CVS changes by file

branch to review (2009-04-14 to 2009-04-21) v204

• java/src/edu/ucsc/genome/qa/cgiCheck/TrackCheck.java
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Changed hard-coded hgwbeta to target.machine so that mysql machine is found in props file.
• java/src/edu/ucsc/genome/qa/cgiCheck/full.props
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Changed machine to hgsqlbeta, the new sql server that hgwbeta is using.
• java/src/edu/ucsc/genome/qa/cgiCheck/hgw1.props
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Changed machine to hgsqlbeta, the new sql server that hgwbeta is using.
• java/src/edu/ucsc/genome/qa/lib/HgConf.java
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Honor HGDB_CONF environment variable.
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.39 lines changed: 1, context: html, text, full: html, text
    fix bug
  • 1.38 lines changed: 6, context: html, text, full: html, text
    set collab server to use public multiz
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    fix a bug I introduced in the last checkin(s/d use sqlConnect not hAllocConn
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.62 lines changed: 4, context: html, text, full: html, text
    Added link to hgTrackUi into the preamble text.
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.89 lines changed: 4, context: html, text, full: html, text
    HTC-116 was removed as this should be the already existing HCT-116
  • 1.88 lines changed: 1, context: html, text, full: html, text
    Fix syntax err
  • 1.87 lines changed: 7, context: html, text, full: html, text
    Add cell colors, loosely based on GNF conventions
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.16 lines changed: 5, context: html, text, full: html, text
    Add fragLength so to be specified by replicate
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.178 lines changed: 4, context: html, text, full: html, text
    If dateSubmitted is ddf ctime, then dateRestricted should use the same.
  • 1.177 lines changed: 120, context: html, text, full: html, text
    Support for DDF level fragLength for Alignments to RawSignal. Now creating metadata setting for trackDb and new fileDb.ra
• src/hg/gsid/gsidMember/bio.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added SSL_library_init() which is apparently necessary with newer versions of SSL
• src/hg/gsid/gsidMember/gsidMember.c
  • 1.36 lines changed: 6, context: html, text, full: html, text
    oops cannot mix malloc and freez
• src/hg/gsid/gsidMember/paypalSignEncrypt.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    oops cannot mix malloc and freez
• src/hg/gsid/gsidMember/paypalSignEncrypt.h
  • 1.3 lines changed: 1, context: html, text, full: html, text
    oops cannot mix malloc and freez
• src/hg/hgBlat/hgBlat.c
  • 1.127 lines changed: 15, context: html, text, full: html, text
    using cmpStringsWithEmbeddedNumbers() which is a bit more general
• src/hg/hgTables/bedList.c
  • 1.66 lines changed: 1, context: html, text, full: html, text
    Use new constant for 'No results' message.
• src/hg/hgTables/compositeTrack.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    64 bytes is no longer big enough to accomodate <tableName>_sel with the giant wgEncode table names.
• src/hg/hgTables/filterFields.c
  • 1.74 lines changed: 1, context: html, text, full: html, text
    I misunderstood what Jim Wanted. 'Limit data output to' some number of rows should work with bigWig
  • 1.73 lines changed: 9, context: html, text, full: html, text
    Exclude bigWig from option to limit data output to some number of rows
• src/hg/hgTables/gffOut.c
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Use new constant for 'No results' message.
• src/hg/hgTables/hgTables.c
  • 1.184 lines changed: 22, context: html, text, full: html, text
    Cleaned up another hPrintf vs. fprintf unnecessary duplication and used new constant for 'No results' message.
• src/hg/hgTables/hgTables.h
  • 1.137 lines changed: 1, context: html, text, full: html, text
    Added a constant for our 'No results' message.
• src/hg/hgTables/seqOut.c
  • 1.22 lines changed: 19, context: html, text, full: html, text
    Print our usual 'No results' method instead of blank screen when no results (thx Katrina).
• src/hg/hgTracks/simpleTracks.c
  • 1.75 lines changed: 7, context: html, text, full: html, text
    Removing some 5-year-old code that became buggy when we started resolving position to chr:start-end before drawing tracks. A user managed to trigger this by using chr:start-end item names, and viewing the item positions, wrongly turning blue items red.
