All File Changes
v295_base to v296_preview (2014-02-03 to 2014-02-10) v296
- src/hg/encode3/eap/eapAddStep/eapAddStep.c
- lines changed 17, context: html, text, full: html, text
Added replicated peaks steps and removing some debugging uglies.
- src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c
- lines changed 231, context: html, text, full: html, text
Renaming eapAnalysis structure to eapRun and eapAnalysisJson to eapRunAddJson
- src/hg/encode3/eap/eapAnalysisJson/eapRunAddJson.c
- lines changed 231, context: html, text, full: html, text
Renaming eapAnalysis structure to eapRun and eapAnalysisJson to eapRunAddJson
- lines changed 2, context: html, text, full: html, text
Renaming analysisId to runId
- lines changed 231, context: html, text, full: html, text
Adding a bunch of missing utils and renaming eapAnalysisJson to eapRunAddJson.
- src/hg/encode3/eap/eapAnalysisJson/makefile
- lines changed 1, context: html, text, full: html, text
Renaming eapAnalysis structure to eapRun and eapAnalysisJson to eapRunAddJson
- lines changed 4, context: html, text, full: html, text
Adding a bunch of missing utils and renaming eapAnalysisJson to eapRunAddJson.
- src/hg/encode3/eap/eapDaemon/eapDaemon.c
- lines changed 4, context: html, text, full: html, text
Coping with change from eapParaQueues constant to eapParaDirs() function call needed as part of separating the ENC/TST/DEV versions of the parasol dirs.
- src/hg/encode3/eap/eapFinish/eapFinish.c
- lines changed 7, context: html, text, full: html, text
Renaming eapAnalysis back to eapRun.
- lines changed 2, context: html, text, full: html, text
Renaming analysisId to runId
- lines changed 6, context: html, text, full: html, text
Coping with change from eapParaQueues constant to eapParaDirs() function call needed as part of separating the ENC/TST/DEV versions of the parasol dirs. Minor rejiggering of how tags are transfered from inputs to output including adding the technical_replicate and paired_end field, and making the experiment field robust in the presence of a control input.
- lines changed 8, context: html, text, full: html, text
Moved 'edwUserFOrPipeline' to library, but to eap library.
- src/hg/encode3/eap/eapMonitor/eapMonitor.c
- lines changed 77, context: html, text, full: html, text
Quite a number of changes combined here. Implementing a new column to show the average job length in minutes of a step. Coping with change from eapParaQueues constant to eapParaDirs() function call needed as part of separating the ENC/TST/DEV versions of the parasol dirs. Moving step count from status to lesser used info sub-command.
- lines changed 2, context: html, text, full: html, text
Making it so a command can be 4 chars wider without disrupting spacing.
- src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c
- lines changed 231, context: html, text, full: html, text
Adding a bunch of missing utils and renaming eapAnalysisJson to eapRunAddJson.
- lines changed 78, context: html, text, full: html, text
Reworking it so that inputs (or outputs) of same name get bundled together in JSON list
- lines changed 254, context: html, text, full: html, text
Fairly large scale changes here. It now just produced a json file rather than attaching json to a row in the database. It also generates json for the software and step objects as well as the run object and some versioning objects.
- lines changed 1, context: html, text, full: html, text
Fixing small issue in seconds field of timestamp where it would show :1 instead of the :01 that was wanted.
- src/hg/encode3/eap/eapRunAddJson/makefile
- lines changed 4, context: html, text, full: html, text
Adding a bunch of missing utils and renaming eapAnalysisJson to eapRunAddJson.
- src/hg/encode3/eap/eapSchedule/eapSchedule.c
- lines changed 192, context: html, text, full: html, text
Implementing first cut at wig pooler step that gets called at the replicate matching stage.
- lines changed 148, context: html, text, full: html, text
A lot of new code written to attempt to find the best replicates to use when creating replicated peaks, and also just to run the new program, edwReplicatedPeaks, that does the careful intersection plus data transfer from the individual replicates to the replicated peaks. I think the best-two-replicates code may take some tweaking still. The current logic is to pick the most recent file in either replicate as the file used for that replicate, and then to use enrichments and depth of coverage to pick the best file from all other replicates.
