CVS changes by file

review to branch (2010-02-23 to 2010-03-02) v226

• src/getgene/makefile
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.5 lines changed: 1, context: html, text, full: html, text
    add StrainA1552 track
• src/hg/archaeStuff/scripts/archaeBrowser/PrecomputedTrack.pm
  • 1.10 lines changed: 16, context: html, text, full: html, text
    allow start=end and fewer than 6 columns for precomputed bed track
• src/hg/checkHgFindSpec/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/hg/checkTableCoords/makefile
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.28 lines changed: 2, context: html, text, full: html, text
    back.gif needed to be a relative path
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Fix mispelling of Tenenbaum
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.15 lines changed: 21, context: html, text, full: html, text
    Report treatment in a separate column instead of as an experimental factor, by request of NHGRI
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/upload.rhtml
  • 1.20 lines changed: 2, context: html, text, full: html, text
    not doing allow reloads automatically for admins because its unneeded
• src/hg/hgGene/hgGene.c
  • 1.119 lines changed: 4, context: html, text, full: html, text
    Removing another dependency on hgg_gene for a purely informational page.
  • 1.118 lines changed: 64, context: html, text, full: html, text
    Making it so can bring up the methods page without a gene specified.
• src/hg/hgGene/hgGene.h
  • 1.50 lines changed: 1, context: html, text, full: html, text
    Removing another dependency on hgg_gene for a purely informational page.
  • 1.49 lines changed: 1, context: html, text, full: html, text
    Making it so can bring up the methods page without a gene specified.
• src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changed human db from hg18 to hg19
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changed human db from hg18 to hg19
• src/hg/hgGene/hgGeneData/Mouse/mm9/otherOrgs.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    changed human db from hg18 to hg19
• src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
  • 1.6 lines changed: 1, context: html, text, full: html, text
    changed human db from hg18 to hg19
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changed human db from hg18 to hg19
• src/hg/hgGene/info.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Removing another dependency on hgg_gene for a purely informational page.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.515 lines changed: 5, context: html, text, full: html, text
    Added option to (not) display item names in bam tracks. Also, when coloring by alignment qual and not pairing, sort by score.
• src/hg/hgTracks/bamTrack.c
  • 1.27 lines changed: 30, context: html, text, full: html, text
    Added option to (not) display item names in bam tracks. Also, when coloring by alignment qual and not pairing, sort by score.
  • 1.26 lines changed: 10, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/inc/hui.h
  • 1.145 lines changed: 1, context: html, text, full: html, text
    Added option to (not) display item names in bam tracks. Also, when coloring by alignment qual and not pairing, sort by score.
• src/hg/inc/knetUdc.h
  • 1.1 lines changed: 10, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/inc/versionInfo.h
  • 1.167 lines changed: 1, context: html, text, full: html, text
    "New version number v226"
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAPublicBrowser.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed a typo that borked the browser
• src/hg/instinct/hgMicroscope/microscope.as
  • 1.2 lines changed: 1, context: html, text, full: html, text
    featureDb support
• src/hg/instinct/hgMicroscope/microscope.sql
  • 1.2 lines changed: 1, context: html, text, full: html, text
    featureDb support
• src/hg/instinct/hgMicroscope/microscope/microscopeSearch.c
  • 1.2 lines changed: 71, context: html, text, full: html, text
    featureDb support
• src/hg/instinct/hgMicroscope/microscopeLoad/loadTCGA.csh
  • 1.1 lines changed: 7, context: html, text, full: html, text
    Added loader script
• src/hg/instinct/hgMicroscope/microscopeLoad/microscopeLoad.c
  • 1.2 lines changed: 13, context: html, text, full: html, text
    FeatureDb support
• src/hg/js/cpJsFiles.pl
  • 1.4 lines changed: 15, context: html, text, full: html, text
    make local links in destDir to avoid problems for mirrors who rsync --links and have a different htdocs path than we do
• src/hg/js/hgGateway.js
  • 1.2 lines changed: 1, context: html, text, full: html, text
    turn on autowidth so strings don't get squashed in pulldown
• src/hg/js/hgTracks.js
  • 1.58 lines changed: 9, context: html, text, full: html, text
    safari/chrome tweaks
  • 1.57 lines changed: 6, context: html, text, full: html, text
    turn off cache in hgTrackUi call
  • 1.56 lines changed: 36, context: html, text, full: html, text
    POST => GET to fix problem on chrom with settings dialog; cleanup getDb code; handle IMAGEv2_DRAG_REORDER == false
• src/hg/lib/bamFile.c
  • 1.20 lines changed: 16, context: html, text, full: html, text
    If compiling with KNETFILE_HOOKS (samtools extension that lets us hook in udc for URL I/O), don't cd to trash while loading the index -- if udc.cacheDir is a relative path, then that breaks, and if using udc we don't need samtools' index-caching.
