tue Jan 23 15:04:24 2018 -0800
    documenting uuid dependency, now also comitting the html version of mirrorManual.txt
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 2, context: html, text, full: html, text
    2dd8a7c76222be274a2f9f2308c232da0d011c54 Wed Jan 24 17:04:13 2018 -0800
    Adding port number to mysql command example, refs #20874
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 24, context: html, text, full: html, text
    4b8ba2cfec3666d658121a82d297c1e07fcf629b Tue Jan 23 15:11:36 2018 -0800
    ongoing work on hgCollection
  • lines changed 25, context: html, text, full: html, text
    106e8022559428926af59dde22e697ca3d96ddce Sat Jan 27 09:41:18 2018 -0800
    ongoing work on hgCollection
  • lines changed 1, context: html, text, full: html, text
    2691eecdd8bcd7819218ce0f1c62ecc7c4ef4612 Sun Jan 28 17:30:40 2018 -0800
    hgCollection tweaks
• src/hg/htdocs/style/HGStyle.css
  • lines changed 12, context: html, text, full: html, text
    d29cbd245e572e71bfd24136e921b7ed2b4cf9d3 Sun Jan 28 23:34:29 2018 -0800
    Moving sort arrows to the left of each heading, refs #20841
• src/hg/htdocs/training/index.html
  • lines changed 44, context: html, text, full: html, text
    6bad77744a38fd22a76bd7428ddc79e9e84bf976 Thu Jan 25 14:22:00 2018 -0800
    dropping SDiego workshops, adding ESHG Milan
• src/hg/inc/annoStreamDbPslPlus.h
  • lines changed 24, context: html, text, full: html, text
    d0f46600984eb50b3ede404e5fa240093c68ce68 Thu Sep 28 10:10:57 2017 -0700
    annoStreamDbPslPlus: join the appropriate tables for either refGene or ncbiRefSeq* to get PSL+CDS+seq info. Still need to implement the right-join support in annoStreamDb!
• src/hg/inc/gpFx.h
  • lines changed 19, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/inc/jksql.h
  • lines changed 12, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/inc/joiner.h
  • lines changed 9, context: html, text, full: html, text
    78fd01e7d81e12b132a1a9d2238015c67e25475f Thu Sep 28 10:02:48 2017 -0700
    Added option to structure joinerPair routeList as a tree using joinerPairListToTree() and new child pointer, so that if one pair's b is the same table as another pair's a, the second pair becomes the child of the first pair. This enables us to generate more efficient SQL joins.
• src/hg/inc/soTerm.h
  • lines changed 2, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/inc/variantProjector.h
  • lines changed 17, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/js/hgCollection.js
  • lines changed 16, context: html, text, full: html, text
    4b8ba2cfec3666d658121a82d297c1e07fcf629b Tue Jan 23 15:11:36 2018 -0800
    ongoing work on hgCollection
  • lines changed 97, context: html, text, full: html, text
    106e8022559428926af59dde22e697ca3d96ddce Sat Jan 27 09:41:18 2018 -0800
    ongoing work on hgCollection
• src/hg/js/utils.js
  • lines changed 11, context: html, text, full: html, text
    106e8022559428926af59dde22e697ca3d96ddce Sat Jan 27 09:41:18 2018 -0800
    ongoing work on hgCollection
• src/hg/lib/annoFormatVep.c
  • lines changed 90, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 314, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/annoStreamDb.c
  • lines changed 6, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
  • lines changed 38, context: html, text, full: html, text
    c54488382199f754b2226109da2995eb16dff19b Thu Sep 28 10:06:31 2017 -0700
    Call joinerPairListToTree on sqlRouteList and use tree structure to make more efficient joins. Also use 'full' keyword to do joins instead of left joins (more efficient).
  • lines changed 25, context: html, text, full: html, text
    869708731727a455813ab88e67d46be978ab77b0 Fri Jan 12 14:48:37 2018 -0800
    Added new config parameters rightJoinDtf and rightJoinMainField to give the option of limiting rows to those that join with some other table. The motivation for this is wanting to get only the rows of ncbiRefSeqPsl that join with ncbiRefSeqCurated.
