All File Changes

v301_base to v302_preview (2014-06-09 to 2014-06-16) v302

• src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
  • lines changed 1, context: html, text, full: html, text
    Doing enrichment calcs straight up bigBed types.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 55, context: html, text, full: html, text
    Adding 'bed_' type formats.
• src/hg/encode3/encodeDataWarehouse/edwUndeprecate/edwUndeprecate.c
  • lines changed 57, context: html, text, full: html, text
    Your basic command line undeprecator.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 1, context: html, text, full: html, text
    Add dm6 to edwAssembly, edwEnrichTarget, and edwQaContamTarget tables.Add dm6 to specialAsm[] in edwLib.c
    
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 5, context: html, text, full: html, text
    Add dm6 to edwAssembly, edwEnrichTarget, and edwQaContamTarget tables.Add dm6 to specialAsm[] in edwLib.c
    
• src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/edwSolexaToSangerFastq.c
  • lines changed 4, context: html, text, full: html, text
    Fixing signedness.
• src/hg/encode3/validateManifest/VERSION.TXT
  • lines changed 1, context: html, text, full: html, text
    vm releasing v1.9
  • lines changed 1, context: html, text, full: html, text
    adding dm6 to vm v1.9
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 1, context: html, text, full: html, text
    adding dm6 to vm v1.9
• src/hg/hgc/hgc.c
  • lines changed 21, context: html, text, full: html, text
    Extended URL trackDb setting to new tokens for item start and stop. Currently coded to use 1 bases coordinates for both start and stop. Redmine #13218
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    Track name should not have dashes in it, because SQL table names do not allow it. Can't think of a reason that hub tracks (which are file-names) couldn't have dashes, but consistency is simplicity.
• src/hg/inc/versionInfo.h
  • lines changed 2, context: html, text, full: html, text
    maintain the new copyright message in versionInfo.h refs #13415
• src/hg/js/ajax.js
  • lines changed 56, context: html, text, full: html, text
    Polished for jshint. Some minor reformatting included.
  • lines changed 5, context: html, text, full: html, text
    Fixed setTimeouts (thanks Angie) and marked some code as possibly DEAD.
• src/hg/js/alleles.js
  • lines changed 44, context: html, text, full: html, text
    Polished for jshint.
  • lines changed 4, context: html, text, full: html, text
    Fixed setTimeouts (thanks Angie) and marked some code as possibly DEAD.
• src/hg/js/autocomplete.js
  • lines changed 24, context: html, text, full: html, text
    jsbeautifier
  • lines changed 9, context: html, text, full: html, text
    jshinted. #13255
  • lines changed 2, context: html, text, full: html, text
    Removing jshint comment
  • lines changed 1, context: html, text, full: html, text
    Fix a few double eq/noteqs not found by jshint
• src/hg/js/ddcl.js
  • lines changed 245, context: html, text, full: html, text
    Polished for jshint. Minor reformatting. Fixed atleast one bug.
  • lines changed 19, context: html, text, full: html, text
    Fixed setTimeout (thanks Angie) and retooled where the output of a bug that was fixed yesterday was relied upon downstream.
• src/hg/js/hgGateway.js
  • lines changed 9, context: html, text, full: html, text
    jsbeautifier
  • lines changed 1, context: html, text, full: html, text
    jshinted. #13255
• src/hg/js/hgHubConnect.js
  • lines changed 18, context: html, text, full: html, text
    jsbeautifier
  • lines changed 4, context: html, text, full: html, text
    jshinted. #13255
  • lines changed 1, context: html, text, full: html, text
    Removing jshint comment
  • lines changed 34, context: html, text, full: html, text
    Had to merge in change from master, and clean up a bit.
  • lines changed 1, context: html, text, full: html, text
    Fix a few double eq/noteqs not found by jshint
• src/hg/js/hgTracks.js
  • lines changed 347, context: html, text, full: html, text
    Polished for jshint, which uncovered a couple minor bugs. Minimal reformatting. Plan to check in a reformatted version of the file soon.
  • lines changed 206, context: html, text, full: html, text
    Formatting changes to be laid on top of jshint polishing.
  • lines changed 1, context: html, text, full: html, text
    Fix for the (non-jshint related) bug where hiding then revisualizing a track without an intervening full page reload resultsin in an error. Redmine #13165.
  • lines changed 8, context: html, text, full: html, text
    Fix bug where gene suggest was failing to make UCSC genes visible. Redmine #13304.
  • lines changed 5, context: html, text, full: html, text
    Extended last fix to a couple more places that were relying upon creating hidden inputs, where adding to the queued cart vars makes more sense. Related to but not exactly redmine #13304.
  • lines changed 6, context: html, text, full: html, text
    Tightened the screws on several descrete cases where comparison to undefined might have been acting on undeclared variable. I have looked through all the js files I altered for jshint and only found these few cases which might (but in practice probably don't) trigger exceptions.
  • lines changed 6, context: html, text, full: html, text
    Backing out several of the previous 'tightening screws' changes. In particular typeof(thing.var) !== 'undefined' if thing.var === null. I thought I tested this eariler, but now it is breaking sortTable, as reported by QA.
• src/hg/js/hgVarAnnogrator.js
  • lines changed 18, context: html, text, full: html, text
    Got jshint to run cleanly. It uncovered a bug -- I was comparing atypeof to 'list' which is incorrect. JQuery has a handy $isArray().
    (As of 1.7 it also has $.isNumeric() but we can't use that yet.)
    
