CVS changes by file

review to branch (2009-09-22 to 2009-09-29) v216

• src/cdnaAli/findCdna/findCdna.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/gfServer/gfServer.c
  • 1.55 lines changed: 10, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.81 lines changed: 23, context: html, text, full: html, text
    Updated new Pog genome to version 3
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.18 lines changed: 1, context: html, text, full: html, text
    fix bug in checking existance of .ptt in ncbi download when loading COG info
• src/hg/archaeStuff/scripts/archaeBrowser/GenePrediction.pm
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Added chmod GeneMark_heuristic.mat
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Fixed for poly-n runs
• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.20 lines changed: 149, context: html, text, full: html, text
    add trnablat track
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.48 lines changed: 4, context: html, text, full: html, text
    add trnablat track
• src/hg/archaeStuff/tooltip/tooltip.c
  • 1.1 lines changed: 681, context: html, text, full: html, text
    fixed blastx track
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.17 lines changed: 17, context: html, text, full: html, text
    add bounds output
  • 1.16 lines changed: 1, context: html, text, full: html, text
    oops, default should be to use 32 bits
  • 1.15 lines changed: 122, context: html, text, full: html, text
    added -bed12, -max, and -zero options. Made default counting unit size and unsigned long
• src/hg/bedSplitOnChrom/bedSplitOnChrom.c
  • 1.3 lines changed: 14, context: html, text, full: html, text
    add a little optimization to avoid hash search on each line
  • 1.2 lines changed: 25, context: html, text, full: html, text
    added a couple of options to facilitate use in ENCODE pipeline
• src/hg/borfBig/borfBig.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/encode/DAFs/BroadChipSeq.daf
  • 1.1 lines changed: 39, context: html, text, full: html, text
    Broad DAFs need to be checked in and need to use dafVersion 1.1
• src/hg/encode/DAFs/BroadChipSeqControl.daf
  • 1.1 lines changed: 33, context: html, text, full: html, text
    Broad DAFs need to be checked in and need to use dafVersion 1.1
• src/hg/encode/DAFs/DukeDNaseSeq.DAF
  • 1.3 lines changed: 7, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.2 lines changed: 13, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UncFAIREseq.DAF
  • 1.4 lines changed: 7, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.3 lines changed: 13, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UtaChIPseq.DAF
  • 1.4 lines changed: 7, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.3 lines changed: 14, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UtaInput.DAF
  • 1.4 lines changed: 1, context: html, text, full: html, text
    DukeUNC/UT needs base overlap signal
  • 1.3 lines changed: 12, context: html, text, full: html, text
    Duke/UNC/UT should be using dafVersion 1.1 now.
• src/hg/encode/DAFs/UwChIPseq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    UW should provide replicates for peaks to be consistent
• src/hg/encode/DAFs/YDHChipSeq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Yale signal is bedGraph
• src/hg/encode/DAFs/YDHChipSeqTreatment.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Yale signal is bedGraph
• src/hg/encode/converters/pairedTagToBed12/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a program to convert a pairedTag file into a bed12 with a couple of sequences
• src/hg/encode/converters/pairedTagToBed12/pairedTagToBed12.c
  • 1.1 lines changed: 83, context: html, text, full: html, text
    a program to convert a pairedTag file into a bed12 with a couple of sequences
• src/hg/encode/converters/tagToBed12/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a program to convert a tagAlign file into a bed12 with a couple of sequences
• src/hg/encode/converters/tagToBed12/tagToBed12.c
  • 1.1 lines changed: 82, context: html, text, full: html, text
    a program to convert a tagAlign file into a bed12 with a couple of sequences
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.130 lines changed: 26, context: html, text, full: html, text
    Added Antibody HA and cell HGF
  • 1.129 lines changed: 1, context: html, text, full: html, text
    Changing H1 ES or H1_ES to H1-hESC for clarity
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.92 lines changed: 1, context: html, text, full: html, text
    allowing renames
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/list.rhtml
  • 1.23 lines changed: 3, context: html, text, full: html, text
    fixing dates to include year
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • 1.45 lines changed: 2, context: html, text, full: html, text
    allowing renames
  • 1.44 lines changed: 10, context: html, text, full: html, text
    fixing dates to include year
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.26 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/encode/validateFiles/validateFiles.c
  • 1.27 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/gsBig/gsBig.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/gsid/gsidTable/gsidTable.c
  • 1.49 lines changed: 15, context: html, text, full: html, text
    Fine tuned Table View display.
