All File Changes

v279_preview to v279_preview2 (2013-01-29 to 2013-02-05) v279

• src/gfServer/gfServer.c
  • lines changed 25, context: html, text, full: html, text
    Jim shortens it.
• src/hg/encode/encodeCvTerm/encodeCvTerm.c
  • lines changed 49, context: html, text, full: html, text
    Tool for extracting info from ENCODE controlled vocabulary file entries. Used in building Track #10042: Uniform TFBS
• src/hg/encode/encodeCvTerm/makefile
  • lines changed 15, context: html, text, full: html, text
    Tool for extracting info from ENCODE controlled vocabulary file entries. Used in building Track #10042: Uniform TFBS
• src/hg/encode/makefile
  • lines changed 2, context: html, text, full: html, text
    Tool for extracting info from ENCODE controlled vocabulary file entries. Used in building Track #10042: Uniform TFBS
  • lines changed 10, context: html, text, full: html, text
    Sort dirs list
• src/hg/hgTables/galaxy.c
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Galaxy MAF documentation.
  • lines changed 1, context: html, text, full: html, text
    Escaped the percent sign in the link to Galaxy.
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 6, context: html, text, full: html, text
    Code Review #10076 - Undoing much of e92495a7 because Tim made me lookagain at why I was getting the composite back from tdbForTrack.
    
  • lines changed 26, context: html, text, full: html, text
    Native VCF tracks don't have bigDataUrl & need a proper call to bbiNameFromSettingOrTableChrom.
• src/hg/hgc/numtsClick.c
  • lines changed 8, context: html, text, full: html, text
    Track #8533 NumtS tracks: Add logic to numtsClick.c to handle the shortened name in 'numtSMitochondrion' table. For example, old NumtS data for or hg18, hg19 and mm9 have name like Mms_NumtS_096_b1, and all new species like dog and cow now have a shorten name like 'SS_NumtS_246')
• src/hg/hgc/peakClusters.c
  • lines changed 31, context: html, text, full: html, text
    Fix ordering of list of assayed cells in Clusters tracks like #9954: DNase Clusters V2
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 10, context: html, text, full: html, text
    Putting downloads link in alphabetical order RM#10065, code review
  • lines changed 124, context: html, text, full: html, text
    Adding a section for Analysis Working Group download links to ENCODE Download pate, RM#10047
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 4, context: html, text, full: html, text
    Per request of data contributor for cerSim1, changed institution affiliation for Oliver Ryder. Also clarified in a few places that this is the southern white rhinoceros, tho left it as white rhinoceros in most places to match our database entry.
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link, per Pauline.
  • lines changed 14, context: html, text, full: html, text
    Fixed broken links (redmine #9984)
  • lines changed 7, context: html, text, full: html, text
    Fixed more broken links (redmine 9984)
  • lines changed 19, context: html, text, full: html, text
    Updated some links; fixed ordering of baboon releases (redmine #9984)
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 7, context: html, text, full: html, text
    Per request of data contributor for cerSim1, changed institution affiliation for Oliver Ryder. Also clarified in a few places that this is the southern white rhinoceros, tho left it as white rhinoceros in most places to match our database entry.
• src/hg/htdocs/images/greenChecksmCtr.png
  • lines changed 0, context: html, text, full: html, text
    Added vertically-centered green check box png image, used by mirror selector menu.
• src/hg/htdocs/indexNews.html
  • lines changed 7, context: html, text, full: html, text
    Per request of data contributor for cerSim1, changed institution affiliation for Oliver Ryder. Also clarified in a few places that this is the southern white rhinoceros, tho left it as white rhinoceros in most places to match our database entry.
• src/hg/inc/hdb.h
  • lines changed 6, context: html, text, full: html, text
    Code Review #10076 - Undoing much of e92495a7 because Tim made me lookagain at why I was getting the composite back from tdbForTrack.
    
• src/hg/js/hgVarAnnogrator.js
  • lines changed 104, context: html, text, full: html, text
    Javascript robustness: added "use strict" as suggested by Brian C; added pragmas for jslint and got jslint to pass again.
• src/hg/js/subCfg.js
  • lines changed 3, context: html, text, full: html, text
    Removed invalid warn message. Denisovan Modern Derived track trilled over it (redmine 8886). When views exist but none are configurable, then assertion was wrong.
• src/hg/lib/geoMirror.c
  • lines changed 2, context: html, text, full: html, text
    Added vertically-centered green check box png image, used by mirror selector menu.
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    Code Review #10076 - Undoing much of e92495a7 because Tim made me lookagain at why I was getting the composite back from tdbForTrack.
    