• src/hg/lib/annoStreamDbPslPlus.c
  • lines changed 185, context: html, text, full: html, text
    d0f46600984eb50b3ede404e5fa240093c68ce68 Thu Sep 28 10:10:57 2017 -0700
    annoStreamDbPslPlus: join the appropriate tables for either refGene or ncbiRefSeq* to get PSL+CDS+seq info. Still need to implement the right-join support in annoStreamDb!
  • lines changed 3, context: html, text, full: html, text
    dd285f81141e45dabf1caf0f90723810f2c6f8a1 Fri Jan 12 14:50:04 2018 -0800
    Use the new annoStreamDb params rightJoinDtf and rightJoinMainField to restrict ncbiRefSeqPsl rows to only those that appear in the selected genePred table (e.g. ncbiRefSeqCurated).
• src/hg/lib/facetField.c
  • lines changed 4, context: html, text, full: html, text
    a3b2294493e8cd9cd4721072fcd3f3919b482ec6 Mon Jan 29 01:44:07 2018 -0800
    making safer sql query strings.
• src/hg/lib/gpFx.c
  • lines changed 82, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/hAnno.c
  • lines changed 14, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/hgFind.c
  • lines changed 2, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/lib/hgHgvs.c
  • lines changed 14, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/hui.c
  • lines changed 14, context: html, text, full: html, text
    4b8ba2cfec3666d658121a82d297c1e07fcf629b Tue Jan 23 15:11:36 2018 -0800
    ongoing work on hgCollection
• src/hg/lib/jksql.c
  • lines changed 16, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/lib/joiner.c
  • lines changed 58, context: html, text, full: html, text
    78fd01e7d81e12b132a1a9d2238015c67e25475f Thu Sep 28 10:02:48 2017 -0700
    Added option to structure joinerPair routeList as a tree using joinerPairListToTree() and new child pointer, so that if one pair's b is the same table as another pair's a, the second pair becomes the child of the first pair. This enables us to generate more efficient SQL joins.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    d0f46600984eb50b3ede404e5fa240093c68ce68 Thu Sep 28 10:10:57 2017 -0700
    annoStreamDbPslPlus: join the appropriate tables for either refGene or ncbiRefSeq* to get PSL+CDS+seq info. Still need to implement the right-join support in annoStreamDb!
• src/hg/lib/soTerm.c
  • lines changed 2, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/spDb.c
  • lines changed 1, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 36, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt
  • lines changed 8, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/tests/sqlCheck.c
  • lines changed 2, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/lib/variant.c
  • lines changed 49, context: html, text, full: html, text
    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/variantProjector.c
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    380a1b308bd3bb4f4e52d89ef9e1ccb962892bab Tue Oct 3 14:10:37 2017 -0700
    Major changes to annoGratorGpVar, annoFormatVep and gpFx.c with the addition of functional effect prediction to variantProjector using PSL+CDS from annoStreamDbPslPlus, which enables accurate predictions even when the genome and transcript have indel differences. struct gpFx includes new members exonCount, txRef and txAlt so that gpFx and variantProjector can compute those and send them forward to annoFormatVep, instead of annoFormatVep computing them assuming that genome and transcript match perfectly. annoGratorGpVar passes forward the new gpFx members in output columns and, when input is PSL+CDS instead of genePred, uses variantProjector instead of gpFx to do functional predictions.