  • 1.48 lines changed: 8, context: html, text, full: html, text
    Turn off sorting for dnaSeqs and aaSeqs.
• src/hg/gsid/gsidTable/gsidTable.h
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed a bug that was hidden for years.
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra.v3
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Updated to be the same as last checked in for ART release.
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra.v3B
  • 1.3 lines changed: 10, context: html, text, full: html, text
    Turn off visibility for most of immuno cols per GSID layout design.
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Updated to present precisely like the layout design by GSID.
• src/hg/hgCustom/hgCustom.c
  • 1.132 lines changed: 2, context: html, text, full: html, text
    Initialize orgForm.clade to empty string instead of NULL (oops!) which causes segfault on solaris. orgForm.clade is overwritten w/selected value when mainForm select is changed, and ignored if genome or db is changed, so initializing to stub value is fine.
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Adding some configuration so hg19 known genes details page works.
• src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Adding some configuration so hg19 known genes details page works.
• src/hg/hgGene/microarray.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed bug in memory management Andy recently introduced where the geneId was freed after the microarray section leaving subsequent sections with garbage geneId.
  • 1.16 lines changed: 5, context: html, text, full: html, text
    Fixed the problem with the missing Affy Exon data from known genes. The problem stems from the removal of the requirement to have a lookup table in the Gene Sorter. In this case, that table would have been called "knownToKnown" but is simply "null" in the columnDb.ra
• src/hg/hgGene/rnaStructure.c
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgGene/wikiTrack.c
  • 1.24 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgGenome/mainPage.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgKnownGeneList/hgKnownGeneList.c
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgPcr/hgPcr.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgSession/hgSession.c
  • 1.52 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTables/identifiers.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.503 lines changed: 1, context: html, text, full: html, text
    snp125: Add a persistent shadow variable to the list of gene tracks, so we can distinguish between a 'clicked to deselect all' vs. 'hasn't made any selections'. Should cart.c make multshad variables persistent?
  • 1.502 lines changed: 5, context: html, text, full: html, text
    Settle on a single function to determine chainNormScoreDb()
  • 1.501 lines changed: 8, context: html, text, full: html, text
    Eliminate use of chainDbNormScoreAvailable() function and use the trackDb variable instead
• src/hg/hgTracks/chainTrack.c
  • 1.37 lines changed: 5, context: html, text, full: html, text
    Settle on a single function to determine chainNormScoreDb()
• src/hg/hgTracks/config.c
  • 1.84 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTracks/cytoBandTrack.c
  • 1.11 lines changed: 7, context: html, text, full: html, text
    Cleanup recommended by Angie a week ago.
• src/hg/hgTracks/hgTracks.c
  • 1.1600 lines changed: 5, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTracks/imageV2.c
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Removed a define dependency
• src/hg/hgTracks/rnaPLFoldTrack.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgTracks/simpleTracks.c
  • 1.107 lines changed: 1, context: html, text, full: html, text
    Bug in imageV2 found by Ann a week ago
  • 1.106 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
  • 1.105 lines changed: 1, context: html, text, full: html, text
    make barb colors be the same color as the line and box.
• src/hg/hgc/bamClick.c
  • 1.10 lines changed: 10, context: html, text, full: html, text
    Added bamGetQueryQuals for displaying sequence quality scores.
  • 1.9 lines changed: 10, context: html, text, full: html, text
    Added bamShowFlagsEnglish to explain the flag bits.
• src/hg/hgc/hgc.c
  • 1.1576 lines changed: 11, context: html, text, full: html, text
    snp125: Add a persistent shadow variable to the list of gene tracks, so we can distinguish between a 'clicked to deselect all' vs. 'hasn't made any selections'. Should cart.c make multshad variables persistent?
  • 1.1575 lines changed: 5, context: html, text, full: html, text
    Settle on a single function to determine chainNormScoreDb()
  • 1.1574 lines changed: 7, context: html, text, full: html, text
    Eliminate use of chainDbNormScoreAvailable() function and use the trackDb variable instead
  • 1.1573 lines changed: 39, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgc/hgdpClick.c
  • 1.8 lines changed: 9, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/hgc/lowelab.c
  • 1.37 lines changed: 5, context: html, text, full: html, text
    adding description to cdd
  • 1.36 lines changed: 100, context: html, text, full: html, text
    Moved functions to loweutils.c
• src/hg/inc/bamFile.h
  • 1.10 lines changed: 3, context: html, text, full: html, text
    Added bamGetQueryQuals for displaying sequence quality scores.
