CVS changes by file

review to branch (2010-03-16 to 2010-03-23) v227

• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.7 lines changed: 4, context: html, text, full: html, text
    add Vogel's transcriptome tracks to H. pylori
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.29 lines changed: 1, context: html, text, full: html, text
    add self homolog track
  • 1.28 lines changed: 2, context: html, text, full: html, text
    change blastx cutoff
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.12 lines changed: 15, context: html, text, full: html, text
    add genetree function
• src/hg/archaeStuff/scripts/archaeBrowser/Phylo.pm
  • 1.5 lines changed: 192, context: html, text, full: html, text
    add self homolog track
  • 1.4 lines changed: 1, context: html, text, full: html, text
    use genePred.tab to get gene count instead of da
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fix remove temp file problem
  • 1.2 lines changed: 81, context: html, text, full: html, text
    change dos LF to unix LF
  • 1.1 lines changed: 331, context: html, text, full: html, text
    add genetree function
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.54 lines changed: 10, context: html, text, full: html, text
    add self homolog track
  • 1.53 lines changed: 5, context: html, text, full: html, text
    add genetree function
• src/hg/encode/DAFs/2.0/broadChipSeq.daf
  • 1.2 lines changed: 41, context: html, text, full: html, text
    Consistency in layout
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
  • 1.1 lines changed: 26, context: html, text, full: html, text
    
• src/hg/encode/DAFs/2.0/nhgriElnitskiBiPro.daf
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Undossified
• src/hg/encode/DAFs/2.0/uwChipSeq.daf
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Undossified
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.29 lines changed: 19, context: html, text, full: html, text
    Preferably use the new metaTbl over the trackDb and fileDb.ra settings.
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.73 lines changed: 22, context: html, text, full: html, text
    fixed problem with reading config after chdir
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • 1.6 lines changed: 10, context: html, text, full: html, text
    fixed problem with reading config after chdir
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • 1.3 lines changed: 61, context: html, text, full: html, text
    new types support, warnings now added to notes file
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.216 lines changed: 1, context: html, text, full: html, text
    Corrected the BTO URL for MDA-MB-231
  • 1.215 lines changed: 80, context: html, text, full: html, text
    Added 5 new cell lines to cv.ra.
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.28 lines changed: 10, context: html, text, full: html, text
    Add support for DAF dataAgreementSuffix field
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.215 lines changed: 19, context: html, text, full: html, text
    added support for bigWig validation
• src/hg/encode/encodeValidate/test/expected/chipseq/README.txt
  • 1.8 lines changed: 5, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/encodeValidate/test/expected/chipseq/load.ra
  • 1.8 lines changed: 9, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/encodeValidate/test/expected/chipseq/trackDb.ra
  • 1.11 lines changed: 14, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/encodeValidate/test/input/chipseq/FoxP2_SL167.align_25.hg18.1.txt.BED
  • 1.1 lines changed: 49, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/encodeValidate/test/input/chipseq/FoxP2_SL167.align_25.hg18.2.txt.BED
  • 1.1 lines changed: 51, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/encodeValidate/test/input/chipseq/SL_167_peak_caller.ChIP.peaks
  • 1.1 lines changed: 99, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip-Test-Jun08.DDF
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/encodeValidate/test/input/chipseq/StanfordChip.DAF
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Restoring input files for chipseq test (removed due to excessive size?) and adjusting output to match
• src/hg/encode/validateFiles/validateFiles.c
  • 1.36 lines changed: 53, context: html, text, full: html, text
    add support for validating bigWig
  • 1.35 lines changed: 66, context: html, text, full: html, text
    add a check in BAM validation to require that chroms be specified and that they are the correct chroms with the right sizes
• src/hg/hgCustom/hgCustom.c
  • 1.140 lines changed: 10, context: html, text, full: html, text
    Use knetUdc (put udc underneath samtools' network code) if KNETFILE_HOOKS.
• src/hg/hgGateway/hgGateway.c
  • 1.116 lines changed: 3, context: html, text, full: html, text
    Generalize survey link
• src/hg/hgTracks/hgTracks.c
  • 1.1635 lines changed: 3, context: html, text, full: html, text
    Generalize survey link
• src/hg/hgc/bamClick.c
  • 1.20 lines changed: 10, context: html, text, full: html, text
    Use knetUdc (put udc underneath samtools' network code) if KNETFILE_HOOKS.