- src/hg/encode3/eap/eapToHub/eapToHub.c
- lines changed 503, context: html, text, full: html, text
This is far from working, but there's enough good work here to be worth protecting under source control.
- lines changed 104, context: html, text, full: html, text
Added a few more fields to the composite track, and starting to generate track stanzas for views and subtracks. Still a ways to go before it generates a working trackDb though!
- src/hg/encode3/eap/fix/eapDepricateUntracked/eapDepricateUntracked.c
- lines changed 104, context: html, text, full: html, text
Worked well enough for something just to make test database prettier....
- src/hg/encode3/eap/fix/eapDepricateUntracked/makefile
- lines changed 4, context: html, text, full: html, text
Worked well enough for something just to make test database prettier....
- src/hg/encode3/eap/hardQueries/notFromMyBam
- lines changed 30, context: html, text, full: html, text
Starting to build collection of queries that take like half an hour to build.
- src/hg/encode3/eap/inc/eapDb.h
- lines changed 40, context: html, text, full: html, text
Changing from eapAnalysis to eapRun.
- src/hg/encode3/eap/inc/eapLib.h
- lines changed 1, context: html, text, full: html, text
Replacing eapParaQueues constant with calls to eapParaDirs(conn).
- lines changed 3, context: html, text, full: html, text
Added function to get email of pipeline daemon. Shortened a number of directories as a weak attempt to improve my carpel tunnel outlook, and also to make it so that can have more files mentioned in a command line without it overflowing parasol limits. The wig pooling command still has one case that overflows though.
- src/hg/encode3/eap/lib/eapDb.as
- lines changed 4, context: html, text, full: html, text
Changing from eapAnalysis to eapRun.
- src/hg/encode3/eap/lib/eapDb.c
- lines changed 49, context: html, text, full: html, text
Changing from eapAnalysis to eapRun.
- src/hg/encode3/eap/lib/eapDb.sql
- lines changed 6, context: html, text, full: html, text
Changing from eapAnalysis to eapRun.
- src/hg/encode3/eap/lib/eapLib.c
- lines changed 17, context: html, text, full: html, text
Replacing eapParaQueues constant with calls to eapParaDirs(conn).
- lines changed 9, context: html, text, full: html, text
Added function to get email of pipeline daemon. Shortened a number of directories as a weak attempt to improve my carpel tunnel outlook, and also to make it so that can have more files mentioned in a command line without it overflowing parasol limits. The wig pooling command still has one case that overflows though.
- src/hg/encode3/eap/makefile
- lines changed 6, context: html, text, full: html, text
Adding a bunch of missing utils and renaming eapAnalysisJson to eapRunAddJson.
- src/hg/encode3/eap/notes/sampleBam/makefile
- lines changed 3, context: html, text, full: html, text
Moving sampleBam from notes to oneShot
- src/hg/encode3/eap/notes/sampleBam/sampleBam.c
- lines changed 109, context: html, text, full: html, text
Moving sampleBam from notes to oneShot
- src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
- lines changed 2, context: html, text, full: html, text
Making program able to deal with things like 'male.hg19' that have crept into the ucscDb field in addition to plain 'hg19'
- src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
- lines changed 17, context: html, text, full: html, text
Moving several routines from edwMakeValidFile to the library where they could be used by others, routines required to generate a license plate name.
- lines changed 1, context: html, text, full: html, text
Coping with edwLicensePlateHead(conn)/edwLicensePlatePrefix change.
- src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
- lines changed 71, context: html, text, full: html, text
Put in a first draft, currently ifdefed out, of routine to mail user when validation finishes. Coping with edwLicensePlateHead(conn)/edwLicensePlatePrefix change.
- src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
- lines changed 3, context: html, text, full: html, text
Coping with edwLicensePlateHead(conn)/edwLicensePlatePrefix change.
- src/hg/encode3/encodeDataWarehouse/fix/edwFixTstToTstff/edwFixTstToTstff.c
- lines changed 82, context: html, text, full: html, text
Good enough for a one shot job.