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Added bamShowFlagsEnglish to explain the flag bits.
• src/hg/inc/bed12wSeq.h
  • 1.1 lines changed: 96, context: html, text, full: html, text
    a header file for bed12 plus a pair of sequences
• src/hg/inc/cddDesc.h
  • 1.1 lines changed: 66, context: html, text, full: html, text
    adding cdd description table
• src/hg/inc/chainDb.h
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Settle on a single function to determine chainNormScoreDb()
• src/hg/inc/hui.h
  • 1.139 lines changed: 3, context: html, text, full: html, text
    Settle on a single function to determine chainNormScoreDb()
• src/hg/inc/loweutils.h
  • 1.1 lines changed: 11, context: html, text, full: html, text
    moving core functions to lib
• src/hg/inc/versionInfo.h
  • 1.156 lines changed: 1, context: html, text, full: html, text
    "New version number v216"
• src/hg/instinct/bioInt2/factorGraph/hgFactorGraph
  • 1.8 lines changed: 0, context: html, text, full: html, text
    Updating digma binary
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.73 lines changed: 2, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.11 lines changed: 28, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.19 lines changed: 20, context: html, text, full: html, text
    
• src/hg/js/hui.js
  • 1.35 lines changed: 44, context: html, text, full: html, text
    Fixed matrix CB normalize to do it's best for dimension Z
• src/hg/lib/bamFile.c
  • 1.9 lines changed: 17, context: html, text, full: html, text
    Added bamGetQueryQuals for displaying sequence quality scores.
  • 1.8 lines changed: 35, context: html, text, full: html, text
    Added bamShowFlagsEnglish to explain the flag bits.
• src/hg/lib/bed12wSeq.as
  • 1.1 lines changed: 18, context: html, text, full: html, text
    bed12 plus a couple of sequences at the end
• src/hg/lib/bed12wSeq.c
  • 1.1 lines changed: 294, context: html, text, full: html, text
    bed12 plus a couple of sequences at the end
• src/hg/lib/bed12wSeq.sql
  • 1.1 lines changed: 24, context: html, text, full: html, text
    bed12 plus a couple of sequences at the end
• src/hg/lib/cddDesc.as
  • 1.1 lines changed: 10, context: html, text, full: html, text
    adding cdd description table
• src/hg/lib/cddDesc.c
  • 1.1 lines changed: 150, context: html, text, full: html, text
    adding cdd description table
• src/hg/lib/cddDesc.sql
  • 1.1 lines changed: 16, context: html, text, full: html, text
    adding cdd description table
• src/hg/lib/chainDb.c
  • 1.13 lines changed: 23, context: html, text, full: html, text
    Settle on a single function to determine chainNormScoreDb()
• src/hg/lib/customFactory.c
  • 1.104 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/customPp.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    adding missing https
• src/hg/lib/customTrack.c
  • 1.178 lines changed: 1, context: html, text, full: html, text
    Making error message a little more informative, and not an 'internal error' since it is in response to erronious input, not software error.
  • 1.177 lines changed: 5, context: html, text, full: html, text
    autocreated custom trackNames now exclude all special chars and append a uniquifier number
• src/hg/lib/hdb.c
  • 1.415 lines changed: 10, context: html, text, full: html, text
    Patching things to look for all_mrna when chr1_mrna doesn't exist and the like.
• src/hg/lib/hgFind.c
  • 1.222 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/hui.c
  • 1.240 lines changed: 16, context: html, text, full: html, text
    Settle on a single function to determine chainNormScoreDb()
  • 1.239 lines changed: 23, context: html, text, full: html, text
    Eliminate the call to chainDbNormScoreAvailable() and instead use the trackDb variable
  • 1.238 lines changed: 6, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/jksql.c
  • 1.136 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/lib/loweutils.c
  • 1.1 lines changed: 96, context: html, text, full: html, text
    moving core functions to lib
• src/hg/lib/makefile
  • 1.397 lines changed: 2, context: html, text, full: html, text
    add a few files to the library (yay! it's even bigger now ;-)
  • 1.396 lines changed: 1, context: html, text, full: html, text
    adding cddDesc.o
  • 1.395 lines changed: 2, context: html, text, full: html, text
    Adding loweutils.o
• src/hg/lib/trackDbCustom.c
  • 1.71 lines changed: 1, context: html, text, full: html, text
    Using hTableOrSplitExists() instead of just hTableExists() to get composite tracks to properly work with split tables
• src/hg/lib/web.c
  • 1.171 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/liftOver/liftOver.c
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/doc/ce7.txt
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Reset default position
• src/hg/makeDb/doc/ce8.txt
  • 1.3 lines changed: 72, context: html, text, full: html, text
    Tried to get the sanger genes up, not complete
• src/hg/makeDb/doc/danRer6.txt
  • 1.9 lines changed: 20, context: html, text, full: html, text
    Finish lastz oryLat2 <-> danRer6
• src/hg/makeDb/doc/encodeDccHg18/yaleUpdate9-30.notes.txt
  • 1.1 lines changed: 902, context: html, text, full: html, text
    Complete lists of files and tables for ENCODE Yale TFSB release 2 which should occur after the 9-30-2009 data freeze. Notes were too long to include directly in pushQ entry.