• src/hg/lib/visiGene.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/makeDb/genbank/etc/align.dbs
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    82d73c2c6e4b20647907695429977ed3b8a0c2af Thu Jan 25 09:07:43 2018 -0800
    adding petMar3 to the update alignments refs #20819
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    82d73c2c6e4b20647907695429977ed3b8a0c2af Thu Jan 25 09:07:43 2018 -0800
    adding petMar3 to the update alignments refs #20819
• src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/makeDb/genbank/src/lib/gbSql.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/makeDb/schema/all.joiner
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    589a3d046558e3241a68aef952ca45c85cc83437 Thu Jan 25 09:30:03 2018 -0800
    adding rules for petMar3 refs #20819
• src/hg/makeDb/schema/joinerRoute/joinerRoute.c
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    a842f599b275e1b92a826ce0c6812711a646eef3 Thu Sep 28 10:13:25 2017 -0700
    joinerRoute: util to display the paths that joinerFindRouteThroughAll finds to join a list of tables. Sometimes it's not what you'd expect and you may want to tweak all.joiner.
• src/hg/makeDb/schema/joinerRoute/makefile
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    a842f599b275e1b92a826ce0c6812711a646eef3 Thu Sep 28 10:13:25 2017 -0700
    joinerRoute: util to display the paths that joinerFindRouteThroughAll finds to join a list of tables. Sometimes it's not what you'd expect and you may want to tweak all.joiner.
• src/hg/makeDb/trackDb/blastHg18KG.html
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    02df6896714390d5c118357c94c60bf4b2d2f9be Thu Jan 25 14:51:26 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/blatFugu.html
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    d33573b77dda431383fb63411682c6c3f8e41b3c Mon Jan 22 12:05:31 2018 -0800
    Fixing broken links for dm1, no Redmine.
• src/hg/makeDb/trackDb/cgapSage.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/chainNet.html
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    193503db3f8e682b6c33840fa9ecd04f6575fcb5 Fri Jan 26 09:01:13 2018 -0800
    Fixing broken links for monDom5, no Redmine.
• src/hg/makeDb/trackDb/contrastGene.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/makeDb/trackDb/cpgIslandSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm1/anophelesEcores.html
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    d33573b77dda431383fb63411682c6c3f8e41b3c Mon Jan 22 12:05:31 2018 -0800
    Fixing broken links for dm1, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm1/flyreg.html
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    d33573b77dda431383fb63411682c6c3f8e41b3c Mon Jan 22 12:05:31 2018 -0800
    Fixing broken links for dm1, no Redmine.
• src/hg/makeDb/trackDb/drosophila/dm1/pscreen.html
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    d33573b77dda431383fb63411682c6c3f8e41b3c Mon Jan 22 12:05:31 2018 -0800
    Fixing broken links for dm1, no Redmine.
• src/hg/makeDb/trackDb/drosophila/mzDy1Dp2Ag1_phast.html
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    d33573b77dda431383fb63411682c6c3f8e41b3c Mon Jan 22 12:05:31 2018 -0800
    Fixing broken links for dm1, no Redmine.
• src/hg/makeDb/trackDb/fosEndPairs.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/genscan.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/HInvGeneMrna.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/affyU133Plus2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/darned.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/decodeRmap.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/eioJcviNAS.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/encodeRegions.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/evofold.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/gad.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hapmapSnps.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/acembly.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/affyExonArray.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/allHg19RS_BW.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/burgeRnaSeqGemMapperAlign.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/consIndelsHgMmCanFam.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/crispr.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/dhcBamDenisova.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/dhcHumDerDenAnc.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/dhcVcfModern.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/evsEsp6500.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/exac.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/genomicSuperDups.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/gwipsvizRiboseq.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/hinv70Composite.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/lincRNAs.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/targetScanS.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/tfbsConsSites.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3Accessibility.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/uMassBrainHistone.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli5.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/vegaGeneComposite.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release4.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDNAseSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDnaMethylSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeExonArraySuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV24lift37.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeHistoneSuper.html
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClusteredV3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSeqSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.patch.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release4.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hg19/wgRna.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hgIkmc.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hgdpGeo.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/hgmd.html
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    0018c7cce9eb36ad49b7502e88cd6c757539c26b Mon Jan 22 10:57:02 2018 -0800
    Updating hgmd reference to more recent version, refs #15536
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/hiSeqDepth.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/iscaComposite.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/laminB1Super.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/lovd.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/ntHumChimpCodingDiff.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/ntOoaHaplo.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/ntSssTop5p.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/ntSssZScorePMVar.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/numtSeq.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/omimGene2.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/omimLocation.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/phastBias.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/polyA.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/rgdQtl.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/snp141.shared.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/snp142.shared.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/snp144.shared.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/snp146.shared.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/snp147.shared.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/snp150.shared.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/human/vistaEnhancers.html
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• src/hg/makeDb/trackDb/jaxQtlMapped.html
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• src/hg/makeDb/trackDb/nestedRepeats.html
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    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/ntSeqReads.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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    193503db3f8e682b6c33840fa9ecd04f6575fcb5 Fri Jan 26 09:01:13 2018 -0800
    Fixing broken links for monDom5, no Redmine.