• src/hg/hgc/hgc.c
  • 1.1605 lines changed: 38, context: html, text, full: html, text
    Updated logic for tRNAs to fix problems with image file names containing '?'.
• src/hg/hgc/lowelab.c
  • 1.47 lines changed: 219, context: html, text, full: html, text
    add selfHomologs track
  • 1.46 lines changed: 38, context: html, text, full: html, text
    rearrange refseq detail page section order
  • 1.45 lines changed: 243, context: html, text, full: html, text
    rework refseq track detail page; add gene tree
• src/hg/inc/geneTree.h
  • 1.1 lines changed: 62, context: html, text, full: html, text
    add geneTree table
• src/hg/inc/hui.h
  • 1.146 lines changed: 3, context: html, text, full: html, text
    Added support for hgTrackUi to support metadata from metaTbl instead of trackDb
• src/hg/inc/jksql.h
  • 1.87 lines changed: 3, context: html, text, full: html, text
    Thought this quick lookup of row count would help
• src/hg/inc/metaTbl.h
  • 1.4 lines changed: 21, context: html, text, full: html, text
    Added support routines for hgTrackUi using metaTbl
  • 1.3 lines changed: 18, context: html, text, full: html, text
    The most useful query yet: all objs that contain every var=val pair provided.
  • 1.2 lines changed: 51, context: html, text, full: html, text
    Extended API for query and print functions
  • 1.1 lines changed: 194, context: html, text, full: html, text
    Finally making progress on a metadata table.
• src/hg/inc/versionInfo.h
  • 1.168 lines changed: 1, context: html, text, full: html, text
    "New version number v227"
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.80 lines changed: 5, context: html, text, full: html, text
    added simple scale to proportions plot
  • 1.79 lines changed: 89, context: html, text, full: html, text
    added proportions summary view
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.86 lines changed: 14, context: html, text, full: html, text
    added proportions summary view
  • 1.85 lines changed: 2, context: html, text, full: html, text
    support adjustBenjaminiHochberg
• src/hg/instinct/hgHeatmap2/hgHeatmap2.h
  • 1.52 lines changed: 4, context: html, text, full: html, text
    added proportions summary view
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenGBMBio.ra
  • 1.5 lines changed: 24, context: html, text, full: html, text
    columnDb_intgenGBMBio.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.26 lines changed: 4, context: html, text, full: html, text
    fixed an oops
  • 1.25 lines changed: 4, context: html, text, full: html, text
    columnDb_intgenGBMBio.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.38 lines changed: 1, context: html, text, full: html, text
    fixed an oops
  • 1.37 lines changed: 1, context: html, text, full: html, text
    columnDb_intgenGBMBio.ra
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.81 lines changed: 6, context: html, text, full: html, text
    fixed error handling
  • 1.80 lines changed: 15, context: html, text, full: html, text
    added proportions summary view
  • 1.79 lines changed: 1, context: html, text, full: html, text
    add Benjamini-Hochberg
• src/hg/lib/geneTree.as
  • 1.1 lines changed: 6, context: html, text, full: html, text
    add geneTree table
• src/hg/lib/geneTree.c
  • 1.1 lines changed: 124, context: html, text, full: html, text
    add geneTree table
• src/hg/lib/geneTree.sql
  • 1.1 lines changed: 12, context: html, text, full: html, text
    add geneTree table
• src/hg/lib/hdb.c
  • 1.423 lines changed: 4, context: html, text, full: html, text
    third times the charm. hTrackDb now returns list sorted by priority
  • 1.422 lines changed: 7, context: html, text, full: html, text
    fixing my earlier fix. The "right" solution is to make sure that we keep the list in the right order when we return the list.
  • 1.421 lines changed: 5, context: html, text, full: html, text
    remove slReverse to fix problem with menus in hgTables being in the opposite order. Used to be that pruneEmpties ended up flipping the list
• src/hg/lib/hui.c
  • 1.265 lines changed: 49, context: html, text, full: html, text
    Added support for hgTrackUi to support metadata from metaTbl instead of trackDb
• src/hg/lib/jksql.c
  • 1.139 lines changed: 9, context: html, text, full: html, text
    Thought this quick lookup of row count would help
• src/hg/lib/makefile
  • 1.405 lines changed: 1, context: html, text, full: html, text
    add geneTree.c for creating gene tree
  • 1.404 lines changed: 1, context: html, text, full: html, text
    Finally making progress on a metadata table.
