CVS changes by file

review to branch (2009-05-19 to 2009-05-26) v207

• src/hg/archaeStuff/data/blat-servers.tab
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Ferax down, switching those servers to lowedev
• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.3 lines changed: 1, context: html, text, full: html, text
    add tRNA_Blat track
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.99 lines changed: 1, context: html, text, full: html, text
    Fix misspelling - Thanks Angie
  • 1.98 lines changed: 1, context: html, text, full: html, text
    Misnamed a protocol
  • 1.97 lines changed: 24, context: html, text, full: html, text
    Added approved protocols
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.22 lines changed: 53, context: html, text, full: html, text
    Added code for a protocol setting in cv.ra which is needed for lab specific protocols on tier 3 cell lines
• src/hg/hgTables/asObj.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/bedList.c
  • 1.68 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/bigBed.c
  • 1.9 lines changed: 5, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/bigWig.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/compositeTrack.c
  • 1.17 lines changed: 27, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/correlate.c
  • 1.77 lines changed: 3, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/custom.c
  • 1.41 lines changed: 8, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/filterFields.c
  • 1.75 lines changed: 6, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/hgTables.c
  • 1.186 lines changed: 13, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/hgTables.h
  • 1.138 lines changed: 18, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/intersect.c
  • 1.51 lines changed: 2, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/joining.c
  • 1.54 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/maf.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/mainPage.c
  • 1.144 lines changed: 3, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/microarrayTables.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/rangeHistogram.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/schema.c
  • 1.60 lines changed: 4, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/seqOut.c
  • 1.23 lines changed: 2, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/sumStats.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTables/wiggle.c
  • 1.73 lines changed: 9, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.490 lines changed: 1, context: html, text, full: html, text
    'Maximum' display mode is needed where there is a mult0view, not when dimensions exist.
  • 1.489 lines changed: 3, context: html, text, full: html, text
    Added by-1000genomes validation string for dbSNP 130.
• src/hg/hgTracks/bedTrack.c
  • 1.11 lines changed: 18, context: html, text, full: html, text
    simplify code and add warning about assuming seq1,seq2 are in row[6] and row[7] respectively
  • 1.10 lines changed: 87, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.9 lines changed: 2, context: html, text, full: html, text
    get rid of colon between +/- strands and split on space, by popular demand
  • 1.8 lines changed: 30, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
  • 1.7 lines changed: 71, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
• src/hg/hgTracks/cds.c
  • 1.96 lines changed: 6, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.95 lines changed: 32, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
• src/hg/hgTracks/cds.h
  • 1.22 lines changed: 1, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
• src/hg/hgTracks/simpleTracks.c
  • 1.81 lines changed: 1, context: html, text, full: html, text
    display sequence or sequence different to the genome using a bed or bigBed which has the sequence in the name (eg tagAlign) in a similar manner to PSL files (by loading the BED as a linkedFeature like a PSL)
  • 1.80 lines changed: 112, context: html, text, full: html, text
    Added decipher tracks.
• src/hg/hgc/hgc.c
  • 1.1546 lines changed: 80, context: html, text, full: html, text
    Added decipher section.
  • 1.1545 lines changed: 2, context: html, text, full: html, text
    Increased string size for snp125 observed allele (blob not varchar!).
• src/hg/inc/hdb.h
  • 1.167 lines changed: 28, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/inc/hui.h
  • 1.130 lines changed: 4, context: html, text, full: html, text
    Make filterBySetCfgUi() publicly available
  • 1.129 lines changed: 3, context: html, text, full: html, text
    Added multiViewCount()
• src/hg/inc/trackDb.h
  • 1.49 lines changed: 4, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
• src/hg/inc/versionInfo.h
  • 1.147 lines changed: 1, context: html, text, full: html, text
    "New version number v207"
• src/hg/instinct/bioInt2/bioController.h
  • 1.7 lines changed: 15, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioGeneLevel.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDriver.c
  • 1.4 lines changed: 137, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDriver.h
  • 1.7 lines changed: 26, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.41 lines changed: 1, context: html, text, full: html, text
    Fixed get correlation
  • 1.40 lines changed: 61, context: html, text, full: html, text
    Changed objects to use prototype for memory and speed
• src/hg/instinct/bioInt2/bioPathwayLevel.c
  • 1.2 lines changed: 9, context: html, text, full: html, text
    fixed script
  • 1.1 lines changed: 527, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioSetLevel.c
  • 1.3 lines changed: 92, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/grabData.c
  • 1.6 lines changed: 24, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/makefile
  • 1.11 lines changed: 13, context: html, text, full: html, text
    initial commit
  • 1.10 lines changed: 3, context: html, text, full: html, text
    Changed objects to use prototype for memory and speed
• src/hg/instinct/bioInt2/pathwayNullDist.c
  • 1.2 lines changed: 88, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/populateDb.c
  • 1.11 lines changed: 141, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.instinct.ra
  • 1.4 lines changed: 24, context: html, text, full: html, text
    Added ispy u133a data
• src/hg/instinct/hgHeatmap2/hgToolTip.c
  • 1.7 lines changed: 16, context: html, text, full: html, text
    fixed bug with tool tip and sample/patient ids
• src/hg/lib/cart.c
  • 1.107 lines changed: 1, context: html, text, full: html, text
    Angie pointed out that my last ci erroneously presumes oldVars is never NULL
• src/hg/lib/decipherRaw.sql
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Added decipherRaw.sql.