• src/hg/makeDb/trackDb/recombRate.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
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• src/hg/makeDb/trackDb/rgdRatQtl.html
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    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/rmsk.html
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    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/tRNAs.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
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    99b28beeb1d3a1edd69d53c952d26ade867e0b33 Thu Jan 25 14:46:48 2018 -0800
    Fixing broken links found by the broken link report, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndPairs.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndSingles.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/ctgPos2.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/gold.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/danRer4/rhMap.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/makeDb/trackDb/zebrafish/vegaGeneZfish.html
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    2afd38725a11a00b29f6b23053054d629662ff34 Tue Jan 23 10:08:26 2018 -0800
    Fixing broken links for danRer4, no Redmine.
• src/hg/oneShot/galtFixUtf8Chars/README
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    14f4d515795bfc338d059ad87a58c9ad9d6fbbee Wed Jan 24 16:09:23 2018 -0800
    Utility to convert utf8 chars to latin1. Not currently in use.
• src/hg/oneShot/galtFixUtf8Chars/galtFixUtf8Chars.c
  • lines changed 424, context: html, text, full: html, text
    14f4d515795bfc338d059ad87a58c9ad9d6fbbee Wed Jan 24 16:09:23 2018 -0800
    Utility to convert utf8 chars to latin1. Not currently in use.
• src/hg/oneShot/galtFixUtf8Chars/makefile
  • lines changed 3, context: html, text, full: html, text
    14f4d515795bfc338d059ad87a58c9ad9d6fbbee Wed Jan 24 16:09:23 2018 -0800
    Utility to convert utf8 chars to latin1. Not currently in use.
• src/hg/oneShot/galtFixUtf8Chars/userName.log
  • lines changed 588, context: html, text, full: html, text
    14f4d515795bfc338d059ad87a58c9ad9d6fbbee Wed Jan 24 16:09:23 2018 -0800
    Utility to convert utf8 chars to latin1. Not currently in use.
• src/hg/oneShot/galtFixUtf8Chars/utf8.text
  • lines changed 128, context: html, text, full: html, text
    14f4d515795bfc338d059ad87a58c9ad9d6fbbee Wed Jan 24 16:09:23 2018 -0800
    Utility to convert utf8 chars to latin1. Not currently in use.
• src/hg/oneShot/galtFixUtf8Chars/win1252.text
  • lines changed 128, context: html, text, full: html, text
    14f4d515795bfc338d059ad87a58c9ad9d6fbbee Wed Jan 24 16:09:23 2018 -0800
    Utility to convert utf8 chars to latin1. Not currently in use.
