CVS changes by file

branch to review (2009-03-10 to 2009-03-17) v202

• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.28 lines changed: 2, context: html, text, full: html, text
    fixed typo
• src/hg/archaeStuff/scripts/archaeBrowser/ProteinDb.pm
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed typo
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    plug the memory leak, > 100bytes per input line, fatal for ENCODE
• src/hg/checkTableCoords/tests/input/pslCTCBad.psl
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Fixed formatting error (too many tabs) that was tolerated when hgLoadPsl wrote its own .tab file for loading but caused trouble when hgLoadPsl (with -nobin and -noSort) sent this file directly to mysql.
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.59 lines changed: 10, context: html, text, full: html, text
    added an option to not do downloads (and implicitly not do table load) so that I could regenerate pushq and whatever else gets done, because I loaded 16 GB of data and got a mysql error on the trackDb step immediaetly after the load was complete.
  • 1.58 lines changed: 1, context: html, text, full: html, text
    Change link to static terms doc to absolute path, avoiding problems with releasing index.html to RR
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.14 lines changed: 10, context: html, text, full: html, text
    noAutoCreate setting at top-level of daf to control generation of autoRawSignal files, and downloadOnly setting in DAF views to control whether files are loaded or not
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.168 lines changed: 7, context: html, text, full: html, text
    validate all of wiggle files
  • 1.167 lines changed: 69, context: html, text, full: html, text
    adding downloadOnly property to Views in DAF, adding validateFiles support in broadPeak, fastq, tagAlign so can validate CSHL data in reasonable time
  • 1.166 lines changed: 21, context: html, text, full: html, text
    mods to keep massive sorts under control; sort files independently with mem limit, then do merge sort of all
• src/hg/encode/makefile
  • 1.11 lines changed: 1, context: html, text, full: html, text
    add validateFiles to makefile directory list
• src/hg/encode/validateFiles/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    first version of a validator for encode, currently supports tagAlign and pairedTagAlign, much faster than Perl adn does extra checking on start<end, chrom, chromSize, etc
• src/hg/encode/validateFiles/validateFiles.c
  • 1.11 lines changed: 3, context: html, text, full: html, text
    mods to usage message
  • 1.10 lines changed: 36, context: html, text, full: html, text
    added bedGraph as bedType variant and modified usage text
  • 1.9 lines changed: 49, context: html, text, full: html, text
    adding narrow and gapped peaks
  • 1.8 lines changed: 62, context: html, text, full: html, text
    support for broadPeak
  • 1.7 lines changed: 138, context: html, text, full: html, text
    improved usage message, continue after error in # columns, add csqual, put colorSpace as option
  • 1.6 lines changed: 11, context: html, text, full: html, text
    provide colorspace as option to include chars 0-3 in DNA
  • 1.5 lines changed: 53, context: html, text, full: html, text
    making everythign use linefile so .gz/.bzip2 files handled automatically
  • 1.4 lines changed: 128, context: html, text, full: html, text
    fix so comment lines only appear at top of fastq, and added csfasta format
  • 1.3 lines changed: 117, context: html, text, full: html, text
    support for fastq
  • 1.2 lines changed: 1, context: html, text, full: html, text
    add -type= to main usage line
  • 1.1 lines changed: 328, context: html, text, full: html, text
    first version of a validator for encode, currently supports tagAlign and pairedTagAlign, much faster than Perl adn does extra checking on start<end, chrom, chromSize, etc
• src/hg/hgGateway/hgGateway.c
  • 1.111 lines changed: 3, context: html, text, full: html, text
    Disable CT for CGB servers for the time being.
• src/hg/hgGene/hgGene.c
  • 1.114 lines changed: 3, context: html, text, full: html, text
    Disabled the otherOrg section for CGB server for the time being.
• src/hg/hgGenome/hgGenome.c
  • 1.63 lines changed: 2, context: html, text, full: html, text
    fix - erase cart do-commands just in case of errAbort
• src/hg/hgNotAvail/hgNotAvail.c
  • 1.1 lines changed: 86, context: html, text, full: html, text
    Created hgNotAvail.c.