• src/hg/makeDb/doc/gasAcu1.txt
  • 1.39 lines changed: 94, context: html, text, full: html, text
    Finish tetNig2 chain/net
• src/hg/makeDb/doc/hg18.txt
  • 1.384 lines changed: 107, context: html, text, full: html, text
    Genome Variants: added Korean (SJK). Added base counts to 1000 Genomes SNPs.
• src/hg/makeDb/doc/hg19.txt
  • 1.39 lines changed: 464, context: html, text, full: html, text
    Working on the 46way conservation, oryCun2 lastz chain net cavPor3 synNet and reload cavPor3 extra large chain tables
• src/hg/makeDb/doc/monDom5.txt
  • 1.16 lines changed: 452, context: html, text, full: html, text
    Added multiz/phastCons make instructions.
• src/hg/makeDb/doc/ornAna1.txt
  • 1.28 lines changed: 5, context: html, text, full: html, text
    add automatic generation of upstream files to genbank configuration
• src/hg/makeDb/doc/oryCun2.txt
  • 1.3 lines changed: 83, context: html, text, full: html, text
    Finish off repeat tracks, lastz run with hg19
• src/hg/makeDb/doc/oryLat2.txt
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Finish lastz oryLat2 <-> danRer6
  • 1.15 lines changed: 136, context: html, text, full: html, text
    add automatic generation of upstream files to genbank conf, and danRer6 swap lastz running and tetNig2 lastz done
• src/hg/makeDb/doc/proteins/090821.txt
  • 1.1 lines changed: 305, context: html, text, full: html, text
    Built new version of proteins database on top of corresponding swissProt database.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.3 lines changed: 26, context: html, text, full: html, text
    Finishing up build and database integration. Will need to add more knownTo and XyzDistance tables as the hg19 database in general is built up.
  • 1.2 lines changed: 29, context: html, text, full: html, text
    Done with first pass of the build. Now for some testing....
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.103 lines changed: 1, context: html, text, full: html, text
    Added oryCun2 - Oryctolagus cuniculus - Rabbit
  • 1.102 lines changed: 2, context: html, text, full: html, text
    Added macEug1 - Macropus eugenii - Wallaby and Papio Hamadryas - Baboon
  • 1.101 lines changed: 1, context: html, text, full: html, text
    removed rn5
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.351 lines changed: 38, context: html, text, full: html, text
    Adding rabbit and wallaby oryCun2 and macEug1
  • 1.350 lines changed: 18, context: html, text, full: html, text
    Adding Baboon papHam1
  • 1.349 lines changed: 17, context: html, text, full: html, text
    removed rn5
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.108 lines changed: 1, context: html, text, full: html, text
    Added oryCun2 - Oryctolagus cuniculus - Rabbit
  • 1.107 lines changed: 2, context: html, text, full: html, text
    Added macEug1 - Macropus eugenii - Wallaby and Papio Hamadryas - Baboon
  • 1.106 lines changed: 1, context: html, text, full: html, text
    removed rn5
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.73 lines changed: 2, context: html, text, full: html, text
    Adding Wallaby Macropus eugenii
  • 1.72 lines changed: 2, context: html, text, full: html, text
    Adding Baboon Papio hamadryas hamadryas
• src/hg/makeDb/hgCountAlign/hgCountAlign.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/hgLoadMaf/hgLoadMaf.c
  • 1.27 lines changed: 14, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/hgMrnaRefseq/hgMrnaRefseq.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgCGAP/hgCGAP.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgKegg/hgKegg.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgKegg2/hgKegg2.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgKegg3/hgKegg3.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/outside/samHit/samHit.c
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/makeDb/schema/all.joiner
  • 1.736 lines changed: 9, context: html, text, full: html, text
    Added wgEncodeGencode V3 tables
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • 1.10 lines changed: 6, context: html, text, full: html, text
    set hg18 chainnets to o_db
  • 1.9 lines changed: 6, context: html, text, full: html, text
    changed name of chainnets for monDom4 to o_db
  • 1.8 lines changed: 12, context: html, text, full: html, text
    reduced size of block for guinea pig chains by using override
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.36 lines changed: 12, context: html, text, full: html, text
    added overrides for chain/net monDom4/5
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.8 lines changed: 79, context: html, text, full: html, text
    pgSnp: added pgSjk, moved 1000 Genomes NA* from pgSnpHgwdev to pgSnp.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.420 lines changed: 17, context: html, text, full: html, text
    pgSnp: added pgSjk, moved 1000 Genomes NA* from pgSnpHgwdev to pgSnp.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.545 lines changed: 16, context: html, text, full: html, text
    Removed release alpha lines for Affy RNA Loc sep-09 update tables.