• src/hg/lib/hdb.c
  • 1.403 lines changed: 61, context: html, text, full: html, text
    Libified findTdbForTable, findTypeForTable, trackIsType, hIsBigBed from hgTables so that other code can easily determine if a track is a bigBed.
• src/hg/lib/hui.c
  • 1.204 lines changed: 1, context: html, text, full: html, text
    forgot or
  • 1.203 lines changed: 3, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.202 lines changed: 4, context: html, text, full: html, text
    The same NO_VALUE protextion is needed for the float version
  • 1.201 lines changed: 38, context: html, text, full: html, text
    handle implied 'scoreFilter' setting and assume that filter at limits is the same as no filter
  • 1.200 lines changed: 5, context: html, text, full: html, text
    Need to not limit min/max default score if 'NO_VALUE' was passed in.
  • 1.199 lines changed: 52, context: html, text, full: html, text
    Added multiViewCount(), support for boxedCfg setting, moved multiView call up a level.
  • 1.198 lines changed: 98, context: html, text, full: html, text
    Fixed scoreFilter defaults code and matrix rendering when dimension row/column has no accociated subtrack
  • 1.197 lines changed: 3, context: html, text, full: html, text
    adding a new trackDb.ra option to get the sequence from the name column of a bed file (plus fixing a logic flaw in case an invalid setting was chosen)
• src/hg/lib/snp125Ui.c
  • 1.32 lines changed: 12, context: html, text, full: html, text
    Added by-1000genomes validation string for dbSNP 130.
• src/hg/lib/trackDbCustom.c
  • 1.66 lines changed: 6, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
• src/hg/makeDb/doc/hg18.txt
  • 1.362 lines changed: 126, context: html, text, full: html, text
    Added updates to phastCons44way and Elements, six tables updated
• src/hg/makeDb/doc/hg19.txt
  • 1.18 lines changed: 58, context: html, text, full: html, text
    Running some recip bests, and started Medaka oryLat2
  • 1.17 lines changed: 330, context: html, text, full: html, text
    Fugu Fr2, Bushbaby OtoGar1 lastz done, Baboon PapHam1 running, SGP and GeneID Genes loaded. 4-way multiz done for UCSC gene build
• src/hg/makeDb/doc/mm9.txt
  • 1.94 lines changed: 21, context: html, text, full: html, text
    Swap to hg19 lastz done
• src/hg/makeDb/genbank/etc/hgdownload-copy
  • 1.3 lines changed: 1, context: html, text, full: html, text
    user rsh for download rsync
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed bug in passing wrong param
  • 1.1 lines changed: 28, context: html, text, full: html, text
    modifyied rsync of download to use locking mechanism used by other genbank scripts
• src/hg/makeDb/genbank/etc/hgdownload.crontab
  • 1.18 lines changed: 1, context: html, text, full: html, text
    only rsync download files every 6 hours
  • 1.17 lines changed: 4, context: html, text, full: html, text
    modifyied rsync of download to use locking mechanism used by other genbank scripts
• src/hg/makeDb/genbank/etc/hgnfs1.crontab
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fixed typo in previous change
  • 1.4 lines changed: 1, context: html, text, full: html, text
    modifyied rsync of download to use locking mechanism used by other genbank scripts
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.94 lines changed: 1, context: html, text, full: html, text
    added ignore entry
• src/hg/makeDb/genbank/src/copy/gbCopyDownload
  • 1.2 lines changed: 150, context: html, text, full: html, text
    modifyied rsync of download to use locking mechanism used by other genbank scripts
• src/hg/makeDb/genbank/src/copy/gbCopyStep
  • 1.18 lines changed: 12, context: html, text, full: html, text
    modifyied rsync of download to use locking mechanism used by other genbank scripts
• src/hg/makeDb/genbank/src/copy/makefile
  • 1.6 lines changed: 2, context: html, text, full: html, text
    added new script to makefile
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.42 lines changed: 15, context: html, text, full: html, text
    modifyied rsync of download to use locking mechanism used by other genbank scripts
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.77 lines changed: 11, context: html, text, full: html, text
    Added ispy u133a data
• src/hg/makeDb/schema/all.joiner
  • 1.715 lines changed: 62, context: html, text, full: html, text
    Fixup hg19 so it is much cleaner
  • 1.714 lines changed: 11, context: html, text, full: html, text
    added rules for two new UCSC to Ensembl mapping tables for hg18,hg19.
