All File Changes

v365_preview2 to v365_base (2018-04-30 to 2018-05-07) v365

• src/hg/cirm/cdw/README
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    66a10b319053c2c36e8a6764e67ed8d907044e3a Wed May 2 17:06:39 2018 -0700
    CIRM: adding the daemon startup scripts to the repo, together with my modifications that rsync the genome onto the ramdisk, refs #21391
• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
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    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
  • lines changed 12, context: html, text, full: html, text
    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 2, context: html, text, full: html, text
    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 31, context: html, text, full: html, text
    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/restartDaemons/cirm01-restartDaemons
  • lines changed 11, context: html, text, full: html, text
    66a10b319053c2c36e8a6764e67ed8d907044e3a Wed May 2 17:06:39 2018 -0700
    CIRM: adding the daemon startup scripts to the repo, together with my modifications that rsync the genome onto the ramdisk, refs #21391
• src/hg/cirm/cdw/restartDaemons/hgwdev-restartDaemons
  • lines changed 16, context: html, text, full: html, text
    66a10b319053c2c36e8a6764e67ed8d907044e3a Wed May 2 17:06:39 2018 -0700
    CIRM: adding the daemon startup scripts to the repo, together with my modifications that rsync the genome onto the ramdisk, refs #21391
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 26, context: html, text, full: html, text
    031adb2c7dea4c4b45e8a440b7e040b8738590c6 Thu May 3 12:58:27 2018 -0700
    Announcing the GENCODE V28 annotation release for hg19 and hg38. refs #21299 and #21266
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    bd1a670e7c90cf8b1209e0ebeddd6437df2e7006 Thu May 3 14:14:54 2018 -0700
    Making a small edit the the GENCODE V28 news announcement, no Redmine.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 56, context: html, text, full: html, text
    2e442a42970561ee964f41a7a192f2e7c7ae8ea5 Thu May 3 09:41:05 2018 -0700
    new pubs from progress report
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    031adb2c7dea4c4b45e8a440b7e040b8738590c6 Thu May 3 12:58:27 2018 -0700
    Announcing the GENCODE V28 annotation release for hg19 and hg38. refs #21299 and #21266
• src/hg/htdocs/training/index.html
  • lines changed 30, context: html, text, full: html, text
    71ebc8c102a450e4044ee4b13021ccd476c59430 Mon Apr 30 21:05:14 2018 -0700
    removed RNA-seq, Leuven, added HNGRI, Novartis workshops
• src/hg/inc/versionInfo.h
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    ba4364c153babdfd10240d96af82658f83da163f Mon May 7 10:37:31 2018 -0700
    New version number v365
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    66793150423c86143303a2322e0453ef4dd55359 Mon May 7 08:59:50 2018 -0700
    Fix for IE not supporting String.startsWith, refs #21196
• src/hg/lib/trackDbCustom.c
  • lines changed 4, context: html, text, full: html, text
    7d50cb16e1ab201dfaead9f47d63fb3636ae5020 Wed May 2 14:41:09 2018 -0700
    Replacing an assert that caused blank page with an errAbort message linking to trackDb doc. refs #21386
• src/hg/makeDb/doc/go.txt
  • lines changed 39, context: html, text, full: html, text
    b25042c6de3edc4ffd47bba0df029351242f682a Fri May 4 15:20:48 2018 -0700
    final knownGene changes.