  • 1.544 lines changed: 181, context: html, text, full: html, text
    add LogSignal tracks for Hannon lab
  • 1.543 lines changed: 4, context: html, text, full: html, text
    Oops. Turned off some Yale RNAseq tracks
  • 1.542 lines changed: 61, context: html, text, full: html, text
    Added 5 Yale RNA-seq tracks
  • 1.541 lines changed: 18, context: html, text, full: html, text
    reload wiggles for Hannon lab
  • 1.540 lines changed: 94, context: html, text, full: html, text
    Fixed some colors and converted H1_ES to H1-hESC for clarity
  • 1.539 lines changed: 63, context: html, text, full: html, text
    Three new experiments for YDH-Peggy Farnham
  • 1.538 lines changed: 246, context: html, text, full: html, text
    UW Exon Affy submissions added
  • 1.537 lines changed: 159, context: html, text, full: html, text
    Hannon lab short rna edits
  • 1.536 lines changed: 150, context: html, text, full: html, text
    Update dataVersion from Fall to Sep 2009
  • 1.535 lines changed: 22, context: html, text, full: html, text
    shortened and editing some labels for Affy/CSHL exons
  • 1.534 lines changed: 342, context: html, text, full: html, text
    new Hannon lab short RNA data
  • 1.533 lines changed: 289, context: html, text, full: html, text
    Tracy and Tim have been straightening out UW
  • 1.532 lines changed: 849, context: html, text, full: html, text
    drop all the old Hannon lab stuff so I can start over
  • 1.531 lines changed: 588, context: html, text, full: html, text
    Tracy Ballinger added new UW Dnase-seq and UW ChIPseq tracks
  • 1.530 lines changed: 1, context: html, text, full: html, text
    move Gis Pet to variation
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Fixed broken link, typo and ref
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.51 lines changed: 7, context: html, text, full: html, text
    set vertChainNet track to go beyond dev and turned on four tracks for default
• src/hg/makeDb/trackDb/lowelab/caldMaqu1/trackDb.ra
  • 1.15 lines changed: 2, context: html, text, full: html, text
    add pyroOgun03 to multiz
• src/hg/makeDb/trackDb/lowelab/description-template.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    add tRNA blat track
• src/hg/makeDb/trackDb/lowelab/pyrAer1/trackDb.ra
  • 1.56 lines changed: 1, context: html, text, full: html, text
    Update multiz track
  • 1.55 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroArse1/trackDb.ra
  • 1.26 lines changed: 2, context: html, text, full: html, text
    add pyroOgun03 to multiz
• src/hg/makeDb/trackDb/lowelab/pyroCali1/trackDb.ra
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/pyroIsla1/trackDb.ra
  • 1.29 lines changed: 2, context: html, text, full: html, text
    add pyroOgun03 to multiz
• src/hg/makeDb/trackDb/lowelab/pyroOgun03/multizPbacTtxCmaTpe.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    Details page for multiz track
• src/hg/makeDb/trackDb/lowelab/pyroOgun03/trackDb.ra
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Update multiz track
  • 1.1 lines changed: 13, context: html, text, full: html, text
    New selfz track
• src/hg/makeDb/trackDb/lowelab/therNeut1/trackDb.ra
  • 1.9 lines changed: 2, context: html, text, full: html, text
    add pyroOgun03 to multiz
• src/hg/makeDb/trackDb/lowelab/therTena1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    change to therNeut0 for multiz
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.87 lines changed: 8, context: html, text, full: html, text
    Adding cdd search
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.68 lines changed: 8, context: html, text, full: html, text
    changed name of old possum chains to o_db
  • 1.67 lines changed: 6, context: html, text, full: html, text
    moved override block with others
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • 1.8 lines changed: 5, context: html, text, full: html, text
    Changed codon translation table per andy.