• src/hg/lib/metaTbl.as
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Finally making progress on a metadata table.
• src/hg/lib/metaTbl.c
  • 1.4 lines changed: 228, context: html, text, full: html, text
    Added support routines for hgTrackUi using metaTbl
  • 1.3 lines changed: 298, context: html, text, full: html, text
    The most useful query yet: all objs that contain every var=val pair provided.
  • 1.2 lines changed: 311, context: html, text, full: html, text
    Extended API for query and print functions
  • 1.1 lines changed: 767, context: html, text, full: html, text
    Finally making progress on a metadata table.
• src/hg/lib/metaTbl.sql
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Finally making progress on a metadata table.
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.3 lines changed: 203, context: html, text, full: html, text
    Completed genbank, cgpIslans, BLAT server
  • 1.2 lines changed: 176, context: html, text, full: html, text
    Complete repeat mask, simple repeat, fix gap using comp.gap
• src/hg/makeDb/doc/hg18.txt
  • 1.405 lines changed: 38, context: html, text, full: html, text
    Changed file names to match table names and added downloads and metadata in trackDb for CRG Mapability subtracks.
• src/hg/makeDb/doc/hg19.txt
  • 1.91 lines changed: 41, context: html, text, full: html, text
    Changed file names to match table names and added downloads and metadata in trackDb for CRG Mapability subtracks.
• src/hg/makeDb/doc/mm9.txt
  • 1.128 lines changed: 25, context: html, text, full: html, text
    IKMC Genes (komp) update.
• src/hg/makeDb/doc/proteins/090821.txt
  • 1.2 lines changed: 48, context: html, text, full: html, text
    Updated Reactome tables in proteom DB using V32 data files from Reactome.
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.113 lines changed: 1, context: html, text, full: html, text
    Adding felCatV17e - Cat - Felis catus
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.365 lines changed: 17, context: html, text, full: html, text
    Adding felCatV17e support
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.117 lines changed: 1, context: html, text, full: html, text
    Adding felCatV17e - Cat - Felis catus
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.102 lines changed: 265, context: html, text, full: html, text
    fixed incorrect syntax in last change
  • 1.101 lines changed: 1554, context: html, text, full: html, text
    added ignore entries, removed old ones
• src/hg/makeDb/metaTblUpdate/makefile
  • 1.2 lines changed: 23, context: html, text, full: html, text
    Added metaTblPrint and keeping in one directory for now.
  • 1.1 lines changed: 19, context: html, text, full: html, text
    Initial check-in of utility to update/add/remove metaTbl entries.
• src/hg/makeDb/metaTblUpdate/metaTblPrint.c
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Altered API to put sql connection inside lib API
  • 1.2 lines changed: 70, context: html, text, full: html, text
    The most useful query yet: all objs that contain every var=val pair provided.
  • 1.1 lines changed: 150, context: html, text, full: html, text
    Initial print functionality but just starting to test
• src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Altered API to put sql connection inside lib API
  • 1.3 lines changed: 0, context: html, text, full: html, text
    This should get undossified. Why isn't it
  • 1.2 lines changed: 36, context: html, text, full: html, text
    Undossified and using changed API
  • 1.1 lines changed: 141, context: html, text, full: html, text
    Initial check-in of utility to update/add/remove metaTbl entries.
• src/hg/makeDb/trackDb/README
  • 1.104 lines changed: 11, context: html, text, full: html, text
    Fixed the syntax of the release tag setting (thanks, markd) and made a few more small edits.
  • 1.103 lines changed: 3, context: html, text, full: html, text
    Added a note about how release tags get parsed. Thanks, Brian.