• src/hg/makeDb/doc/hg19.txt
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    8f464f40e845042a1eb41457ef63ae95add33a7d Tue May 1 19:03:41 2018 -0700
    fixed bug building wgEncodeGencodeEntrezGeneV28lift37 #21299
  • lines changed 81, context: html, text, full: html, text
    97fd0abb1650feea6e15f5ca7c4bcb2c8d5bfca9 Thu May 3 07:19:29 2018 -0700
    lastz chainNet to panPan2 per user request refs #21358
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 27, context: html, text, full: html, text
    4b93818730b7a3747465cba6d223ac79aa3ab94a Fri May 4 14:39:18 2018 -0700
    start of update for rmskJoined track, refs #18273
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 89, context: html, text, full: html, text
    78fee663a12b57c8dc3ada9eb9528deab55d5716 Tue May 1 07:23:18 2018 -0700
    oviAri4/hg38 chain/net done, refs #17247
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 23, context: html, text, full: html, text
    5e862a2effa06b00553ed47137aacf0943611746 Mon Apr 30 13:52:03 2018 -0700
    Done with oviAri3 to oviAri4, refs #17247
• src/hg/makeDb/doc/oviAri4/initialBuild.txt
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    3fe991acf3aa086d255e910c6d4ba7b8a82d49b5 Thu May 3 13:31:18 2018 -0700
    oviAri4 ready for QA, refs #17247
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes17.csh
  • lines changed 46, context: html, text, full: html, text
    b25042c6de3edc4ffd47bba0df029351242f682a Fri May 4 15:20:48 2018 -0700
    final knownGene changes.
• src/hg/makeDb/hgKgGetText/hgKgGetText.c
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    b25042c6de3edc4ffd47bba0df029351242f682a Fri May 4 15:20:48 2018 -0700
    final knownGene changes.
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 1, context: html, text, full: html, text
    8f464f40e845042a1eb41457ef63ae95add33a7d Tue May 1 19:03:41 2018 -0700
    fixed bug building wgEncodeGencodeEntrezGeneV28lift37 #21299
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    f41f09f252d3e21aa478799b0fe74ebb5480c9fb Fri May 4 15:00:52 2018 -0700
    losen requirements for matches of knownGene to ucscRetroInfo6
• src/hg/makeDb/trackDb/blastHg16KG.html
  • lines changed 1, context: html, text, full: html, text
    06217c715454d91fa9271f4c8644f44ed2a26a8d Thu May 3 13:17:21 2018 -0700
    Updating redirected links for ci1, uiLinks cronjob.
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 8, context: html, text, full: html, text
    db54508a9cc19b08e4eaef5e054d6f44a8d09008 Tue May 1 10:15:20 2018 -0700
    Updating redirected links for felCat4, uiLinks cronjob.
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 7, context: html, text, full: html, text
    ac3e1d2b6e2bcb58d921561589199e234752208a Tue May 1 10:32:56 2018 -0700
    Updating redirected links for bosTau4, uiLinks cronjob.
• src/hg/makeDb/trackDb/cow/bosTau4/nscanGene.html
  • lines changed 4, context: html, text, full: html, text
    ac3e1d2b6e2bcb58d921561589199e234752208a Tue May 1 10:32:56 2018 -0700
    Updating redirected links for bosTau4, uiLinks cronjob.
• src/hg/makeDb/trackDb/cow/bosTau4/phastConsElements5way.html
  • lines changed 5, context: html, text, full: html, text
    ac3e1d2b6e2bcb58d921561589199e234752208a Tue May 1 10:32:56 2018 -0700
    Updating redirected links for bosTau4, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 8, context: html, text, full: html, text
    d1b0514c2d2685cbd6cae549f8365482af3184ab Tue May 1 11:07:31 2018 -0700
    tweaking oviAri4 chainNet definitions refs #17247
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    e861279221fda6033b6a2a0aa0d5d9fc3422d5fe Wed May 2 10:23:40 2018 -0700
    Adding beta release tags for the GENCODE V28 release for hg38 and hg19, refs #21266 and #21299
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    b8acf1f4f9601e579622dd85a951ef513aa06515 Wed May 2 12:43:12 2018 -0700
    Removing alpha,beta tags now that the track is on hgwbeta-public, refs #21266 and #21299
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    82e5f4b859a69478e522ca0e135f27de4415408f Thu May 3 14:17:26 2018 -0700