• src/hg/hgNotAvail/makefile
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Created makefile.
• src/hg/hgSession/hgSession.c
  • 1.49 lines changed: 3, context: html, text, full: html, text
    Added Browser and Email links after session-update message - thanks b0b for the suggestion!
• src/hg/hgTables/bedList.c
  • 1.63 lines changed: 2, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.62 lines changed: 2, context: html, text, full: html, text
    Fixing problem in bigWig custom track output. Testing (seems to work) with subtrack merge.
  • 1.61 lines changed: 18, context: html, text, full: html, text
    Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken.
• src/hg/hgTables/bigBed.c
  • 1.4 lines changed: 57, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Polishing bigBed status page a little.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding parameter to bedAsDef.
  • 1.1 lines changed: 127, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
• src/hg/hgTables/bigWig.c
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Putting up message about limits of subtrack merge in summary status page. Getting more extended intersection options back.
  • 1.2 lines changed: 66, context: html, text, full: html, text
    Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken.
  • 1.1 lines changed: 266, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/compositeTrack.c
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
• src/hg/hgTables/correlate.c
  • 1.74 lines changed: 6, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.73 lines changed: 6, context: html, text, full: html, text
    Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken.
  • 1.72 lines changed: 0, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/correlate.h
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.15 lines changed: 23, context: html, text, full: html, text
    Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken.
• src/hg/hgTables/filterFields.c
  • 1.65 lines changed: 7, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.64 lines changed: 1, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/gffOut.c
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
• src/hg/hgTables/hgTables.c
  • 1.176 lines changed: 2, context: html, text, full: html, text
    Adding microarray stuff to output microarray names in the microarrayGroupings.ra file. Also put in some bits to output the microarray groupings themselves but that's incomplete currently.
  • 1.175 lines changed: 30, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.174 lines changed: 12, context: html, text, full: html, text
    Added logic to disable other functions of TB (besides view table schema) for CGB servers.
  • 1.173 lines changed: 62, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
• src/hg/hgTables/hgTables.h
  • 1.129 lines changed: 11, context: html, text, full: html, text
    Adding microarray stuff to output microarray names in the microarrayGroupings.ra file. Also put in some bits to output the microarray groupings themselves but that's incomplete currently.
  • 1.128 lines changed: 11, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.127 lines changed: 16, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
  • 1.126 lines changed: 0, context: html, text, full: html, text
    Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken.
  • 1.125 lines changed: 46, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/identifiers.c
  • 1.27 lines changed: 3, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
• src/hg/hgTables/intersect.c
  • 1.48 lines changed: 6, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.47 lines changed: 3, context: html, text, full: html, text
    Putting up message about limits of subtrack merge in summary status page. Getting more extended intersection options back.
  • 1.46 lines changed: 1, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.45 lines changed: 103, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/joining.c
  • 1.52 lines changed: 2, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
• src/hg/hgTables/mainPage.c
  • 1.139 lines changed: 19, context: html, text, full: html, text
    Adding microarray stuff to output microarray names in the microarrayGroupings.ra file. Also put in some bits to output the microarray groupings themselves but that's incomplete currently.
  • 1.138 lines changed: 1, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.137 lines changed: 0, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/makefile
  • 1.53 lines changed: 1, context: html, text, full: html, text
    Adding microarray stuff to output microarray names in the microarrayGroupings.ra file. Also put in some bits to output the microarray groupings themselves but that's incomplete currently.
  • 1.52 lines changed: 1, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
  • 1.51 lines changed: 2, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/microarrayTables.c
  • 1.1 lines changed: 43, context: html, text, full: html, text
    Adding microarray stuff to output microarray names in the microarrayGroupings.ra file. Also put in some bits to output the microarray groupings themselves but that's incomplete currently.
• src/hg/hgTables/schema.c
  • 1.54 lines changed: 55, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
• src/hg/hgTables/seqOut.c
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
• src/hg/hgTables/sumStats.c
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.24 lines changed: 10, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTables/wiggle.c
  • 1.71 lines changed: 1, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.70 lines changed: 2, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.69 lines changed: 4, context: html, text, full: html, text
    Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken.