- src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
- lines changed 16, context: html, text, full: html, text
Moving several routines from edwMakeValidFile to the library where they could be used by others, routines required to generate a license plate name. Added convenience wrapper to get an edwAssembly from it's ID.
- lines changed 9, context: html, text, full: html, text
Added edwSubmitFromId function. Revised edwLicensePlateHead to cope with TST->TSTFF change for Stanford compatibility. Added edwSubmitIsValidated. Improved some comments.
- src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
- lines changed 53, context: html, text, full: html, text
Moving several routines from edwMakeValidFile to the library where they could be used by others, routines required to generate a license plate name. Added convenience wrapper to get an edwAssembly from it's ID.
- lines changed 21, context: html, text, full: html, text
Added edwSubmitFromId function. Revised edwLicensePlateHead to cope with TST->TSTFF change for Stanford compatibility. Added edwSubmitIsValidated. Improved some comments.
- src/hg/encode3/encodeDataWarehouse/lib/restartDaemons
- lines changed 2, context: html, text, full: html, text
Disengaging old style analysis daemon.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
- src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.as
- lines changed 58, context: html, text, full: html, text
Adding back old table defs since have to rerun this and they are gone. Fixing bug in eapStepSwVersion table where it was using the edw version of the swVersion, not the eap one.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.c
- lines changed 941, context: html, text, full: html, text
Adding back old table defs since have to rerun this and they are gone. Fixing bug in eapStepSwVersion table where it was using the edw version of the swVersion, not the eap one.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwAnalysis.h
- lines changed 302, context: html, text, full: html, text
Adding back old table defs since have to rerun this and they are gone. Fixing bug in eapStepSwVersion table where it was using the edw version of the swVersion, not the eap one.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwToEap1.c
- lines changed 15, context: html, text, full: html, text
Adding back old table defs since have to rerun this and they are gone. Fixing bug in eapStepSwVersion table where it was using the edw version of the swVersion, not the eap one.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/makefile
- lines changed 1, context: html, text, full: html, text
Adding in separate module for old style tables.
- src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
- lines changed 27, context: html, text, full: html, text
Mostly improving commenting. Favoring 'Input' controls over other controls per Eurie's suggestion, but there aren't input controls to test it on, so I'm not sure if this part works yet.
- src/hg/encode3/encodeDataWarehouse/oneShot/sampleBam/makefile
- lines changed 3, context: html, text, full: html, text
Moving sampleBam from notes to oneShot
- src/hg/encode3/encodeDataWarehouse/oneShot/sampleBam/sampleBam.c
- lines changed 109, context: html, text, full: html, text
Moving sampleBam from notes to oneShot
- lines changed 2, context: html, text, full: html, text
Fixing usage message to reflect what is, rather than what we want.
- src/hg/encode3/encodeDataWarehouse/utils/edwReplicatedPeaks/edwReplicatedPeaks.c
- lines changed 299, context: html, text, full: html, text
Needs more testing, but works in at least three cases.
- lines changed 1, context: html, text, full: html, text
Added version to usage message.
- src/hg/hgBlat/hgBlat.c
- lines changed 1, context: html, text, full: html, text
Making hgPcr and hgBlat work in the browserbox. To do this, the gfblat lib needs to be able to split a filename that is actually a URL
- src/hg/hgPcr/hgPcr.c
- lines changed 1, context: html, text, full: html, text
Making hgPcr and hgBlat work in the browserbox. To do this, the gfblat lib needs to be able to split a filename that is actually a URL
- src/hg/hgSelect/hgSelect.c
- lines changed 1, context: html, text, full: html, text
incorrect if() statement construction refs #11681
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 2, context: html, text, full: html, text
Changes from code review.
- src/hg/hgTracks/factorSource.c
- lines changed 20, context: html, text, full: html, text
Support multiple canonical motifs for a TF. Also simplify hgc code for motifs. refs #9092
- lines changed 1, context: html, text, full: html, text
Comment as requested in code review
- lines changed 1, context: html, text, full: html, text
Remove direction arrows in dense mode. Agreeing with Brian's suggest during code review that it's busy and problematic if overlaps are on both directions. refs #9092
- lines changed 2, context: html, text, full: html, text
Changes from code review.