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Forgot a period.
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Added phastCons parameters to the description.
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Fixed a bad sentence.
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Changed the description for the conservation track to reflect the correct phastCons tree model creation procedure in this case, which was NOT to use 4D sites like in the human conservation track.
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Updated species list to reflect make doc.
  • 1.2 lines changed: 43, context: html, text, full: html, text
    Fixed up references section (used text from calJac1 multiz page).
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.19 lines changed: 58, context: html, text, full: html, text
    added chain vars for all orgs
  • 1.18 lines changed: 6, context: html, text, full: html, text
    added some parameters for zfish chain
  • 1.17 lines changed: 6, context: html, text, full: html, text
    added chainnet priority overrides for separate chainnetGalGal3 tracks
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Added speciesCodonDefault to multiz9way entry.
  • 1.15 lines changed: 4, context: html, text, full: html, text
    added details about mm9 chain
  • 1.14 lines changed: 18, context: html, text, full: html, text
    Brooke and Bob want it to be opposite of the Conservation line-up (which I think is incorrect:-)
  • 1.13 lines changed: 71, context: html, text, full: html, text
    ordered chain/net tracks wrt the opossum and each-other.
  • 1.12 lines changed: 6, context: html, text, full: html, text
    moved chimp chainnets next to orang
• src/hg/makeDb/trackDb/orangutan/trackDb.ra
  • 1.6 lines changed: 1, context: html, text, full: html, text
    changed netMonDom4 shortLabel to say Net, not Chain
• src/hg/makeDb/trackDb/platypus/ornAna1/priority.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    moved monDom4 chainnet blocks from priority.ra to trackDb.ra and changed shortLabel to o_db
• src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
  • 1.11 lines changed: 9, context: html, text, full: html, text
    moved monDom4 chainnet blocks from priority.ra to trackDb.ra and changed shortLabel to o_db
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.47 lines changed: 5, context: html, text, full: html, text
    added matrix for possum chain
  • 1.46 lines changed: 8, context: html, text, full: html, text
    moved override to bottom of track block
• src/hg/makeDb/trackDb/snp130.html
  • 1.10 lines changed: 7, context: html, text, full: html, text
    Added description of repetitive sequence highlighting in re-alignment of flanking sequences.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.535 lines changed: 4, context: html, text, full: html, text
    Properly release lable the ornAna1 chain and net composite and separate tracks
  • 1.534 lines changed: 2, context: html, text, full: html, text
    added matrix to possum.chainPonAbe2 track
• src/hg/makeDb/trackDb/wallaby/macEug1/description.html
  • 1.1 lines changed: 129, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/wallaby/macEug1/gap.html
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/wallaby/macEug1/gold.html
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/wallaby/macEug1/trackDb.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    Initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/xenTro/priority.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    set hg18 chainnets to o_db
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
  • 1.20 lines changed: 7, context: html, text, full: html, text
    set hg18 chainnets to o_db
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
  • 1.16 lines changed: 11, context: html, text, full: html, text
    combined chainnets for hg18 from priority.ta into trackDb.ra and set shortLabel to o_db
• src/hg/makeDb/trackDb/zebrafish/danRer5/priority.ra
  • 1.6 lines changed: 6, context: html, text, full: html, text
    combined chainnets for hg18 from priority.ta into trackDb.ra and set shortLabel to o_db
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • 1.23 lines changed: 6, context: html, text, full: html, text
    moved possum net back with other mammals
  • 1.22 lines changed: 10, context: html, text, full: html, text
    combined chainnets for hg18 from priority.ta into trackDb.ra and set shortLabel to o_db
• src/hg/mouseStuff/chainSplit/chainSplit.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/mouseStuff/netSplit/netSplit.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/near/hgClusterGenes/hgClusterGenes.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/near/hgNear/hgNearData/Human/hg19/acc.html
  • 1.1 lines changed: 2, context: html, text, full: html, text
    Making directory for config files for hg19
• src/hg/phyloGif/phyloGif.c
  • 1.23 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgAliasKgXref/kgAliasKgXref.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgAliasM/kgAliasM.c
  • 1.9 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgAliasRefseq/kgAliasRefseq.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgPepMrna/kgPepMrna.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgPick/kgPick.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgProtAlias/kgProtAlias.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgXref/kgXref.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/kgXref2/kgXref2.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/lib/doTracks.c
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Corrected an early termination bug for AA Anomalies track.