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    Buf too small! Needed to expand for track with 177x91 trackUi matrix: #10042 Uniform TFBS
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 222, context: html, text, full: html, text
    Rename make doc to make it easier to find
  • lines changed 231, context: html, text, full: html, text
    First cut track load and display. ENCODE Track #10042: Uniform TFBS
• src/hg/makeDb/doc/encodeDccHg19/awgUniform.txt
  • lines changed 185, context: html, text, full: html, text
    Rename make doc to make it easier to find
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 1, context: html, text, full: html, text
    Correction to a comment
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #10098 (GWAS Catalog): bimonthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 60, context: html, text, full: html, text
    Ran hg19-panTro4 for user, using same params as for panTro3.
  • lines changed 40, context: html, text, full: html, text
    Track #10098 (GWAS Catalog): bimonthly update.
• src/hg/makeDb/doc/susScr2.txt
  • lines changed 5, context: html, text, full: html, text
    Track #8533: Description file for susScr2's NumtS tracks.
• src/hg/makeDb/genbank/src/dbload/dumpTableStats
  • lines changed 1, context: html, text, full: html, text
    add a ten second sleep between calls to dump mySQL table status (per Hiram)
• src/hg/makeDb/schema/all.joiner
  • lines changed 64, context: html, text, full: html, text
    Added Denisova tables to ignored section.
• src/hg/makeDb/trackDb/README
  • lines changed 33, context: html, text, full: html, text
    adding back in the Variable Substitution section per Brooke's code review #10067
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 5, context: html, text, full: html, text
    Correcting broken URL for cv.ra based on ChronJob report
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 5, context: html, text, full: html, text
    Copying alpha cv.ra to beta and public: Correcting broken URL for cv.ra based on ChronJob report
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 5, context: html, text, full: html, text
    Copying alpha cv.ra to beta and public: Correcting broken URL for cv.ra based on ChronJob report
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Modified canFam2/3 release tags for hg19 -> canFam3 chain/net track (redmine #8826)
  • lines changed 32, context: html, text, full: html, text
    Track #7043 (SNPs for mm10): Moved up search specs for snp137 to top-level trackDb.ra for sharing with mouse. (Thanks Luvina!)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    First cut track load and display. ENCODE Track #10042: Uniform TFBS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
  • lines changed 4905, context: html, text, full: html, text
    First cut track load and display. ENCODE Track #10042: Uniform TFBS
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    add URL for Coriell Del Dup track, and remove trailing spaces in file, redmine 6530
• src/hg/makeDb/trackDb/pig/susScr2/numtSeqSusScr2.html
  • lines changed 77, context: html, text, full: html, text
    Track #8533: Description file for susScr2's NumtS tracks.
  • lines changed 4, context: html, text, full: html, text
    Change the department in Italian to English.
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    Track #8533 Add search rules for NumtS tables for susScr2.
• src/hg/makeDb/trackDb/qPcrPrimers.html
  • lines changed 2, context: html, text, full: html, text
    Decided that 'UCSC Gene' should be 'UCSC Genes'.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed References section in html; made other minor html corrections; removed release tag from .ra file (redmine #9135)
  • lines changed 32, context: html, text, full: html, text
    Track #7043 (SNPs for mm10): Moved up search specs for snp137 to top-level trackDb.ra for sharing with mouse. (Thanks Luvina!)
• src/hg/makeDb/trackDb/ucscGenePfam.html
  • lines changed 35, context: html, text, full: html, text
    add detail page of ucscGenePfam track (#9135)
  • lines changed 9, context: html, text, full: html, text
    some additions as suggested by Steve (#9135)
  • lines changed 25, context: html, text, full: html, text
    Fixed References section in html; made other minor html corrections; removed release tag from .ra file (redmine #9135)
• src/hg/oneShot/freen/freen.c
  • lines changed 1, context: html, text, full: html, text
    Removing extranious blank line.
• src/hg/pslCDnaFilter/algo.txt
  • lines changed 20, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/cDnaStats.c
  • lines changed 2, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 7, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/decayMinCoverTest/filt.out
  • lines changed 1, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/globalBestTest/filt.out
  • lines changed 2, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/filt.out
  • lines changed 1, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/hapLocalTest/filt.out
  • lines changed 1, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/hapLocalXenoTest/filt.out
  • lines changed 2, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/localBestTest/filt.out
  • lines changed 2, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/overlapTest/drop.psl
  • lines changed 5, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/overlapTest/filt.out
  • lines changed 4, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/overlapTest/keep.psl
  • lines changed 5, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/overlapTest/weird.psl
  • lines changed 2, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/uniqueMappedHapTest/filt.out
  • lines changed 1, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/uniqueMappedTest/filt.out
  • lines changed 1, context: html, text, full: html, text
    Minor changes relative to previous weird overlap change. Print stats in the order the filters happen and fixed test output
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/drop.psl
  • lines changed 7, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/filt.out
  • lines changed 5, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/keep.psl
  • lines changed 1, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnMinCoverTest/weird.psl
  • lines changed 0, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/drop.psl
  • lines changed 7, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/filt.out
  • lines changed 4, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/keep.psl
  • lines changed 1, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/expected/weirdOverlapMultAlnTest/weird.psl
  • lines changed 0, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/input/weirdOverlapMultAln.psl
  • lines changed 8, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/pslCDnaFilter/tests/makefile
  • lines changed 16, context: html, text, full: html, text
    Fixed handling of multiple indentical overlapping alignments create by mappingproteins via mRNAs, along with a couple of weird alignments. This results in
    all alignments being kept. The weird overlap was moved until later so that
    -bestOverlap and other filters still work.
    