• src/hg/hgc/hgc.c
  • 1.1527 lines changed: 2, context: html, text, full: html, text
    Removing bedLoadNBin, which duplicated lots of code in bedLoadN for no good reason.
  • 1.1526 lines changed: 8, context: html, text, full: html, text
    tagAlign tables have 'sequence' column instead of 'name' column, but otherwise are BED 6 and should be interpretable like that
• src/hg/hgc/hgcData/links.ra
  • 1.27 lines changed: 3, context: html, text, full: html, text
    MMR link changed
• src/hg/inc/bed.h
  • 1.55 lines changed: 260, context: html, text, full: html, text
    Separating out basicBed module from bed module, so that basicBed can live in src/lib and be clear that it has no database dependence.
  • 1.54 lines changed: 3, context: html, text, full: html, text
    Removing bedLoadNBin, which duplicated lots of code in bedLoadN for no good reason.
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.28 lines changed: 76, context: html, text, full: html, text
    Added cookie to save state
  • 1.27 lines changed: 101, context: html, text, full: html, text
    Added drilldown mode and fixed query stuff for current API
• src/hg/instinct/bioInt2/bioIntUI.c
  • 1.16 lines changed: 128, context: html, text, full: html, text
    updated
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/index.html
  • 1.33 lines changed: 3, context: html, text, full: html, text
    Added tutorial video and fixed heights on elements
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.70 lines changed: 2, context: html, text, full: html, text
    Added tutorial video and fixed heights on elements
• src/hg/js/utils.js
  • 1.18 lines changed: 1, context: html, text, full: html, text
    validateInt had a bad error message when alpha was entered
• src/hg/lib/bed.c
  • 1.65 lines changed: 1247, context: html, text, full: html, text
    Separating out basicBed module from bed module, so that basicBed can live in src/lib and be clear that it has no database dependence.
  • 1.64 lines changed: 43, context: html, text, full: html, text
    Removing bedLoadNBin, which duplicated lots of code in bedLoadN for no good reason.
• src/hg/lib/gsidSubjInfo3.sql
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Moved comment field to the end.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Getting ready for the next wave of new data items.
• src/hg/lib/hdb.c
  • 1.401 lines changed: 2, context: html, text, full: html, text
    tagAlign tables have 'sequence' column instead of 'name' column, but otherwise are BED 6 and should be interpretable like that
  • 1.400 lines changed: 2, context: html, text, full: html, text
    Use the more efficient hDbExists in hTableOrSplitExists, and move the sqlDatabaseExists into hDbExists.
• src/hg/lib/hui.c
  • 1.185 lines changed: 2, context: html, text, full: html, text
    Changing downloads path for easier FTP access
• src/hg/makeDb/doc/taeGut1.txt
  • 1.16 lines changed: 30, context: html, text, full: html, text
    added taeGut1 N-SCAN
• src/hg/makeDb/genbank/doc/config.html
  • 1.24 lines changed: 11, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.335 lines changed: 2, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignIServerClean
  • 1.6 lines changed: 70, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignIServerCopy
  • 1.5 lines changed: 90, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • 1.24 lines changed: 175, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • 1.24 lines changed: 49, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fix bug where mgc/orfeone psl tables were not updated when clones were deleted from MGC
• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.h
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fix bug where mgc/orfeone psl tables were not updated when clones were deleted from MGC
• src/hg/makeDb/genbank/src/dbload/gbMetaData.c
  • 1.48 lines changed: 13, context: html, text, full: html, text
    fix bug where mgc/orfeone psl tables were not updated when clones were deleted from MGC
• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
  • 1.12 lines changed: 2, context: html, text, full: html, text
    fixed change on type of accession in refLink
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.41 lines changed: 8, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/py/genbank/GenomePartition.py
  • 1.1 lines changed: 159, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/py/genbank/GenomeSeqs.py
  • 1.4 lines changed: 29, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/py/genbank/__init__.py
  • 1.3 lines changed: 5, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/schema/all.joiner
  • 1.704 lines changed: 1, context: html, text, full: html, text
    Removed line about vegaPep.name needing full and unique whatevers. The vegaPep table only exists in danRer5.
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Fixed links to Baylor.