• src/hg/makeDb/trackDb/README
  • 1.73 lines changed: 16, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.72 lines changed: 4, context: html, text, full: html, text
    added 'colorByStrand' option which specifies a + and - strand color to override the main 'color', currently works for bed/bigBed tracks which have base coloring
  • 1.71 lines changed: 14, context: html, text, full: html, text
    adding new baseColor options to get the sequence from the name field (eg tagAlign tracks), and updated the track type list
• src/hg/makeDb/trackDb/chainMonDom5.html
  • 1.1 lines changed: 84, context: html, text, full: html, text
    Added top-level trackDb blocks and html files for monDom5 nets and chains.
• src/hg/makeDb/trackDb/human/decipher.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    added info about consent
  • 1.2 lines changed: 12, context: html, text, full: html, text
    adjusted line lenghts to fit on screen
  • 1.1 lines changed: 20, context: html, text, full: html, text
    Added decipher.html.
• src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    changed 32P-gamma-ATP to gamma-32P-ATP
• src/hg/makeDb/trackDb/human/hg18/snpArray.html
  • 1.15 lines changed: 3, context: html, text, full: html, text
    changed to make it more clear where to get info about SV affy chip
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.393 lines changed: 6, context: html, text, full: html, text
    Updated phastCons44way tables and elements to new version from Adam's lab
  • 1.392 lines changed: 7, context: html, text, full: html, text
    set 3 snpArray subrtracks to on by default
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.310 lines changed: 48, context: html, text, full: html, text
    Added pairedTagAlign baseColor option controlled by 'seq1Seq2' option to baseColorUseSequence
  • 1.309 lines changed: 4, context: html, text, full: html, text
    Reregenerated Yale LargeFrag with fragLength=575
  • 1.308 lines changed: 48, context: html, text, full: html, text
    ReRegenerated Open Chromatin Raw Signals and finally got FAIRE HeLa-S3 Peaks which were accidentally missing
  • 1.307 lines changed: 11, context: html, text, full: html, text
    getting rid of offending colon cancer
  • 1.306 lines changed: 11, context: html, text, full: html, text
    first cut of RIKEN colorByStrand settings
  • 1.305 lines changed: 27, context: html, text, full: html, text
    Cleaned up mapability track
  • 1.304 lines changed: 18, context: html, text, full: html, text
    error with the Riken Polysome data, should be PolyA-
  • 1.303 lines changed: 44, context: html, text, full: html, text
    Show bases different to teh genome in the RIKEN tagAligns
  • 1.302 lines changed: 4, context: html, text, full: html, text
    fix missing metadata fields for some HA control tracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.2 lines changed: 53, context: html, text, full: html, text
    Terry provided his methods
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Removed duplicated paragraph.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.19 lines changed: 24, context: html, text, full: html, text
    Add multiz4way for UCSC Genes construction
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.456 lines changed: 1, context: html, text, full: html, text
    hid decipher track by default
  • 1.455 lines changed: 35, context: html, text, full: html, text
    Moved the entry for the uniqueness track farther up the file, with the other track entries.
  • 1.454 lines changed: 9, context: html, text, full: html, text
    Added decipher track.
• src/hg/makeDb/trackDb/human/uniqueness.html
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Reworded to use the passive voice, for consistency with other tracks.
