All File Changes
v365_preview2 to v365_base (2018-04-30 to 2018-05-07) v365
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- src/hg/cirm/cdw/README
- lines changed 6, 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/cdwMakePairedEndQa/cdwMakePairedEndQa.c
- lines changed 75, 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/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
- lines changed 5, context: html, text, full: html, text
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
- lines changed 1, context: html, text, full: html, text
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
- lines changed 6, context: html, text, full: html, text
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
- lines changed 973, context: html, text, full: html, text
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
- lines changed 5, context: html, text, full: html, text
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
- 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
- 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/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
- 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/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
- 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/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
- lines changed 3, context: html, text, full: html, text
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
- lines changed 1, context: html, text, full: html, text
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
- 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/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
- lines changed 4, 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_.
- 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_.
- lines changed 2, context: html, text, full: html, text
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
- lines changed 6, context: html, text, full: html, text
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
- lines changed 6, context: html, text, full: html, text
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
- lines changed 1, context: html, text, full: html, text
ba4364c153babdfd10240d96af82658f83da163f Mon May 7 10:37:31 2018 -0700
New version number v365
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
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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- files changed: 63