• src/hg/makeDb/trackDb/cpgIslandExt.html
  • 1.18 lines changed: 1, context: html, text, full: html, text
    slightly edited text
  • 1.17 lines changed: 2, context: html, text, full: html, text
    slightly edited text
• src/hg/makeDb/trackDb/hiv/trackDb.ra
  • 1.4 lines changed: 8, context: html, text, full: html, text
    reordered tracks to mimic table on description page
• src/hg/makeDb/trackDb/hiv/vax003PosSel.html
  • 1.16 lines changed: 6, context: html, text, full: html, text
    added Credits section.
  • 1.15 lines changed: 4, context: html, text, full: html, text
    removed junk
  • 1.14 lines changed: 42, context: html, text, full: html, text
    collapsed two sections into one (they were redundant)
• src/hg/makeDb/trackDb/hiv/vax004PosSelLoc.html
  • 1.8 lines changed: 6, context: html, text, full: html, text
    added Credits section.
  • 1.7 lines changed: 1481, context: html, text, full: html, text
    Major edits to get rid of the MS Word stuff. And add the correct tables. And add the fully-edited Methods, etc.
• src/hg/makeDb/trackDb/hiv/vax004PosSelRace.html
  • 1.9 lines changed: 6, context: html, text, full: html, text
    added Credits section.
  • 1.8 lines changed: 1398, context: html, text, full: html, text
    removing old junk.
  • 1.7 lines changed: 274, context: html, text, full: html, text
    Major edits to get rid of the MS Word stuff. And add the correct tables. And add the fully-edited Methods, etc.
• src/hg/makeDb/trackDb/hiv/vax004PosSelVac.html
  • 1.8 lines changed: 6, context: html, text, full: html, text
    added Credits section.
  • 1.7 lines changed: 1436, context: html, text, full: html, text
    Major edits to get rid of the MS Word stuff. And add the correct tables. And add the fully-edited Methods, etc.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.254 lines changed: 14, context: html, text, full: html, text
    Updated to of UNC FAIRE peak tracks
  • 1.253 lines changed: 41, context: html, text, full: html, text
    wiggle data for +/- strands
  • 1.252 lines changed: 2, context: html, text, full: html, text
    Helicos description
  • 1.251 lines changed: 683, context: html, text, full: html, text
    A small number of new metadata tags and a very large number of changed ones. Turns out that the metadata generation code did not calc the dataUnrestricted properly
  • 1.250 lines changed: 41, context: html, text, full: html, text
    Consistency on Affy and Riken track labeling
  • 1.249 lines changed: 218, context: html, text, full: html, text
    Added a lot more metadata settings for Most of Mike's tracks
  • 1.248 lines changed: 0, context: html, text, full: html, text
    format cleanup -- need to make sure this is in validator
  • 1.247 lines changed: 193, context: html, text, full: html, text
    Big cleanup of RNA track labels
  • 1.246 lines changed: 54, context: html, text, full: html, text
    Shrink short labels on Riken Cage track
  • 1.245 lines changed: 475, context: html, text, full: html, text
    Added a lot of metadata settings for Broad, Duke/UNC/UT-A, Elnitski, HudsunAlpha, Yale
  • 1.244 lines changed: 74, context: html, text, full: html, text
    Additional coloring by cell type
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.html
  • 1.3 lines changed: 28, context: html, text, full: html, text
    fixups
  • 1.2 lines changed: 5, context: html, text, full: html, text
    fixups
  • 1.1 lines changed: 124, context: html, text, full: html, text
    Helicos description
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.6 lines changed: 8, context: html, text, full: html, text
    updated from Piero
  • 1.5 lines changed: 3, context: html, text, full: html, text
    fix up contact
  • 1.4 lines changed: 4, context: html, text, full: html, text
    updated message about technologies
• src/hg/makeDb/trackDb/human/hg19/gold.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    edited types based on Deanna Church's input
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.451 lines changed: 1, context: html, text, full: html, text
    One more tweak to hgdpXpehh view limits (thx Brooke!).
  • 1.450 lines changed: 2, context: html, text, full: html, text
    Adjusted hgdpXpehh view limits (thx Brooke).