    Adding the 'Updated' pennantIcon for the GENCODE V28 release for hg38 and hg19, refs #21266 and #21299.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV28lift37.ra
  • lines changed 1, context: html, text, full: html, text
    70bc2fb35cf9a8a2bf193f581c8d1505d49e17f9 Wed May 2 12:54:31 2018 -0700
    Hiding the new lifted GENCODE V28 tracks for hg19 by default, refs #21299
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    82e5f4b859a69478e522ca0e135f27de4415408f Thu May 3 14:17:26 2018 -0700
    Adding the 'Updated' pennantIcon for the GENCODE V28 release for hg38 and hg19, refs #21266 and #21299.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    e861279221fda6033b6a2a0aa0d5d9fc3422d5fe Wed May 2 10:23:40 2018 -0700
    Adding beta release tags for the GENCODE V28 release for hg38 and hg19, refs #21266 and #21299
  • lines changed 1, context: html, text, full: html, text
    b8acf1f4f9601e579622dd85a951ef513aa06515 Wed May 2 12:43:12 2018 -0700
    Removing alpha,beta tags now that the track is on hgwbeta-public, refs #21266 and #21299
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    82e5f4b859a69478e522ca0e135f27de4415408f Thu May 3 14:17:26 2018 -0700
    Adding the 'Updated' pennantIcon for the GENCODE V28 release for hg38 and hg19, refs #21266 and #21299.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV28.ra
  • lines changed 1, context: html, text, full: html, text
    82e5f4b859a69478e522ca0e135f27de4415408f Thu May 3 14:17:26 2018 -0700
    Adding the 'Updated' pennantIcon for the GENCODE V28 release for hg38 and hg19, refs #21266 and #21299.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    912d19305d35c621b06ec6a8994ffb03c36105f0 Wed May 2 17:14:37 2018 -0700
    tweaking phegeni tdb, refs #21052
• src/hg/makeDb/trackDb/mouse/mm10/knownGeneOld9.html
  • lines changed 22, context: html, text, full: html, text
    b25042c6de3edc4ffd47bba0df029351242f682a Fri May 4 15:20:48 2018 -0700
    final knownGene changes.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    d1b0514c2d2685cbd6cae549f8365482af3184ab Tue May 1 11:07:31 2018 -0700
    tweaking oviAri4 chainNet definitions refs #17247
• src/hg/makeDb/trackDb/nestedRepeats.html
  • lines changed 2, context: html, text, full: html, text
    478a356a31e8537d682ee0b821f5c64a9eb295b3 Fri May 4 09:09:08 2018 -0700
    Updating redirected links for melGal1, uiLinks cronjob.
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    2d9c14af4e401dd1340f82c67e095ebb99543d5e Tue May 1 09:04:35 2018 -0700
    Removing a New trackDb icon to a blog post about the New NCBI RefSeq tracks. RM To Do #21242
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    06d128b093e205b5229a60635d98bc0486c8b2bb Wed May 2 09:11:18 2018 -0700
    Updating redirected links for xenTro2, uiLinks cronjob.
• src/hg/makeDb/trackDb/squirt/ci1/blatCioSav1.html
  • lines changed 1, context: html, text, full: html, text
    06217c715454d91fa9271f4c8644f44ed2a26a8d Thu May 3 13:17:21 2018 -0700
    Updating redirected links for ci1, uiLinks cronjob.
• src/hg/makeDb/trackDb/squirt/ci1/jgiGene.html
  • lines changed 4, context: html, text, full: html, text
    06217c715454d91fa9271f4c8644f44ed2a26a8d Thu May 3 13:17:21 2018 -0700
    Updating redirected links for ci1, uiLinks cronjob.
• src/hg/makeDb/trackDb/squirt/ci1/snapGene.html
  • lines changed 2, context: html, text, full: html, text
    06217c715454d91fa9271f4c8644f44ed2a26a8d Thu May 3 13:17:21 2018 -0700
    Updating redirected links for ci1, uiLinks cronjob.
• src/hg/makeDb/trackDb/squirt/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    06217c715454d91fa9271f4c8644f44ed2a26a8d Thu May 3 13:17:21 2018 -0700
    Updating redirected links for ci1, uiLinks cronjob.
• src/hg/makeDb/trackDb/squirt/xenoMrna.html
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    06217c715454d91fa9271f4c8644f44ed2a26a8d Thu May 3 13:17:21 2018 -0700
    Updating redirected links for ci1, uiLinks cronjob.