• src/hg/lib/hgRelate.c
  • 1.27 lines changed: 4, context: html, text, full: html, text
    fixed backwards logic on including pid in tmp file name
• src/hg/lib/hui.c
  • 1.263 lines changed: 1, context: html, text, full: html, text
    Fixed glarring bug in ABC dimension settings persistence
• src/hg/lib/knetUdc.c
  • 1.1 lines changed: 84, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/lib/makefile
  • 1.402 lines changed: 1, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/hg/makeDb/doc/encodeDccHg18/HudsonalphaMethylSeq.release2.txt
  • 1.1 lines changed: 89, context: html, text, full: html, text
    a file I need to create to get this track through QA
• src/hg/makeDb/doc/encodeDccHg18/broadChipSeqRelease3Lists.txt
  • 1.1 lines changed: 881, context: html, text, full: html, text
    Getting ready to put Broad into the pushQ
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • 1.7 lines changed: 461, context: html, text, full: html, text
    Working through a lot of messy issues in order to get this ready for release 2
• src/hg/makeDb/doc/encodeDccHg18/haibTfsbRelease2Lists.txt
  • 1.4 lines changed: 1, context: html, text, full: html, text
    More ugly unscrambling. And it is not done yet.
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Straightened out mislabeled replicate.
  • 1.2 lines changed: 13, context: html, text, full: html, text
    Straightened out the GM12878/Taf mess, I hope.
  • 1.1 lines changed: 1133, context: html, text, full: html, text
    Release 2 is just about ready for QA
• src/hg/makeDb/doc/encodeDccHg18/uwDnaseSeq.release2.notes.txt
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Needed to include files.txt and md5sum.txt
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • 1.8 lines changed: 151, context: html, text, full: html, text
    Old stuff that needs to be checked in
• src/hg/makeDb/doc/hg18.txt
  • 1.401 lines changed: 99, context: html, text, full: html, text
    Adding H-Inv(7.0) update
  • 1.400 lines changed: 45, context: html, text, full: html, text
    gwasCatalog update
• src/hg/makeDb/doc/hg19.txt
  • 1.87 lines changed: 12, context: html, text, full: html, text
    gwasCatalog update
  • 1.86 lines changed: 43, context: html, text, full: html, text
    Adding UCSC Genes as a target for In Silico PCR on hg19
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.10 lines changed: 56, context: html, text, full: html, text
    Adding some business to help finish up lingering issues.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.64 lines changed: 61, context: html, text, full: html, text
    allow release tags to be comma separated lists with alpha, beta, and public
• src/hg/makeDb/schema/all.joiner
  • 1.774 lines changed: 1, context: html, text, full: html, text
    lowered flyBase2004IdDm rule against hgBalstTab to 96% as it is getting older and was no longer passing at the previous 99%
  • 1.773 lines changed: 1, context: html, text, full: html, text
    Adding kgTargetAli to all.joiner.
• src/hg/makeDb/trackDb/baboon/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    adding cvs ident strings
  • 1.1 lines changed: 3, context: html, text, full: html, text
    adding chain net definitions for marmoset calJac3
• src/hg/makeDb/trackDb/baboon/trackDb.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    adding cvs ident strings
  • 1.1 lines changed: 1, context: html, text, full: html, text
    adding chain net definitions for marmoset calJac3
• src/hg/makeDb/trackDb/bushbaby/trackDb.chainNet.ra
  • 1.2 lines changed: 5, context: html, text, full: html, text
    adding calJac3 chain net
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • 1.15 lines changed: 3, context: html, text, full: html, text
    adding calJac3 definition
• src/hg/makeDb/trackDb/cow/trackDb.ra
  • 1.8 lines changed: 2, context: html, text, full: html, text
    adding cvs ident strings
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.19 lines changed: 5, context: html, text, full: html, text
    adding definition for calJac3 chain net
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra
  • 1.11 lines changed: 5, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
• src/hg/makeDb/trackDb/gorilla/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    adding cvs ident strings
  • 1.1 lines changed: 5, context: html, text, full: html, text
    adding calJac3 chain net definition
• src/hg/makeDb/trackDb/gorilla/trackDb.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    adding cvs ident strings
  • 1.1 lines changed: 1, context: html, text, full: html, text
    adding calJac3 chain net definition
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.470 lines changed: 10, context: html, text, full: html, text