• src/hg/protein/makefile
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Adding pbCalResStdGlobal to parent makefile so we'll spot when it doesn't compile sooner.
• src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Reduced a warn to a verbose 2 since it was complaining about 'U' which is common these days. Also took out a system call to speed it up about 2x.
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/pbCalPi/pbCalPi.c
  • 1.8 lines changed: 43, context: html, text, full: html, text
    Simplified code. Reduced run time from 5 hours to 20 minutes.
• src/hg/protein/pbCalResStd/pbCalResStd.c
  • 1.11 lines changed: 8, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
  • 1.8 lines changed: 10, context: html, text, full: html, text
    Adding database parameter as now required for hAllocConn(). Changing a stderr message to verbose(2 since it was coming up a lot to no bad effect. Bumping up MAXN so can handle 20 million proteins in SwissProt since now up to 9.3 million and previous limit was 10 million. Changing biggest array to be dynamically allocated to avoid linkage error.
• src/hg/protein/pbHgnc/pbHgnc.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/pfamXref/pfamXref.c
  • 1.10 lines changed: 12, context: html, text, full: html, text
    Sped up 10 or 20x by using a hash table instead of repeated sql queries.
  • 1.9 lines changed: 6, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spOrganism/spOrganism.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spToProteins/spToProteins.c
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spm3/spm3.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spm6/spm6.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/protein/spm7/spm7.c
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/qa/apacheMonitor.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/sim4big/sim4big.c
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/sqlToXml/doTest
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Got rid of a test case that depended on a database being constant.
• src/hg/tcga/bamBam/bamBam.c
  • 1.5 lines changed: 139, context: html, text, full: html, text
    updated
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    moved stuff around to make it more flexible
  • 1.3 lines changed: 145, context: html, text, full: html, text
    updated
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    it is alive
  • 1.1 lines changed: 253, context: html, text, full: html, text
    initial commit
• src/hg/tcga/bamBam/bam_dual_pileup.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 167, context: html, text, full: html, text
    moved stuff around to make it more flexible
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    updated
  • 1.1 lines changed: 380, context: html, text, full: html, text
    initial commit
• src/hg/tcga/bamBam/bam_dual_pileup.h
  • 1.3 lines changed: 26, context: html, text, full: html, text
    moved stuff around to make it more flexible
  • 1.2 lines changed: 33, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 77, context: html, text, full: html, text
    initial commit
• src/hg/tcga/bamBam/makefile
  • 1.1 lines changed: 23, context: html, text, full: html, text
    initial commit
• src/hg/tcga/bamVariants/bamVariants.c
  • 1.1 lines changed: 379, context: html, text, full: html, text
    initial commit
• src/hg/tcga/bamVariants/makefile
  • 1.1 lines changed: 23, context: html, text, full: html, text
    initial commit
• src/hg/trfBig/trfBig.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/hg/utils/automation/Encode.pm
  • 1.46 lines changed: 1, context: html, text, full: html, text
    Rename freeze
• src/hg/utils/automation/synBlastp.csh
  • 1.5 lines changed: 2, context: html, text, full: html, text
    fix based on mysql5
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Working around mysql 5 bug.
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/hg/utils/refreshNamedSessionCustomTracks/makefile
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFiles.csh
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Move aside tmp output after failure; keep a lastLog file with most recent successful log.
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSessionCtFilesInner.csh
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Adding uptime command after error/warning messages so we can see whether load is high.
  • 1.1 lines changed: 58, context: html, text, full: html, text
    Adding refreshSessionCtFiles*csh which have been living in ~qateam/bin/scripts, and souped them up to use tmp file names based on hour, and to watch out for signs of multiple refresh jobs happening at once. makeExclusionList.pl now accepts doNotRmFile as an arg instead of hardcoding it.
• src/inc/common.h
  • 1.155 lines changed: 3, context: html, text, full: html, text
    Added eraseNonAlphaNum()
  • 1.154 lines changed: 12, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/isPcr/webPcr/webPcr.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/jkOwnLib/gfBlatLib.c
  • 1.28 lines changed: 4, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/jkOwnLib/gfPcrLib.c
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/bPlusTree.c
  • 1.6 lines changed: 7, context: html, text, full: html, text
    Fixing problem with bptTraverse on larger data sets. Causes problems in bigWig on scaffolded assemblies.