• src/hg/js/hui.js
  • lines changed 286, context: html, text, full: html, text
    Plished for jshint and some reformatting. At least one bug corrected.
  • lines changed 1, context: html, text, full: html, text
    Fix for tool-tip hover on hgTrackUi matrices, as reported by Jonathon.
• src/hg/js/jquery.tablednd.js
  • lines changed 12, context: html, text, full: html, text
    Polished only UCSC changes for jshint. These 3rd party files modified by UCSC do NOT pass jshint. But changes are kept to minimum for later disambiguating.
• src/hg/js/jshint.exclude
  • lines changed 4, context: html, text, full: html, text
    Adding jshint target to js/makefile. In inc/common.mk, JSHINT is setto true (program that simply exits with no error) if not already set,
    so running 'make jshint' is a no-op unless you set JSHINT=jshint in
    your environment.
    
  • lines changed 4, context: html, text, full: html, text
    Removed jshint.exclude file. Removed some unnecessary ifdef's frommakefile, removed the jshint command that used jshint.exclude,
    and made doInstall depend on jshint.
    
• src/hg/js/makefile
  • lines changed 3, context: html, text, full: html, text
    Adding jshint target to js/makefile. In inc/common.mk, JSHINT is setto true (program that simply exits with no error) if not already set,
    so running 'make jshint' is a no-op unless you set JSHINT=jshint in
    your environment.
    
  • lines changed 33, context: html, text, full: html, text
    All UCSC js files should pass jshint as part of make. Do not rely upon jshint.exclude.
  • lines changed 1, context: html, text, full: html, text
    Fix typo in JSHINT env var name.
  • lines changed 11, context: html, text, full: html, text
    Removed jshint.exclude file. Removed some unnecessary ifdef's frommakefile, removed the jshint command that used jshint.exclude,
    and made doInstall depend on jshint.
    