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.75 lines changed: 11, context: html, text, full: html, text
    add tRNA_Blat track
• src/hg/makeDb/trackDb/netMonDom5.html
  • 1.1 lines changed: 80, context: html, text, full: html, text
    Added top-level trackDb blocks and html files for monDom5 nets and chains.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.506 lines changed: 24, context: html, text, full: html, text
    Added top-level trackDb blocks and html files for monDom5 nets and chains.
• src/hg/makeDb/trackDb/worm/ce6/description.html
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Switched to a generic link to wormbase instead of the ws190 link until the old one is functioning again.
• src/hg/makeDb/trackDb/worm/ce6/gap.html
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Switched to a generic link to wormbase instead of the ws190 link until the old one is functioning again.
• src/hg/makeDb/trackDb/worm/ce6/gold.html
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Switched to a generic link to wormbase instead of the ws190 link until the old one is functioning again.
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.50 lines changed: 6, context: html, text, full: html, text
    Added priorities for monDom5 net and chain.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • 1.10 lines changed: 93, context: html, text, full: html, text
    Added -1000GenomesRsIds for adding our own by-1000genomes validation status using a flatfile of 1000Genomes IDs from dbSNP. Also, treat NULL like MISSING, for input from one big sql query instead of from little queries and join commands.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • 1.10 lines changed: 22, context: html, text, full: html, text
    Instead of processing the hgcentral query of session info row by row, slurp the results into memory and then process. Hopefully this will reduce the frequency of losing the connection to hgcentral (currently 4x/day).
• src/utils/qa/browserUsage.csh
  • 1.5 lines changed: 2, context: html, text, full: html, text
    made usage more clear
• src/utils/qa/chain.csh
  • 1.24 lines changed: 12, context: html, text, full: html, text
    Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely.
• src/utils/qa/chain2.csh
  • 1.10 lines changed: 17, context: html, text, full: html, text
    Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely.
• src/utils/qa/checkBOT.csh
  • 1.14 lines changed: 1, context: html, text, full: html, text
    fixed parsing of IPs. thanks pauline
• src/utils/qa/copyExtSeqRows.csh
  • 1.11 lines changed: 5, context: html, text, full: html, text
    cleared up two output messages
  • 1.10 lines changed: 2, context: html, text, full: html, text
    quieting more egreps
  • 1.9 lines changed: 1, context: html, text, full: html, text
    quiet the egrep. this section also works for symlinks (which was untested until now)
  • 1.8 lines changed: 7, context: html, text, full: html, text
    exit at the end of setup run just in case something is wrong and it runs into the real run
  • 1.7 lines changed: 23, context: html, text, full: html, text
    used multi-line echo trick
• src/utils/qa/countPerChrom.csh
  • 1.9 lines changed: 13, context: html, text, full: html, text
    removed need/ability to specify beta as second machine. thanks pauline
• src/utils/qa/getChromlist.csh
  • 1.6 lines changed: 12, context: html, text, full: html, text
    Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely.
• src/utils/qa/igtc.csh
  • 1.22 lines changed: 10, context: html, text, full: html, text
    My preliminary attempt to clean up the 'sqlbeta' substitutions made during the last checkin. It is going to need to be tested during the next run of this script. Most of the variables were not being interpreted.
• src/utils/qa/makeFilledBlockBed.csh
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely.
• src/utils/qa/makeUniProtFile.csh
  • 1.5 lines changed: 18, context: html, text, full: html, text
    sweet tweaks from Brooke
  • 1.4 lines changed: 19, context: html, text, full: html, text
    UniProt has decided that they want to connect using 'org' names rather than 'db' names. I have cautioned them. This fixes the script to produce only 'org' names.
• src/utils/qa/makefile
  • 1.108 lines changed: 0, context: html, text, full: html, text
    it wanted a tab not spaces
  • 1.107 lines changed: 2, context: html, text, full: html, text
    added cvsup to makefile so we can be sure we are building the latest and greatest
• src/utils/qa/net.csh
  • 1.19 lines changed: 5, context: html, text, full: html, text
    Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely.
• src/utils/qa/runBits.csh
  • 1.17 lines changed: 9, context: html, text, full: html, text
    added checking to see if track can pack. set to full in those cases
  • 1.16 lines changed: 8, context: html, text, full: html, text
    Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely.
• src/utils/qa/syncAday.csh
  • 1.9 lines changed: 1, context: html, text, full: html, text
    modified usage statement
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.60 lines changed: 3, context: html, text, full: html, text
    v207 final build

• lines changed: 3936
• files changed: 102