• src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra
  • lines changed 3, context: html, text, full: html, text
    d1b0514c2d2685cbd6cae549f8365482af3184ab Tue May 1 11:07:31 2018 -0700
    tweaking oviAri4 chainNet definitions refs #17247
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
  • lines changed 7, context: html, text, full: html, text
    06d128b093e205b5229a60635d98bc0486c8b2bb Wed May 2 09:11:18 2018 -0700
    Updating redirected links for xenTro2, uiLinks cronjob.
• src/hg/makeDb/trackDb/xenTro/xenTro2/phastConsElements7way.html
  • lines changed 5, context: html, text, full: html, text
    06d128b093e205b5229a60635d98bc0486c8b2bb Wed May 2 09:11:18 2018 -0700
    Updating redirected links for xenTro2, uiLinks cronjob.
• src/hg/utils/automation/doNcbiRefSeq.pl
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    9a9e0448c012df593844f2a16c70ca4526d2cf6f Fri Apr 27 09:34:21 2018 -0700
    Changes to gff3ToRefLink.pl to avoid missing occasional protAcc, pseudo, gene_biotype, gene_synonym. * Instead of accumulating tag values as we go, first parse the GFF into a tree and traverse the tree to find the right level of transcripts to output and the tags for those transcripts. Tolerate some kinds of mismatches, gloss over per-transcript-mapping differences, report other mismatches. * Use raFile prt value as a backup in case GFF is missing protein_id because only a non-coding exon(s) of a coding transcript could be mapped to the reference assembly, so no CDS records in the GFF. * Use hash-membership to select which tags to keep and which model organism external database IDs to extract from Dbxref. no redmine - email thread "ncbiRefSeq QA" in which Braney reported missing NP_.
• src/hg/utils/automation/gff3ToRefLink.pl
  • lines changed 511, context: html, text, full: html, text
    9a9e0448c012df593844f2a16c70ca4526d2cf6f Fri Apr 27 09:34:21 2018 -0700
    Changes to gff3ToRefLink.pl to avoid missing occasional protAcc, pseudo, gene_biotype, gene_synonym. * Instead of accumulating tag values as we go, first parse the GFF into a tree and traverse the tree to find the right level of transcripts to output and the tags for those transcripts. Tolerate some kinds of mismatches, gloss over per-transcript-mapping differences, report other mismatches. * Use raFile prt value as a backup in case GFF is missing protein_id because only a non-coding exon(s) of a coding transcript could be mapped to the reference assembly, so no CDS records in the GFF. * Use hash-membership to select which tags to keep and which model organism external database IDs to extract from Dbxref. no redmine - email thread "ncbiRefSeq QA" in which Braney reported missing NP_.
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    f87ac2bb68a10bfb3cb35f929586797d6ffe9cfd Fri May 4 17:29:01 2018 -0700
    Obscure new instances of reused IDs keep cropping up in various species' GFF from NCBI, but not affecting the RefSeq transcripts. warn instead of die.
• src/hg/utils/automation/openStack/startParaHub.sh
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    3116a40b2f1f4220d323c6d8ad766464452dfb9c Fri May 4 10:43:00 2018 -0700
    Add command line argument for ssh key-pair to openstack parasol install scripts, refs #18874
• src/hg/utils/automation/openStack/startParaNode.sh
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    3116a40b2f1f4220d323c6d8ad766464452dfb9c Fri May 4 10:43:00 2018 -0700
    Add command line argument for ssh key-pair to openstack parasol install scripts, refs #18874
• src/inc/srcVersion.h
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    ba4364c153babdfd10240d96af82658f83da163f Mon May 7 10:37:31 2018 -0700
    New version number v365
• src/utils/qa/weeklybld/buildEnv.csh
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    641480fb928deecb7ae7eae06979453e8b0c5cb8 Mon May 7 10:28:21 2018 -0700
    v365 final build refs #21332
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    2ba328b9dcbee56720f4a9c5d883c1797ede912c Mon May 7 10:36:47 2018 -0700
    v365 final build refs #21332

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