• src/hg/js/subCfg.js
  • lines changed 148, context: html, text, full: html, text
    Polished for jshint. Minor reformatting.
• src/hg/js/ui.dropdownchecklist.js
  • lines changed 6, context: html, text, full: html, text
    Polished only UCSC changes for jshint. These 3rd party files modified by UCSC do NOT pass jshint. But changes are kept to minimum for later disambiguating.
• src/hg/js/utils.js
  • lines changed 591, context: html, text, full: html, text
    Polished for jshint. Minor formatting (e.g. all lines within 100). Strengthened normed(). Marked some code as possibly DEAD.
  • lines changed 3, context: html, text, full: html, text
    Removed 'DEAD CODE?' comment next to setCheckboxList because it is used by hgVai.c.
  • lines changed 35, context: html, text, full: html, text
    Changes at Angie's suggestion during pre-code-review. Redmine #13255.
  • lines changed 5, context: html, text, full: html, text
    Undeclared variables do not pass the 'truthiness' test without error. Redmine #13385.
  • lines changed 28, context: html, text, full: html, text
    Tightened the screws on several descrete cases where comparison to undefined might have been acting on undeclared variable. I have looked through all the js files I altered for jshint and only found these few cases which might (but in practice probably don't) trigger exceptions.
  • lines changed 12, context: html, text, full: html, text
    Backing out several of the previous 'tightening screws' changes. In particular typeof(thing.var) !== 'undefined' if thing.var === null. I thought I tested this eariler, but now it is breaking sortTable, as reported by QA.
• src/hg/lib/trackHub.c
  • lines changed 12, context: html, text, full: html, text
    Partially addresses #11296. Forbid the main known evil setting "idInUrlSql" in hubs.
  • lines changed 36, context: html, text, full: html, text
    strip out parens and carriage returns from trackHub decriptionUrl's. Addroutine to get blat parameters
    