- src/hg/hgTracks/hgTracks.c
- lines changed 5, context: html, text, full: html, text
Revised logic for cytoBandIdeo parentheses per code review, refs #12614
- src/hg/hgTracks/multiWig.c
- lines changed 3, context: html, text, full: html, text
fix crash in multiWig if underlying bigWig file was not found
- src/hg/hgc/hgc.c
- src/hg/hgc/lowelab.c
- lines changed 1, context: html, text, full: html, text
fix empty if() statement warning refs #12209
- src/hg/hgc/peakClusters.c
- lines changed 100, context: html, text, full: html, text
Support multiple canonical motifs for a TF. Also simplify hgc code for motifs. refs #9092
- lines changed 4, context: html, text, full: html, text
Fix problem with missing Description section (occured when factor is missing from motifTarget table. refs #9092
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 6, context: html, text, full: html, text
Additional settings for motifs in factorSource tracks. refs #9092
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 4, context: html, text, full: html, text
Additional settings for motifs in factorSource tracks. refs #9092
- src/hg/htdocs/images/emc.png
- lines changed 0, context: html, text, full: html, text
Adding logo for McGill Epigenomics Center hub. refs #12132
- src/hg/js/autocomplete.js
- lines changed 1, context: html, text, full: html, text
Fixed autocomplete dialog falling beneath the data images in some cases. Redmine #12589
- src/hg/js/hgTracks.js
- lines changed 1, context: html, text, full: html, text
Fixed a comment as per Galt's review #12618
- lines changed 7, context: html, text, full: html, text
Fixed bug that only shows up on Mac-Safari combination, where disabling the highlight dialog doesn't actually disable it. Redmine #12645.
- src/hg/js/makefile
- lines changed 1, context: html, text, full: html, text
use rsync instead of cp --update to avoid errors for cp that doesn't have that option refs #12209
- src/hg/lib/cart.c
- lines changed 2, context: html, text, full: html, text
fix empty if() statement warning refs #12209
- src/hg/lib/customFactory.c
- lines changed 1, context: html, text, full: html, text
fix broken if() statement refs #12209
- src/hg/lib/factorMotifs.as
- lines changed 6, context: html, text, full: html, text
Schema for TF to motif table (e.g. factorbookMotifTarget). refs #9092
- src/hg/lib/grp.sql
- lines changed 1, context: html, text, full: html, text
Adding pubs group to grp table sql file. Now any future assemblies should have the pubs group, refs #12583
- lines changed 1, context: html, text, full: html, text
Changed pubs to pub, refs #12583
- src/hg/lib/hdb.c
- lines changed 18, context: html, text, full: html, text
oops swap comments, thanks for catching, Tim.
- src/hg/lib/jksql.c
- lines changed 73, context: html, text, full: html, text
putting existing code into a new function "sqlTableExistsNoCache" as Ineed this code twice
- lines changed 3, context: html, text, full: html, text
Adding missing NULL check. On hgwdev, without this fix we get a SEGV:- cartReset
- hgTables
- change group to "all tables" --> page draws halfway
Fortunately I don't see that on hgwbeta.
- src/hg/lib/liftOver.c
- lines changed 12, context: html, text, full: html, text
making hgLiftOver work in the browserbox, refs #11957, note 56
- src/hg/makeDb/doc/bosTau7.txt
- lines changed 183, context: html, text, full: html, text
Built snp138 tables for bosTau7 and susScr3. Along the way, severalrefinements to doDbSnp.pl and snpNcbiToUcsc were required. refs #12490
- lines changed 7, context: html, text, full: html, text
Starting work on cytoband for farm animal assembles, correcting section title. refs #12373
- lines changed 190, context: html, text, full: html, text
Resolving merge conflict.
