File Changes for kent
switch to commits view, user indexv295_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/lib/jsonParse.c
- lines changed 1, context: html, text, full: html, text
Fixed a place where data was sent to stdout instead of specified file.
- src/parasol/inc/paraMessage.h
- lines changed 5, context: html, text, full: html, text
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
- lines changed 1, context: html, text, full: html, text
Bumping version and adding note to version.doc.
- src/parasol/lib/paraMessage.c
- lines changed 13, context: html, text, full: html, text
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
- lines changed 5, context: html, text, full: html, text
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
- lines changed 6, context: html, text, full: html, text
Fixing crash on empty message sent to main message queue.
- src/parasol/parasol/parasol.c
- lines changed 5, context: html, text, full: html, text
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
- lines changed 1, context: html, text, full: html, text
Bumping version and adding note to version.doc.
- src/utils/bigWigMerge/bigWigMerge.c
- lines changed 1, context: html, text, full: html, text
Adding version number to usage statement.
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