• src/hg/makeDb/trackDb/lowelab/caldMaqu1/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/methAeol1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/privateTracks.ra
  • 1.18 lines changed: 6, context: html, text, full: html, text
    add track restrictions for YNP collab group
• src/hg/makeDb/trackDb/zebraFinch/nscanGene.html
  • 1.1 lines changed: 68, context: html, text, full: html, text
    added taeGut1 N-SCAN
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/trackDb.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    added taeGut1 N-SCAN
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • 1.11 lines changed: 5, context: html, text, full: html, text
    fix bug with name when lastz input is a 2bit
• src/hg/utils/automation/Encode.pm
  • 1.40 lines changed: 1, context: html, text, full: html, text
    Added fileDb.ra definition
• src/hg/utils/automation/fileServer
  • 1.1 lines changed: 18, context: html, text, full: html, text
    This source found in /cluster/bin/scripts appears to not be in the source tree yet and it is used by the blastz pipeline
• src/inc/asParse.h
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Adding asTypesIsInt and asTypesIsFloating
• src/inc/basicBed.h
  • 1.1 lines changed: 266, context: html, text, full: html, text
    Separating out basicBed module from bed module, so that basicBed can live in src/lib and be clear that it has no database dependence.
• src/inc/bigBed.h
  • 1.12 lines changed: 12, context: html, text, full: html, text
    
• src/lib/asParse.c
  • 1.8 lines changed: 31, context: html, text, full: html, text
    Adding asTypesIsInt and asTypesIsFloating
• src/lib/basicBed.c
  • 1.1 lines changed: 1259, context: html, text, full: html, text
    Separating out basicBed module from bed module, so that basicBed can live in src/lib and be clear that it has no database dependence.
• src/lib/bigBed.c
  • 1.16 lines changed: 40, context: html, text, full: html, text
    removed timing messages. added 'sorted' option to speed up creation of gigabyte sized beds.
  • 1.15 lines changed: 61, context: html, text, full: html, text
    
  • 1.14 lines changed: 82, context: html, text, full: html, text
    Improving error detection of bedToBigBed.
• src/lib/common.c
  • 1.129 lines changed: 78, context: html, text, full: html, text
    Adding numerically away string compares.
• src/lib/linefile.c
  • 1.59 lines changed: 1, context: html, text, full: html, text
    Improving error message in lineFileNeedFullNum
• src/lib/makefile
  • 1.150 lines changed: 2, context: html, text, full: html, text
    Separating out basicBed module from bed module, so that basicBed can live in src/lib and be clear that it has no database dependence.
• src/lib/tests/expected/pipelineWriteErr.err
  • 1.3 lines changed: 2, context: html, text, full: html, text
    fixed test problem due to timing of processes
• src/lib/tests/makefile
  • 1.34 lines changed: 6, context: html, text, full: html, text
    fixed test problem due to timing of processes
• src/lib/udc.c
  • 1.16 lines changed: 11, context: html, text, full: html, text
    removing user:pwd@ from head of afterProtocol so that the sensitive login info is not replicated into the udcCache path
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.4 lines changed: 5, context: html, text, full: html, text
    added sort option, also made changes to bigBed.h + bigBed.c
• src/utils/bigBedSummary/bigBedSummary.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed Wig that should be a Bed in usage message.
• src/utils/qa/checkCoverage.csh
  • 1.7 lines changed: 1, context: html, text, full: html, text
    clarified usage statement a little
• src/utils/qa/checkOffend.csh
  • 1.11 lines changed: 1, context: html, text, full: html, text
    dropped comma from usage statement
• src/utils/qa/doGenbankTests
  • 1.6 lines changed: 18, context: html, text, full: html, text
    Added xenoEst to featureBits and pslCheck lists, removed unused trackList variable, reordered checks so they match priority in hgTracks.
  • 1.5 lines changed: 17, context: html, text, full: html, text
    Added logic to check the database argument.
• src/utils/qa/makeFilledBlockBed.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    clarified usage statement
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.55 lines changed: 2, context: html, text, full: html, text
    v205 preview
• src/utils/qa/weeklybld/doTrackCheckRobot.csh
  • 1.4 lines changed: 2, context: html, text, full: html, text
    need to use hgconf for beta because SQL server is on different host now
• src/utils/qa/weeklybld/doZip.csh
  • 1.8 lines changed: 3, context: html, text, full: html, text
    no js on hgwdownload

• lines changed: 11462
• files changed: 94