    Adding H-Inv(7.0) update
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.896 lines changed: 1709, context: html, text, full: html, text
    Split Broad between alpha and beta
  • 1.895 lines changed: 2, context: html, text, full: html, text
    Still flying blind on beta. Thanks Katrina
  • 1.894 lines changed: 1, context: html, text, full: html, text
    Fixing Beta while flying blind
  • 1.893 lines changed: 33, context: html, text, full: html, text
    Missed a bunch of alpha flags
  • 1.892 lines changed: 2, context: html, text, full: html, text
    Missed 2 alpha tags
  • 1.891 lines changed: 1, context: html, text, full: html, text
    Pointing release beta stanza of wgEncodeUwDnaseSeq to special release 2 html description so that the release 3 desc for the new release doesn't leak back to RR
  • 1.890 lines changed: 522, context: html, text, full: html, text
    Split HAIB TFBS alpha/beta and added 2 tracks
  • 1.889 lines changed: 1297, context: html, text, full: html, text
    Had to split UW DNase into alpha/beta
  • 1.888 lines changed: 5, context: html, text, full: html, text
    Fix a mislabeled replicate for HAIB TFBS. But there is more unscrambling to come
  • 1.887 lines changed: 26, context: html, text, full: html, text
    Hopefully straightened out the GM12878/TAF mess for HAIN TFBS
  • 1.886 lines changed: 22, context: html, text, full: html, text
    Removed 2 duplicated and obsolete tracks from HAIB TFSB
  • 1.885 lines changed: 2, context: html, text, full: html, text
    Updated HAIB TFSB data version in preparation for release2
  • 1.884 lines changed: 120, context: html, text, full: html, text
    removed beta stanzas and release alpha lines to stage wgEncodeGencode tracks
  • 1.883 lines changed: 1, context: html, text, full: html, text
    Fixed one more metadata problem for HAIB TFBS
  • 1.882 lines changed: 6, context: html, text, full: html, text
    Fixed a couple of metadata problems for HAIB TFBS
  • 1.881 lines changed: 8, context: html, text, full: html, text
    removed release alphas from the rest of the ENCODE CSHL Sm RNA-Seq table blocks
  • 1.880 lines changed: 10, context: html, text, full: html, text
    Removing alphas in preparation for staging track on beta.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.21 lines changed: 24, context: html, text, full: html, text
    Working on release 3
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease2.html
  • 1.1 lines changed: 137, context: html, text, full: html, text
    Need to save this release 2 version while working on release 3
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.22 lines changed: 8, context: html, text, full: html, text
    Hopefully straightened out the GM12878/TAF mess for HAIN TFBS
  • 1.21 lines changed: 20, context: html, text, full: html, text
    Added a release note in preparation for release2
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeqRelease1.html
  • 1.1 lines changed: 145, context: html, text, full: html, text
    Need to save release 1 version while release 2 work is going on
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • 1.12 lines changed: 3, context: html, text, full: html, text
    add some release notes
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.alpha.ra
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Removed an erranr % sign, changed the RNA type for HepG2 nlos + from pA- to tot, as for consistent with the metadata
  • 1.3 lines changed: 25, context: html, text, full: html, text
    Cleaned up the long labels
  • 1.2 lines changed: 137, context: html, text, full: html, text
    Cleaned up the colors and the short labels
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Fixed a link
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeqRelease2.html
  • 1.1 lines changed: 114, context: html, text, full: html, text
    added a release2 html so that the RR won't incorrectly have the release3 info while I am QAing it
• src/hg/makeDb/trackDb/human/hg18/wgRna.html
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Fixed a typo.
• src/hg/makeDb/trackDb/human/par.html
  • 1.2 lines changed: 3, context: html, text, full: html, text
    fixed a couple typos.
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.37 lines changed: 9, context: html, text, full: html, text
    adding calJac3 ailMel1 and susScr1 chain and net definitions
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.522 lines changed: 6, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
  • 1.521 lines changed: 28, context: html, text, full: html, text
    add ensGene searchs *without shortCircuit* to human so that Gencode releases with the same id's are searched too!