• src/hg/makeDb/doc/dm6.txt
  • lines changed 90, context: html, text, full: html, text
    lift dm3 flyBaseGene to dm6.
• src/hg/makeDb/doc/hg38.txt
  • lines changed 17, context: html, text, full: html, text
    add scientific name phylo tree file for the 7-way refs #13300
  • lines changed 35, context: html, text, full: html, text
    reload cytoBand track with corrected data refs #13379
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 13, context: html, text, full: html, text
    build procedure for Lamprey genes refs #13358
  • lines changed 45, context: html, text, full: html, text
    build procedure for Lamprey genes refs #13358
• src/hg/makeDb/doc/quickAssembly.txt
  • lines changed 5, context: html, text, full: html, text
    automatic download genbank refs #252
  • lines changed 36, context: html, text, full: html, text
    updating windowMasker sequence refs #252
• src/hg/makeDb/trackDb/acembly.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/affyAllExonProbes.html
  • lines changed 75, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/affyExonTissues.html
  • lines changed 16, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/allenBrainAli.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/baboon/papHam1/gap.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on baboon (papHam1) track description pages.
• src/hg/makeDb/trackDb/baboon/papHam1/gold.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on baboon (papHam1) track description pages.
• src/hg/makeDb/trackDb/ccdsGene.html
  • lines changed 30, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 34, context: html, text, full: html, text
    lift dm3 flyBaseGene to dm6.
• src/hg/makeDb/trackDb/drosophila/droGri1/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on drosophila (droGri1 and droPer1) track description pages.
• src/hg/makeDb/trackDb/drosophila/droGri1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on drosophila (droGri1 and droPer1) track description pages.
• src/hg/makeDb/trackDb/drosophila/droPer1/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on drosophila (droGri1 and droPer1) track description pages.
• src/hg/makeDb/trackDb/grcIncidentDb.html
  • lines changed 1, context: html, text, full: html, text
    incidents now come from a different directory refs #12407
  • lines changed 1, context: html, text, full: html, text
    correct generic URL reference to the GRC directory refs #12407
• src/hg/makeDb/trackDb/human/grcIncidentDb.html
  • lines changed 25, context: html, text, full: html, text
    incidents now come from a different directory refs #12407
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    removed a few lines per code review #13407
• src/hg/makeDb/trackDb/lamprey/petMar2/lampreyGene.html
  • lines changed 2, context: html, text, full: html, text
    made correction to reference link
• src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    add search rule and vis pack for lampreyGenes refs #9153
  • lines changed 2, context: html, text, full: html, text
    fix search rule for lampreyGenes refs #9153
• src/hg/makeDb/trackDb/mouse/affyGnf1m.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/affyGnfU74A.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/affyGnfU74B.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/affyGnfU74C.html
  • lines changed 12, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/affyMOE430.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/affyU74.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/genotypeArrays.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/gnfAtlas2.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/igtc.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/ikmc.html
  • lines changed 37, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/jaxRepTranscript.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 74, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/exoniphy.html
  • lines changed 27, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/knownGene.html
  • lines changed 28, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/knownGeneOld4.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
  • lines changed 74, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/pseudoYale60.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/targetScanS.html
  • lines changed 37, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/transcriptome.html
  • lines changed 16, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/vegaGeneComposite.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on some mouse (mm9) ENCODE track description pages
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release3.html
  • lines changed 9, context: html, text, full: html, text
    Changing links on some mouse (mm9) ENCODE track description pages
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
  • lines changed 16, context: html, text, full: html, text
    Changing links on some mouse (mm9) ENCODE track description pages
  • lines changed 1, context: html, text, full: html, text
    Changing link on mouse (mm9) description page
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on some mouse (mm9) ENCODE track description pages
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.release2.html
  • lines changed 4, context: html, text, full: html, text
    Changing links on some mouse (mm9) ENCODE track description pages
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.html
  • lines changed 15, context: html, text, full: html, text
    Changing links on some mouse (mm9) ENCODE track description pages
• src/hg/makeDb/trackDb/mouse/stsMapMouseNew.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/mouse/xenoRefGene.html
  • lines changed 8, context: html, text, full: html, text
    Changing links on mouse (mm9) track description pages
• src/hg/makeDb/trackDb/pika/ochPri2/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on Pika (ochPri2) track description pages.
• src/hg/makeDb/trackDb/pika/ochPri2/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on Pika (ochPri2) track description pages.
• src/hg/makeDb/trackDb/pika/ochPri2/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on Pika (ochPri2) track description pages.
• src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on rhesus (rheMac3) track description pages.
• src/hg/makeDb/trackDb/rhesus/rheMac3/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on rhesus (rheMac3) track description pages.
• src/hg/makeDb/trackDb/rhesus/rheMac3/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on rhesus (rheMac3) track description pages.
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on worm (ce10) track description pages.
• src/hg/makeDb/trackDb/worm/ce10/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on worm (ce10) track description pages.
• src/hg/makeDb/trackDb/worm/ce10/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on worm (ce10) track description pages.
• src/hg/makeDb/trackDb/worm/ce10/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on worm (ce10) track description pages.
• src/hg/oneShot/freen/freen.c
  • lines changed 37, context: html, text, full: html, text
    Freen finds a lineFileSeek bug.
  • lines changed 40, context: html, text, full: html, text
    testing AUTO SQL
  • lines changed 24, context: html, text, full: html, text
    Fixing merge conflicts
  • lines changed 28, context: html, text, full: html, text
    Demoing autoSql
• src/hg/txGene/txGeneValidation/makefile
  • lines changed 2, context: html, text, full: html, text
    create scripts destination refs #13327
  • lines changed 3, context: html, text, full: html, text
    include DESTDIR on SCRIPTS destination refs #13327
• src/hg/utils/automation/grcUpdate.sh
  • lines changed 92, context: html, text, full: html, text
    new style of processing for GRC incident update track refs #12407
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
  • lines changed 1, context: html, text, full: html, text
    fix a problem with cached hubs in hubPublicCheck
• src/hg/utils/phyloTrees/db.ncbiTaxId.tab
  • lines changed 131, context: html, text, full: html, text
    convenient to have db to taxId relation refs #10272
  • lines changed 221, context: html, text, full: html, text
    not sequence number on db name and with species name and download site refs #10272
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 32, context: html, text, full: html, text
    adding 32 new assemblies now available refs #10272
• src/inc/common.mk
  • lines changed 4, context: html, text, full: html, text
    Adding jshint target to js/makefile. In inc/common.mk, JSHINT is setto true (program that simply exits with no error) if not already set,
    so running 'make jshint' is a no-op unless you set JSHINT=jshint in
    your environment.
    