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.chainNet.ra
  • 1.4 lines changed: 5, context: html, text, full: html, text
    reordering chainNets to match phylo tree
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • 1.17 lines changed: 1, context: html, text, full: html, text
    fixing ordering of chain/net
  • 1.16 lines changed: 3, context: html, text, full: html, text
    reordering chainNets to match phylo tree
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.20 lines changed: 4, context: html, text, full: html, text
    fixing ordering of chain/net
• src/hg/makeDb/trackDb/guineaPig/trackDb.chainNet.ra
  • 1.8 lines changed: 3, context: html, text, full: html, text
    fixing ordering of chain/net
• src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed typo
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.476 lines changed: 1, context: html, text, full: html, text
    added noScoreFilter line to tRNAs so that the score filter doesn't display in hgTrackUi for that track
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.930 lines changed: 1734, context: html, text, full: html, text
    removed public stanzas for Broad Chip Seq tracks, and removed alpha,beta lines from the newer tracks
  • 1.929 lines changed: 1, context: html, text, full: html, text
    fixed some ENCODE Open Chromatin short labels
  • 1.928 lines changed: 333, context: html, text, full: html, text
    for wgEncodeBroadChipSeq tracks, enabling new tables on beta
  • 1.927 lines changed: 7, context: html, text, full: html, text
    fixed some ENCODE Open Chromatin short labels
  • 1.926 lines changed: 359, context: html, text, full: html, text
    changed release alpha to release alpha,beta and release beta,public to release public for release 3 of the Open Chromatin track
  • 1.925 lines changed: 10, context: html, text, full: html, text
    Added metadata information for the CRG Mapability subtracks.
  • 1.924 lines changed: 12, context: html, text, full: html, text
    Remove restriction timestamps from ENCODE Mapability as data restriction has been explicitly waiived by the labs (not part of the main production effort).
  • 1.923 lines changed: 1, context: html, text, full: html, text
    Added missing subTrack label for release alpha version of Mapability track.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra
  • 1.3 lines changed: 76, context: html, text, full: html, text
    some view changes
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.30 lines changed: 1, context: html, text, full: html, text
    In credits, changed link to email Terry Furey to display his name rather than his email address
• src/hg/makeDb/trackDb/human/hg19/encHaibMethylRrbs.html
  • 1.1 lines changed: 69, context: html, text, full: html, text
    first round of doc
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.6 lines changed: 40, context: html, text, full: html, text
    first round of HAIB Methyl Rrbs track
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Added metadata information for the CRG Mapability subtracks.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.105 lines changed: 1, context: html, text, full: html, text
    added noScoreFilter line to tRNAs so that the score filter doesn't display in hgTrackUi for that track
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.38 lines changed: 4, context: html, text, full: html, text
    fixing ordering of chain/net
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • 1.7 lines changed: 5, context: html, text, full: html, text
    fixing ordering of chain/net
  • 1.6 lines changed: 2, context: html, text, full: html, text
    reordering chainNets to match phylo tree
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • 1.13 lines changed: 5, context: html, text, full: html, text
    fixing ordering of chain/net
  • 1.12 lines changed: 5, context: html, text, full: html, text
    Reordering chains and nets
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.89 lines changed: 1, context: html, text, full: html, text
    added noScoreFilter line to tRNAs so that the score filter doesn't display in hgTrackUi for that track
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.35 lines changed: 3, context: html, text, full: html, text
    fixing ordering of chain/net
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • 1.7 lines changed: 4, context: html, text, full: html, text
    fixing ordering of chain/net
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    fixing ordering of chain/net
  • 1.13 lines changed: 1, context: html, text, full: html, text
    changed phylo order
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.58 lines changed: 1, context: html, text, full: html, text
    added noScoreFilter line to tRNAs so that the score filter doesn't display in hgTrackUi for that track
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • 1.16 lines changed: 1, context: html, text, full: html, text
    fixing ordering of chain/net
  • 1.15 lines changed: 3, context: html, text, full: html, text
    fixing ordering of chain/net
  • 1.14 lines changed: 4, context: html, text, full: html, text
    changed phylo priority
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
  • 1.11 lines changed: 5, context: html, text, full: html, text
    aplCal1 release
  • 1.10 lines changed: 5, context: html, text, full: html, text
    Edited.
• src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
  • 1.13 lines changed: 3, context: html, text, full: html, text
    fixing ordering of chain/net
• src/hg/makeDb/trackDb/tRNAs.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    made a few minor edits
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • 1.18 lines changed: 3, context: html, text, full: html, text
    fixing ordering of chain/net
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Reordering chains and nets
• src/hg/mouseStuff/chainToAxt/chainToAxt.c
  • 1.7 lines changed: 53, context: html, text, full: html, text
    support using twobit as well as nib
• src/hg/mouseStuff/chainToAxt/expected/chrM.axt
  • 1.2 lines changed: 12, context: html, text, full: html, text
    fixed broken tests results
• src/hg/ratStuff/mafSplit/mafSplit.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fix from adk. MafSplit was clipping off the first base of every split
• src/hg/ratStuff/mafSplit/makefile
  • 1.4 lines changed: 3, context: html, text, full: html, text
    add test. Prolly need to change the target to something other than test?