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • lines changed 19, context: html, text, full: html, text
    Parse out metaobject name of the experiment control (follows _VS_) from Anshuls TFBS peak filesnames. ENCODE Track #10042: Uniform TFBS
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 3, context: html, text, full: html, text
    Assembly #6352 Rename musPut1 to musFur1.
  • lines changed 200, context: html, text, full: html, text
    Track #9407: Ensembl Genes v70 update.
  • lines changed 1, context: html, text, full: html, text
    Track #9407: Ensembl Genes v70 update corrected choHof1 type.
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 83, context: html, text, full: html, text
    ready to use the new RepeatMasker 4.0.0 version with new types of search engines and correct liftUp for .align files
• src/hg/utils/automation/ensGene/felCat5.ensGene.ra
  • lines changed 9, context: html, text, full: html, text
    Track #9407 Ensembl Genes v70 update ra file for felCat5 and rn5.
  • lines changed 1, context: html, text, full: html, text
    Track 9407 ensembl v70 update: Database name Typo corrected.
• src/hg/utils/automation/ensGene/gadMor1.ensGene.ra
  • lines changed 9, context: html, text, full: html, text
    Track #9407 Add gadMor1 to v70 list.
• src/hg/utils/automation/ensGene/rn5.ensGene.ra
  • lines changed 7, context: html, text, full: html, text
    Track #9407 Ensembl Genes v70 update ra file for felCat5 and rn5.
• src/inc/bits.h
  • lines changed 6, context: html, text, full: html, text
    Corrected bug Angie found in previous checkin. 'Clone' is always a clone. Also changed lmBit routines to require lm, rather than suggest that it is optional.
• src/inc/localmem.h
  • lines changed 5, context: html, text, full: html, text
    Corrected bug Angie found in previous checkin. 'Clone' is always a clone. Also changed lmBit routines to require lm, rather than suggest that it is optional.
• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 47, context: html, text, full: html, text
    Improving way unused monomers get inserted back in output a little.
  • lines changed 10, context: html, text, full: html, text
    Removing some debugging code.
  • lines changed 6, context: html, text, full: html, text
    Making random seed default to 0 rather than time to make results more reproducible. Adding in a NULL check to avoid a seg fault.
• src/lib/bits.c
  • lines changed 12, context: html, text, full: html, text
    Corrected bug Angie found in previous checkin. 'Clone' is always a clone. Also changed lmBit routines to require lm, rather than suggest that it is optional.
• src/lib/localmem.c
  • lines changed 15, context: html, text, full: html, text
    Corrected bug Angie found in previous checkin. 'Clone' is always a clone. Also changed lmBit routines to require lm, rather than suggest that it is optional.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    add pslMap to userApps (#9135)
• src/utils/qa/checkBOT.csh
  • lines changed 32, context: html, text, full: html, text
    Put bottleneck host name in a variable and changed it from genome-bottle to rrnfs1. Replaced calls to ipw with calls to whois. Took out requirement to run on hgwdev. Set variable 'worst' using IPs with session names chopped off instead of raw output from bottleneck. Removed an unecessary echo from an if statement. Changed printout of whois info for worst offender to only print if argument is 'all'. Added PIDs to filename and added an onintr and cleanup instruction.
  • lines changed 1, context: html, text, full: html, text
    Removed path to bottleneck program (it is in a different location on hgwbeta).

• lines changed: 7078
• files changed: 100