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • 1.9 lines changed: 15, context: html, text, full: html, text
    adding all the chain net overrides for calJac3
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.14 lines changed: 2, context: html, text, full: html, text
    adding cvs ident strings
• src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra
  • 1.8 lines changed: 7, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • 1.10 lines changed: 7, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
• src/hg/makeDb/trackDb/medaka/trackDb.ra
  • 1.29 lines changed: 6, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.33 lines changed: 8, context: html, text, full: html, text
    adding calJac3 and oryCun2 chain net definition
• src/hg/makeDb/trackDb/mouseLemur/trackDb.chainNet.ra
  • 1.1 lines changed: 6, context: html, text, full: html, text
    adding definitions for calJac3 chain net
• src/hg/makeDb/trackDb/mouseLemur/trackDb.ra
  • 1.1 lines changed: 3, context: html, text, full: html, text
    adding definitions for calJac3 chain net
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.34 lines changed: 10, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • 1.22 lines changed: 11, context: html, text, full: html, text
    adding calJac3 and ailMel1 chain net definitions
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • 1.12 lines changed: 3, context: html, text, full: html, text
    adding definition for calJac3 chain net
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Adding calJac3 chain net
• src/hg/makeDb/trackDb/simpleRepeat.html
  • 1.14 lines changed: 1, context: html, text, full: html, text
    changed wording slightlyfor clarity
• src/hg/makeDb/trackDb/tarsier/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    adding cvs ident strings
  • 1.1 lines changed: 5, context: html, text, full: html, text
    adding definition for calJac3
• src/hg/makeDb/trackDb/tarsier/trackDb.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    adding cvs ident strings
  • 1.1 lines changed: 1, context: html, text, full: html, text
    adding definition for calJac3
• src/hg/makeDb/trackDb/tetraodon/gaze.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed typo
• src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.chainNet.ra
  • 1.4 lines changed: 3, context: html, text, full: html, text
    overrode chainGasAcu1 parameters due to chainNetTrio results
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.60 lines changed: 6, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.85 lines changed: 3, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
  • 1.84 lines changed: 148, context: html, text, full: html, text
    made individual chain and net tracks use same html as composite track
  • 1.83 lines changed: 242, context: html, text, full: html, text
    adding the new ones for calJac3 13-way
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.621 lines changed: 27, context: html, text, full: html, text
    combined chain and netdanRer5 tracks into composite
  • 1.620 lines changed: 1, context: html, text, full: html, text
    don't let PAR track hide PAR1 genes
• src/hg/qaPushQ/qaPushQ.c
  • 1.123 lines changed: 25, context: html, text, full: html, text
    adding table and file counts as requested
  • 1.122 lines changed: 1, context: html, text, full: html, text
    enabling mary to auto-lock as she reqested
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Enforce capitalization of only the first word in commonName, to match dbDb convention.
• src/hg/visiGene/vgPrepImage/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/inc/common.mk
  • 1.76 lines changed: 5, context: html, text, full: html, text
    I have added some hooks into knetfile.c in our local copy of samtools, so that knetfile can serve as a wrapper on udc (or any other suitable code). If KNETFILE_HOOKS=1 (in addition to USE_BAM=1) this will bring the benefits of udc to bam tracks.
• src/inc/portable.h
  • 1.29 lines changed: 3, context: html, text, full: html, text
    Added touchFile (like touch command).
• src/lib/osunix.c
  • 1.45 lines changed: 19, context: html, text, full: html, text
    Added touchFile (like touch command).
• src/lib/udc.c
  • 1.35 lines changed: 12, context: html, text, full: html, text
    No need to use sparseFile in addition to bitmap file for cache age/timeout, and it causes trouble when bitmap exists but sparseData doesn't (yet). Also, moved verbose() up to where it wouldn't cause segv.
  • 1.34 lines changed: 7, context: html, text, full: html, text
    Another tweak required to make the cache timeout work: when we do fetch info, update the cache file mod times to reset the cache timeout clock.
  • 1.33 lines changed: 9, context: html, text, full: html, text
    When getting updateTime and size from the cache bitmap file, get the real remote update time from the bitmap file contents, not the bitmap fileModTime.
• src/parasol/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/primeMate/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).
• src/utils/qa/chain.csh
  • 1.27 lines changed: 1, context: html, text, full: html, text
    changed call to the new findLevel script (no .csh extension)
  • 1.26 lines changed: 2, context: html, text, full: html, text
    removed a print of a variable not used
• src/utils/qa/chainNetTrio.csh
  • 1.11 lines changed: 3, context: html, text, full: html, text
    added informational statement about what to do when the script finishes
• src/utils/qa/doGenbankTests
  • 1.17 lines changed: 2, context: html, text, full: html, text
    Added more settings that will keep things from failing silently.
• src/utils/qa/findLevel
  • 1.1 lines changed: 111, context: html, text, full: html, text
    Changed findLevel.csh to a bash script to simplify dealing with stderr and stdout. This version throws away errors from tdbQuery (whose errors should be addressed, but not here). Also, this version is not restricted to running from hgwdev.
• src/utils/qa/findLevel.csh
  • 1.21 lines changed: 124, context: html, text, full: html, text
    Removing findLevel.csh. It has been replaced with findLevel.
• src/utils/qa/makefile
  • 1.120 lines changed: 1, context: html, text, full: html, text
    Removing findLevel.csh. It has been replaced with findLevel.
  • 1.119 lines changed: 1, context: html, text, full: html, text
    Added findLevel.
• src/utils/qa/net.csh
  • 1.22 lines changed: 1, context: html, text, full: html, text
    changed call to the new findLevel script (no .csh extension)
  • 1.21 lines changed: 2, context: html, text, full: html, text
    Fixed broken logic for finding out if the chrom list is too long to be useful
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.102 lines changed: 3, context: html, text, full: html, text
    v226 final build
• src/wormAli/makefile
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Adding dependencies to install targets to avoid race conditions when using make -j (parallel).

• lines changed: 8842
• files changed: 108