- src/hg/makeDb/doc/galGal4.txt
- lines changed 6, context: html, text, full: html, text
Starting work on cytoband for farm animal assembles, correcting section title. refs #12373
- src/hg/makeDb/doc/hg19.txt
- lines changed 29, context: html, text, full: html, text
beginning to reload fixed multiz100way tables refs #12260
- lines changed 46, context: html, text, full: html, text
reloaded annotated maf tables and frames for multiz100way redo refs #12260
- src/hg/makeDb/doc/hg38.txt
- lines changed 67, context: html, text, full: html, text
done with mm10 lastz/chain/net refs #11681
- lines changed 53, context: html, text, full: html, text
done with canFam3 lastz/chain/net refs #11681
- src/hg/makeDb/doc/susScr3.txt
- lines changed 126, context: html, text, full: html, text
Built snp138 tables for bosTau7 and susScr3. Along the way, severalrefinements to doDbSnp.pl and snpNcbiToUcsc were required. refs #12490
- lines changed 3, context: html, text, full: html, text
Starting work on cytoband for farm animal assembles, correcting section title. refs #12373
- lines changed 126, context: html, text, full: html, text
Resolving merge conflict.
- src/hg/makeDb/genbank/etc/genbank.conf
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
add hg38 to assemblies updated
- src/hg/makeDb/hgLoadBed/hgLoadBed.c
- lines changed 156, context: html, text, full: html, text
hgLoadBed's -type=bedN[+[P]] option, when N < 9, should imply thatthe 9th column is not to be treated as itemRgb. (There is also
a -notItemRgb option, but really, -type=bedN should be enough.)
I found that -type was processed only inside the main loop of
loadOneBed, intermixed with some autoSql-processing logic.
I moved out the autoSql, field-counting, type-parsing and -checking
logic into separate functions. It turned out that they did not need
to be inside that loop after all; there is enough information to
figure them out up front, and the loop needs only to check that each
line has the predetermined correct number of rows.
- src/hg/makeDb/hgLoadBed/tests/RunTest.sh
- lines changed 1, context: html, text, full: html, text
hgLoadBed's -type=bedN[+[P]] option, when N < 9, should imply thatthe 9th column is not to be treated as itemRgb. (There is also
a -notItemRgb option, but really, -type=bedN should be enough.)
I found that -type was processed only inside the main loop of
loadOneBed, intermixed with some autoSql-processing logic.
I moved out the autoSql, field-counting, type-parsing and -checking
logic into separate functions. It turned out that they did not need
to be inside that loop after all; there is enough information to
figure them out up front, and the loop needs only to check that each
line has the predetermined correct number of rows.
- src/hg/makeDb/hgLoadBed/tests/bed6plus19.txt.gz
- lines changed 0, context: html, text, full: html, text
hgLoadBed's -type=bedN[+[P]] option, when N < 9, should imply thatthe 9th column is not to be treated as itemRgb. (There is also
a -notItemRgb option, but really, -type=bedN should be enough.)
I found that -type was processed only inside the main loop of
loadOneBed, intermixed with some autoSql-processing logic.
I moved out the autoSql, field-counting, type-parsing and -checking
logic into separate functions. It turned out that they did not need
to be inside that loop after all; there is enough information to
figure them out up front, and the loop needs only to check that each
line has the predetermined correct number of rows.
- src/hg/makeDb/hgLoadBed/tests/chrom.sizes
- lines changed 93, context: html, text, full: html, text
hgLoadBed's -type=bedN[+[P]] option, when N < 9, should imply thatthe 9th column is not to be treated as itemRgb. (There is also
a -notItemRgb option, but really, -type=bedN should be enough.)
I found that -type was processed only inside the main loop of
loadOneBed, intermixed with some autoSql-processing logic.
I moved out the autoSql, field-counting, type-parsing and -checking
logic into separate functions. It turned out that they did not need
to be inside that loop after all; there is enough information to
figure them out up front, and the loop needs only to check that each
line has the predetermined correct number of rows.
- src/hg/makeDb/schema/all.joiner
- lines changed 16, context: html, text, full: html, text
Linked tables for TF ChIP V4 track. refs #12551
- lines changed 1, context: html, text, full: html, text
Updating databasesIgnored with some recent dbSNP build databases.