• src/hg/ratStuff/mafSplit/test/makefile
  • 1.1 lines changed: 5, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.bed
  • 1.1 lines changed: 1, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.correct.0.maf
  • 1.1 lines changed: 13, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.correct.1.maf
  • 1.1 lines changed: 13, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.maf
  • 1.1 lines changed: 13, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/regulate/enhancerTraining/enhancers.txt
  • 1.1 lines changed: 36, context: html, text, full: html, text
    Making some notes on enhancers as called by eye looking at ENCODE tracks on hg18 around some genes.
• src/hg/utils/automation/Encode.pm
  • 1.59 lines changed: 3, context: html, text, full: html, text
    Add support for DAF dataAgreementSuffix field
  • 1.58 lines changed: 6, context: html, text, full: html, text
    added function to get the gbdb store dir
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    fixed various issues with error reporting
  • 1.3 lines changed: 28, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
  • 1.2 lines changed: 58, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/utils/gff3ToGenePred/tests/README
  • 1.1 lines changed: 17, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
• src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out
  • 1.1 lines changed: 11, context: html, text, full: html, text
    fixed various issues with error reporting
• src/hg/utils/gff3ToGenePred/tests/expected/multCdsOutOfExonTest.out
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed various issues with error reporting
  • 1.1 lines changed: 3, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/utils/gff3ToGenePred/tests/expected/noIdTest.gp
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
• src/hg/utils/gff3ToGenePred/tests/input/errCases1.gff3
  • 1.1 lines changed: 17, context: html, text, full: html, text
    fixed various issues with error reporting
• src/hg/utils/gff3ToGenePred/tests/input/multCdsOutOfExon.gff3
  • 1.1 lines changed: 11, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/utils/gff3ToGenePred/tests/input/noId.gff3
  • 1.1 lines changed: 12, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
• src/hg/utils/gff3ToGenePred/tests/makefile
  • 1.4 lines changed: 13, context: html, text, full: html, text
    fixed various issues with error reporting
  • 1.3 lines changed: 5, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
  • 1.2 lines changed: 5, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/wikiPlot/makefile
  • 1.9 lines changed: 11, context: html, text, full: html, text
    remove reference to HGCGI in makefile and fix compile warning errors
• src/hg/wikiPlot/wikiPlot.c
  • 1.9 lines changed: 4, context: html, text, full: html, text
    remove reference to HGCGI in makefile and fix compile warning errors
• src/inc/common.h
  • 1.168 lines changed: 9, context: html, text, full: html, text
    Needed another flavor of chopByWhite that respects quotes
• src/inc/nibTwo.h
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    added function to get sequence size
• src/inc/portable.h
  • 1.30 lines changed: 3, context: html, text, full: html, text
    Converted touchFile to maybeTouchFile because ownership of an existing file (not just permissions) can cause problems.
• src/lib/common.c
  • 1.146 lines changed: 74, context: html, text, full: html, text
    Needed another flavor of chopByWhite that respects quotes
• src/lib/gff3.c
  • 1.4 lines changed: 30, context: html, text, full: html, text
    spec unclear where phase is allowed, so don't reject for non-CDS feeatures
• src/lib/nibTwo.c
  • 1.6 lines changed: 9, context: html, text, full: html, text
    added function to get sequence size
• src/lib/osunix.c
  • 1.47 lines changed: 13, context: html, text, full: html, text
    Converted touchFile to maybeTouchFile because ownership of an existing file (not just permissions) can cause problems.
• src/lib/pipeline.c
  • 1.23 lines changed: 120, context: html, text, full: html, text
    wait on process group rather than individual process to prevent deadlocks in certain cases
• src/lib/udc.c
  • 1.37 lines changed: 6, context: html, text, full: html, text
    Grim reaper can take sparseData but not bitmap (esp. when we touch bitmap), so if bitmap exists but sparseData doesn't, get rid of bitmap. To reduce debugging headaches, use maybeTouchFile instead of touchFile.