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 111, context: html, text, full: html, text
    03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800
    do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
  • lines changed 12, context: html, text, full: html, text
    c38255cd365b9742bf47b39954cbd26770bef21f Thu Jan 25 17:29:09 2018 -0800
    changed handling of previous change NCBI immuno segments to just discard the gene-level CDS, as moving them to the transcript level brought out CDS/exon inconsitencies in the NCBI human and mouse files
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.attrs
  • lines changed 77, context: html, text, full: html, text
    03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800
    do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
  • lines changed 194, context: html, text, full: html, text
    c38255cd365b9742bf47b39954cbd26770bef21f Thu Jan 25 17:29:09 2018 -0800
    changed handling of previous change NCBI immuno segments to just discard the gene-level CDS, as moving them to the transcript level brought out CDS/exon inconsitencies in the NCBI human and mouse files
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.gp
  • lines changed 6, context: html, text, full: html, text
    03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800
    do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
  • lines changed 14, context: html, text, full: html, text
    c38255cd365b9742bf47b39954cbd26770bef21f Thu Jan 25 17:29:09 2018 -0800
    changed handling of previous change NCBI immuno segments to just discard the gene-level CDS, as moving them to the transcript level brought out CDS/exon inconsitencies in the NCBI human and mouse files
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.out
  • lines changed 12, context: html, text, full: html, text
    c38255cd365b9742bf47b39954cbd26770bef21f Thu Jan 25 17:29:09 2018 -0800
    changed handling of previous change NCBI immuno segments to just discard the gene-level CDS, as moving them to the transcript level brought out CDS/exon inconsitencies in the NCBI human and mouse files
• src/hg/utils/gff3ToGenePred/tests/input/ncbiSegments.gff3
  • lines changed 35, context: html, text, full: html, text
    03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800
    do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
  • lines changed 89, context: html, text, full: html, text
    c38255cd365b9742bf47b39954cbd26770bef21f Thu Jan 25 17:29:09 2018 -0800
    changed handling of previous change NCBI immuno segments to just discard the gene-level CDS, as moving them to the transcript level brought out CDS/exon inconsitencies in the NCBI human and mouse files
• src/hg/utils/gff3ToGenePred/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800
    do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
  • lines changed 2, context: html, text, full: html, text
    c38255cd365b9742bf47b39954cbd26770bef21f Thu Jan 25 17:29:09 2018 -0800
    changed handling of previous change NCBI immuno segments to just discard the gene-level CDS, as moving them to the transcript level brought out CDS/exon inconsitencies in the NCBI human and mouse files
• src/hg/visiGene/gensat/gensatFixFull/gensatFixFull.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/visiGene/hgVisiGene/visiSearch.c
  • lines changed 7, context: html, text, full: html, text
    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/visiGene/vgChangeContributors/vgChangeContributors.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/visiGene/vgLoadJax/vgLoadJax.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/visiGene/vgProbeTrack/vgProbeTrack.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/visiGene/vgRemoveSubmission/vgRemoveSubmission.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/hg/visiGene/visiGeneLoad/visiGeneLoad.c
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    1f55f129858863d78076fd3818d3841429741121 Mon Jan 29 01:35:45 2018 -0800
    Fixing bug: sqlDyStringAppend() is not safe, and it is not needed. Using sqlDyStringPrintf instead.
• src/inc/gff3.h
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    03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800
    do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
• src/lib/gff3.c
  • lines changed 30, context: html, text, full: html, text
    03d79bf4ff976c1c0f7327d91e8b9d9adc70cefd Tue Jan 23 21:55:36 2018 -0800
    do a better job converting NCBI [CDJV]_gene_segment GFF3 annotations. This avoids split into genePreds. Another evening wasted with bioinformatics file formats
• src/lib/vcf.c
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    675a334117c7a98be59035fdf620ac8ca764fd1e Thu Jan 18 12:11:33 2018 -0800
    isAllNt ignores last base in string so beware; also, isAllNt returns true for "-" (translates it to 'n') but that means the empty string so exclude it from base-trimming.
  • lines changed 21, context: html, text, full: html, text
    e38dd775f9552b3d050b6910c0989be5aba715f1 Fri Jan 19 12:54:23 2018 -0800
    'Variants' with no alternate allele may come in two forms: alt == '.' or alt == ref. In either case, filter down to ref only.
• src/utils/qa/weeklybld/buildEnv.csh
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    02a792711556340c7087f5824188c758f4eb2e4b Mon Jan 29 10:21:45 2018 -0800
    v361 preview1 refs #20889

• lines changed: 5442
• files changed: 251