- src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
- lines changed 35, context: html, text, full: html, text
Changing links on chimp (panTro3) track description pages
- src/hg/makeDb/trackDb/chimp/panTro3/description.html
- lines changed 45, context: html, text, full: html, text
Changing links on chimp (panTro3) track description pages
- src/hg/makeDb/trackDb/chimp/panTro3/gold.html
- lines changed 8, context: html, text, full: html, text
Changing links on chimp (panTro3) track description pages
- src/hg/makeDb/trackDb/human/hg19/cooperDevDelay.html
- lines changed 32, context: html, text, full: html, text
Adding early draft for Cooper Dev. Delay track. refs #9391
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
- lines changed 1, context: html, text, full: html, text
Support multiple canonical motifs for a TF. Also simplify hgc code for motifs. refs #9092
- lines changed 32, context: html, text, full: html, text
Add missing TF factors to filter. refs #12551
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
- lines changed 25, context: html, text, full: html, text
Clarifications and minor additions to TF ChIP V4 track description after review by ZLab (Zhiping Weng). refs #12551
- src/hg/makeDb/trackDb/human/hg38/cpgIslandSuper.html
- lines changed 7, context: html, text, full: html, text
Made changes suggested by Donna in code review (redmine #12612)
- lines changed 1, context: html, text, full: html, text
Removed hyphen (redmine #12612)
- src/hg/makeDb/trackDb/human/hg38/description.html
- lines changed 13, context: html, text, full: html, text
Revised wording in IUPAC and chrM sections (redmine #11706)
- lines changed 18, context: html, text, full: html, text
Added centromere info provided by Karen (redmine #11706)
- lines changed 17, context: html, text, full: html, text
Added Miga reference (redmine #11706)
- lines changed 10, context: html, text, full: html, text
Based on Bob's input, went with Wikipedia's page on IUPAC notation (redmine #11706)
- src/hg/makeDb/trackDb/megabat/pteVam1/description.html
- lines changed 2, context: html, text, full: html, text
Changing links on megabat (pteVam1) track description pages
- src/hg/makeDb/trackDb/megabat/pteVam1/gap.html
- lines changed 1, context: html, text, full: html, text
Changing links on megabat (pteVam1) track description pages
- src/hg/makeDb/trackDb/megabat/pteVam1/gold.html
- lines changed 1, context: html, text, full: html, text
Changing links on megabat (pteVam1) track description pages
- src/hg/makeDb/trackDb/mouse/mm10/hg19ChainNet.ra
- lines changed 17, context: html, text, full: html, text
adding hg38 and reigning in rogue legacy species refs #11681
- src/hg/makeDb/trackDb/mouse/mm10/hg38ChainNet.ra
- lines changed 17, context: html, text, full: html, text
adding hg38 and reigning in rogue legacy species refs #11681
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
- lines changed 14, context: html, text, full: html, text
adding hg38 and reigning in rogue legacy species refs #11681
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
- lines changed 62, context: html, text, full: html, text
adding hg38 and reigning in rogue legacy species refs #11681
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 1, context: html, text, full: html, text
adding hg38 and reigning in rogue legacy species refs #11681
- src/hg/makeDb/trackDb/opossum/monDom5/description.html
- lines changed 3, context: html, text, full: html, text
Changing links on opossum (monDom5) track description pages
- src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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Changing links on yeast (sacCer3) track description pages
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- src/hg/makeDb/trackDb/sacCer/blastHg18KG.html
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- src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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- src/hg/makeDb/trackDb/sacCer/transRegCode.html
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- src/hg/makeDb/trackDb/sacCer/transRegCodeProbe.html
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Changing links on yeast (sacCer3) track description pages
- src/hg/makeDb/trackDb/tagTypes.tab
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
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adding hg38 chain net refs #11681
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
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Built snp138 tables for bosTau7 and susScr3. Along the way, severalrefinements to doDbSnp.pl and snpNcbiToUcsc were required. refs #12490
- src/hg/utils/automation/doDbSnp.pl
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Built snp138 tables for bosTau7 and susScr3. Along the way, severalrefinements to doDbSnp.pl and snpNcbiToUcsc were required. refs #12490
- src/inc/cheapcgi.h
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Fixes #12630. This addresses a bug in + handling in FTP URLs which only have a path part and no query part. Added cgiDecodeFull function to parallel the existing cgiEncodeFull function. These functions ignore the + character when encoding.