  • lines changed 1, context: html, text, full: html, text
    Use true instead of /bin/true for portability (it's /usr/bin/true on BSD/OSX).
  • lines changed 5, context: html, text, full: html, text
    can find libpng.a in usr local lib on Mavericks with homebrew refs #13327
  • lines changed 10, context: html, text, full: html, text
    eliminate need for MACHTYPE setting and correct it when incorrect refs #12209
• src/inc/fq.h
  • lines changed 7, context: html, text, full: html, text
    stylistic changes
• src/lib/fq.c
  • lines changed 8, context: html, text, full: html, text
    stylistic changes
  • lines changed 1, context: html, text, full: html, text
    Fixing signedness warning/error
• src/lib/linefile.c
  • lines changed 8, context: html, text, full: html, text
    Removing an optimization for short seeks in lineFileSeek that was breaking in most cases.
• src/lib/trix.c
  • lines changed 2, context: html, text, full: html, text
    back out quick fix for lineFileSeek problem.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate need for MACHTYPE setting and correct it when incorrect refs #12209
• src/utils/bamMerge/bamMerge.c
  • lines changed 76, context: html, text, full: html, text
    Merges multiple bam files into a single bam file, for testing bamSplitByChrom
  • lines changed 12, context: html, text, full: html, text
    Removed a function that was librarified, updated comments and stylistic errors
• src/utils/bamSplitByChrom/bamSplitByChrom.c
  • lines changed 102, context: html, text, full: html, text
    Created the basic framework for bamSplitByChrom, which will take in a bam file and return a bam file for each chromosome present in the initial file
  • lines changed 49, context: html, text, full: html, text
    Program seems to be running as expceted, has not been tested yet.
  • lines changed 20, context: html, text, full: html, text
    Removed test functions and white space, camel cased variables and added comments.
  • lines changed 16, context: html, text, full: html, text
    Fixed an I/O bug
  • lines changed 3, context: html, text, full: html, text
    Not working for chromosomes with underscores in their name. Working for others.
  • lines changed 31, context: html, text, full: html, text
    Not working for unique chromosomes
  • lines changed 62, context: html, text, full: html, text
    changed structure to increase efficiency, added 'unmapped.bam' to output
  • lines changed 19, context: html, text, full: html, text
    Removed functions that were already in the library,replaced the functions with their counterparts in the library
    
  • lines changed 11, context: html, text, full: html, text
    Added comments and fixed stylistic errors
  • lines changed 29, context: html, text, full: html, text
    Removed memory leak, fixed some stylistic errors
  • lines changed 20, context: html, text, full: html, text
    stylistic changes, testing new option '-unmapped'
  • lines changed 43, context: html, text, full: html, text
    changed bamSplitByChrom so that the outputs are put into a user specified directory
• src/utils/bamToFastq/bamToFastq.c
  • lines changed 61, context: html, text, full: html, text
    Changed comments and librarified functions
  • lines changed 11, context: html, text, full: html, text
    Removed memory leak, fixed some stylistic errors
  • lines changed 2, context: html, text, full: html, text
    stylistic changes
• src/utils/fastqMottTrim/fastqMottTrim.c
  • lines changed 100, context: html, text, full: html, text
    Updated to with new library file'fq', fixed indenting and comment missplacement
    
  • lines changed 8, context: html, text, full: html, text
    stylistic changes
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v302 preview1 refs #13448
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 2, context: html, text, full: html, text
    removing pauline from emails and eliminate ann duplicate email refs #13189
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 2, context: html, text, full: html, text
    removing pauline from emails and eliminate ann duplicate email refs #13189
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    removing pauline from emails and eliminate ann duplicate email refs #13189
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    removing pauline from emails and eliminate ann duplicate email refs #13189
• src/utils/qa/weeklybld/updateCgiVersion.csh
  • lines changed 5, context: html, text, full: html, text
    maintain the new copyright message in versionInfo.h refs #13415

• lines changed: 4718
• files changed: 168