• src/lib/bwgCreate.c
  • 1.16 lines changed: 20, context: html, text, full: html, text
    Making wigToBigWig creation check for overlaps in sections for a better error message rather than the internal error message.
• src/lib/common.c
  • 1.133 lines changed: 18, context: html, text, full: html, text
    Added eraseNonAlphaNum()
  • 1.132 lines changed: 32, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/fa.c
  • 1.38 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/htmlPage.c
  • 1.38 lines changed: 5, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/https.c
  • 1.2 lines changed: 7, context: html, text, full: html, text
    close all extra descriptors to fix fork for mysql5 client
• src/lib/net.c
  • 1.73 lines changed: 7, context: html, text, full: html, text
    close all extra descriptors to fix fork for mysql5 client
  • 1.72 lines changed: 7, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/obscure.c
  • 1.48 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/options.c
  • 1.27 lines changed: 5, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/snof.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/twoBit.c
  • 1.28 lines changed: 6, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/lib/wormdna.c
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/reformat/gbtofa/gbtofa.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/utils/bedClip/makefile
  • 1.2 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/bedGraphToBigWig/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.4 lines changed: 3, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Making printf formating agree in signedness to avoid error on different compilers.
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixup compile error due to incorrect type from sizeof() in a printf format
• src/utils/bedToBigBed/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/bigBedSummary/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/bigBedToBed/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/bigWigInfo/makefile
  • 1.4 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
  • 1.3 lines changed: 2, context: html, text, full: html, text
    adding DESTDIR
• src/utils/bigWigSummary/makefile
  • 1.7 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/bigWigToBedGraph/makefile
  • 1.7 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/ccCp/ccCp.c
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/utils/faCount/makefile
  • 1.7 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/faFrag/makefile
  • 1.8 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/faOneRecord/makefile
  • 1.8 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/faRandomize/makefile
  • 1.4 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/faSize/makefile
  • 1.8 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/faSomeRecords/makefile
  • 1.9 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/faToNib/makefile
  • 1.13 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/faToTwoBit/makefile
  • 1.15 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/htmlCheck/makefile
  • 1.10 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.9 lines changed: 1, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/nibFrag/makefile
  • 1.10 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/qa/bigPush.csh
  • 1.7 lines changed: 1, context: html, text, full: html, text
    tweak to usage
• src/utils/qa/chain.csh
  • 1.25 lines changed: 3, context: html, text, full: html, text
    added call for new getChainLines script
• src/utils/qa/findNewTables.csh
  • 1.10 lines changed: 3, context: html, text, full: html, text
    fixed the way GENBANK list is used
• src/utils/qa/getChainLines.csh
  • 1.2 lines changed: 2, context: html, text, full: html, text
    we do not need the dollar-sign before the variable
  • 1.1 lines changed: 72, context: html, text, full: html, text
    this script gets the two variables needed for the chain description page ($chainMinScore and $chainLinearGap). similar to the getMatrixLines script which gets the $matrix variable
• src/utils/qa/makefile
  • 1.114 lines changed: 1, context: html, text, full: html, text
    new getChainLines script
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.24 lines changed: 1, context: html, text, full: html, text
    happy fiction that preview is really on next branch already
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.80 lines changed: 3, context: html, text, full: html, text
    v216 final build
• src/utils/qa/weeklybld/doNewReview.csh
  • 1.15 lines changed: 4, context: html, text, full: html, text
    making it a little more friendly
• src/utils/qa/weeklybld/makeUserApps.csh
  • 1.6 lines changed: 3, context: html, text, full: html, text
    oops fixed path problem
• src/utils/textHistogram/makefile
  • 1.15 lines changed: 0, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/twoBitInfo/makefile
  • 1.11 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.10 lines changed: 1, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/twoBitToFa/makefile
  • 1.16 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.15 lines changed: 1, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/utils/wigToBigWig/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    adding SOCKETLIB back, apparently needed for solaris and other stuff (this is not SSL related)
  • 1.7 lines changed: 1, context: html, text, full: html, text
    fixing makefiles; getting rid of unnecessary $SOCKETLIB, adding $DESTDIR and removing an unneeded space-char
• src/weblet/counter/counter.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
• src/weblet/hitreport/hitreport.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.

• lines changed: 12096
• files changed: 251