- src/inc/common.mk
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can catch empty if() statement here with Wempty-body refs #12209
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do not need the pthread business on the Mac it causes constant warnings refs #12209
- src/inc/hash.h
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Fixing a couple comments that promise too much.
- src/jkOwnLib/gfInternal.c
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Making hgPcr and hgBlat work in the browserbox. To do this, the gfblat lib needs to be able to split a filename that is actually a URL
- src/lib/basicBed.c
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In bedAsDef(), use lstring instead of string for those 'undocumented fields' which can be larger than varchar(255).
- src/lib/bbiRead.c
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fix broken if() statement refs #12209
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fix problem of disappearing narrow peak discussed in #12558 bynormalizing the statics to reflect that base counts are integers.
- src/lib/cheapcgi.c
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Fixes #12630. This addresses a bug in + handling in FTP URLs which only have a path part and no query part. Added cgiDecodeFull function to parallel the existing cgiEncodeFull function. These functions ignore the + character when encoding.
- src/lib/hash.c
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code review changes, refs #12615
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Fixing a couple comments that promise too much.
- src/lib/htmshell.c
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the TrackCheck robot uses jTidy which is stricter than normalwebbrowsers with the W3C html syntax rules. Attributes should not
contain &, nor < or >. see http://www.w3.org/TR/2006/REC-xml11-20060816/#syntax
- src/lib/jsonParse.c
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Fixed a place where data was sent to stdout instead of specified file.
- src/lib/linefile.c
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fix a bug in how lineFile deals with the udc cache.
- src/lib/maf.c
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fix a problem with maf's that are read from stdin, in which case wedon't want to use udc. Probably we should get udc to work with stdin.
- src/lib/net.c
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Fixes #12630. This addresses a bug in + handling in FTP URLs which only have a path part and no query part. Added cgiDecodeFull function to parallel the existing cgiEncodeFull function. These functions ignore the + character when encoding.
- src/parasol/inc/paraMessage.h
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Moving a check on commands against message size to library since in fact it was already implemented twice, and I needed it a third time.
- src/parasol/inc/paraVersion.h
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Bumping version and adding note to version.doc.
- src/parasol/lib/paraMessage.c
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Moving a check on commands against message size to library since in fact it was already implemented twice, and I needed it a third time.
- src/parasol/para/para.c
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Moving a check on commands against message size to library since in fact it was already implemented twice, and I needed it a third time.
- src/parasol/paraHub/paraHub.c
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Fixing crash on empty message sent to main message queue.
- src/parasol/parasol/parasol.c
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Moving a check on commands against message size to library since in fact it was already implemented twice, and I needed it a third time.
- src/parasol/version.doc
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Bumping version and adding note to version.doc.
- src/product/README.requirements
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code review changes, refs #12615
- src/utils/bigWigCat/bigWigCat.c
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change %i to %d in response to code review
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
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calculated in the bigWig summary calculations
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calculated in the bigWig summary calculations
- src/utils/bigWigCat/tests/expected/tf1.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
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calculated in the bigWig summary calculations
- src/utils/bigWigCat/tests/expected/tf3.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/bigWigCat/tests/expected/tv1.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/bigWigCat/tests/expected/tv10.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/bigWigCat/tests/expected/tv100.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/bigWigMerge/bigWigMerge.c
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Adding version number to usage statement.
- src/utils/qa/weeklybld/buildEnv.csh
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v296 preview1 refs #12535
- src/utils/wigToBigWig/tests/expected/tf1.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected/tv1.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tbg1.sum
- lines changed 1, context: html, text, full: html, text
update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tbg10.sum
- lines changed 1, context: html, text, full: html, text
update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tbg100.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tbg1000.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tbg10000.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
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calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tf3.sum
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update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tv1.sum
- lines changed 1, context: html, text, full: html, text
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calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tv10.sum
- lines changed 1, context: html, text, full: html, text
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calculated in the bigWig summary calculations
- src/utils/wigToBigWig/tests/expected_2/tv100.sum
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calculated in the bigWig summary calculations
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