• src/parasol/gensub2/gensub2.c
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    adding template file syntax help for the check statement
• src/product/README.trackDb
  • 1.6 lines changed: 8, context: html, text, full: html, text
    mention order of trackDb tables and what it does
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    update to talke about how to use trackDb_localTracks table
• src/product/README.udc
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    typo
• src/product/scripts/activeDbList.sh
  • 1.1 lines changed: 18, context: html, text, full: html, text
    can not fetch minimal set of database dumps into goldenPath
• src/product/scripts/beta.cvsup.pl
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    only one directory allowed for argument and indicate where this is all taking place
  • 1.1 lines changed: 209, context: html, text, full: html, text
    initial set of files that can fetch and build kent source tree
• src/product/scripts/browserEnvironment.txt
  • 1.4 lines changed: 15, context: html, text, full: html, text
    add trash file cleaner and TRASHDIR variable to environment fixup readme on the update race condition
  • 1.3 lines changed: 7, context: html, text, full: html, text
    rsync command and hgdownload location are parameters
  • 1.2 lines changed: 2, context: html, text, full: html, text
    can NOW fetch minimal set of database dumps into goldenPath
  • 1.1 lines changed: 78, context: html, text, full: html, text
    initial set of files that can fetch and build kent source tree
• src/product/scripts/fetchFullGbdb.sh
  • 1.2 lines changed: 2, context: html, text, full: html, text
    rsync command and hgdownload location are parameters
  • 1.1 lines changed: 83, context: html, text, full: html, text
    this will fetch all files for a given gbdb directory
• src/product/scripts/fetchFullGoldenPath.sh
  • 1.2 lines changed: 2, context: html, text, full: html, text
    rsync command and hgdownload location are parameters
  • 1.1 lines changed: 85, context: html, text, full: html, text
    can now fetch all files in goldenPath/<db>/database/
• src/product/scripts/fetchMinimalGbdb.sh
  • 1.2 lines changed: 6, context: html, text, full: html, text
    rsync command and hgdownload location are parameters
  • 1.1 lines changed: 94, context: html, text, full: html, text
    can now fetch minimal set of gbdb files
• src/product/scripts/fetchMinimalGoldenPath.sh
  • 1.2 lines changed: 2, context: html, text, full: html, text
    rsync command and hgdownload location are parameters
  • 1.1 lines changed: 88, context: html, text, full: html, text
    can not fetch minimal set of database dumps into goldenPath
• src/product/scripts/kentSrcUpdate.sh
  • 1.1 lines changed: 87, context: html, text, full: html, text
    initial set of files that can fetch and build kent source tree
• src/product/scripts/minimal.db.list.txt
  • 1.1 lines changed: 87, context: html, text, full: html, text
    can not fetch minimal set of database dumps into goldenPath
• src/utils/newProg/newProg.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    cleaning should do A.EXT instead of just A
• src/utils/qa/GS1.csh
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    removed call to updateTimes.csh in localbin dir
• src/utils/qa/comparePublic.csh
  • 1.4 lines changed: 5, context: html, text, full: html, text
    removed rest of files the script makes. thnx, ann
• src/utils/qa/qaEncodeTracks.csh
  • 1.11 lines changed: 2, context: html, text, full: html, text
    stripped white space and new line from tdbQuery output of shortLabel and longLabel
  • 1.10 lines changed: 6, context: html, text, full: html, text
    now that we have encode tables on more than hg18, and in more than one kind of trackDb.ra file, I am switching this script to use tdbQuery.
• src/utils/qa/updateTimes.csh
  • 1.29 lines changed: 15, context: html, text, full: html, text
    b0b hates the labels. Reverting to label only on trackDb_public.
  • 1.28 lines changed: 15, context: html, text, full: html, text
    Added labels to the output lines!
  • 1.27 lines changed: 17, context: html, text, full: html, text
    Added a check for trackDb_public when the table given is trackDb.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.105 lines changed: 3, context: html, text, full: html, text
    v227 final build
• src/utils/qa/weeklybld/makeStrictBeta.csh
  • 1.9 lines changed: 2, context: html, text, full: html, text
    begin support for 3way tagging alpha beta public

• lines changed: 11405
• files changed: 141