  • 1.68 lines changed: 143, context: html, text, full: html, text
    Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.480 lines changed: 2, context: html, text, full: html, text
    allow net tracks to color by gray scale, and fixing chain tracks Ui options
  • 1.479 lines changed: 1, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
  • 1.478 lines changed: 1, context: html, text, full: html, text
    hapmapSnpsUi: incomplete html found by Jim in code review.
  • 1.477 lines changed: 1, context: html, text, full: html, text
    Larger entry field for filter by chromosome on a chain track
• src/hg/hgTracks/bedTrack.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
• src/hg/hgTracks/chainTrack.c
  • 1.32 lines changed: 3, context: html, text, full: html, text
    allow net tracks to color by gray scale, and fixing chain tracks Ui options
  • 1.31 lines changed: 9, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
• src/hg/hgTracks/hgTracks.c
  • 1.1561 lines changed: 5, context: html, text, full: html, text
    Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs
  • 1.1560 lines changed: 2, context: html, text, full: html, text
    Disabled Convert on top bar for CGB servers for the time being.
  • 1.1559 lines changed: 5, context: html, text, full: html, text
    Disable TB on CGB servers.
• src/hg/hgTracks/netTrack.c
  • 1.24 lines changed: 41, context: html, text, full: html, text
    allow net tracks to color by gray scale, and fixing chain tracks Ui options
• src/hg/hgTracks/simpleTracks.c
  • 1.71 lines changed: 14, context: html, text, full: html, text
    No longer default subtrack list when all are unselected.
  • 1.70 lines changed: 9, context: html, text, full: html, text
    Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs
  • 1.69 lines changed: 1, context: html, text, full: html, text
    Registered pgSnpHgwdev (Belinda's Genome Variants subtracks that should remain on hgwdev for now.
• src/hg/hgc/hgc.c
  • 1.1518 lines changed: 32, context: html, text, full: html, text
    Extra vertical whitespace between alt. pcr matches as suggested by Brooke. For HapMap SNPs (Phase III), show average of populations' allele frequencies instead of sum of all individual alleles.
  • 1.1517 lines changed: 2, context: html, text, full: html, text
    Changed hAllocate() to hAllocConnTrack() to fix a bug on CGB servers due to the logicalDb.
• src/hg/inc/bed.h
  • 1.52 lines changed: 4, context: html, text, full: html, text
    Adding parameter to bedAsDef.
  • 1.51 lines changed: 3, context: html, text, full: html, text
    Adding bedAsDef.
• src/hg/inc/chainCart.h
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
• src/hg/inc/hdb.h
  • 1.165 lines changed: 15, context: html, text, full: html, text
    Removing function prototype for a nonexistant function.
• src/hg/inc/hui.h
  • 1.121 lines changed: 22, context: html, text, full: html, text
    allow net tracks to color by gray scale, and fixing chain tracks Ui options
  • 1.120 lines changed: 3, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
• src/hg/inc/trackDb.h
  • 1.45 lines changed: 2, context: html, text, full: html, text
    Checked in cfgNetAlign to get passed compiler error
  • 1.44 lines changed: 2, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
• src/hg/inc/wiggle.h
  • 1.85 lines changed: 6, context: html, text, full: html, text
    Adding wigCompareFromString and wigCompareValFilter.
• src/hg/instinct/bioIntegrator/bioIntDriver.c
  • 1.13 lines changed: 15, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/bioMeta.c
  • 1.2 lines changed: 93, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    updated
• src/hg/instinct/bioIntegrator/populateDb.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    updated
• src/hg/js/hui.js
  • 1.22 lines changed: 32, context: html, text, full: html, text
    Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs
• src/hg/lib/bed.c
  • 1.62 lines changed: 21, context: html, text, full: html, text
    Adding parameter to bedAsDef.
  • 1.61 lines changed: 42, context: html, text, full: html, text
    Adding bedAsDef.
• src/hg/lib/cart.c
  • 1.104 lines changed: 10, context: html, text, full: html, text
    Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs
• src/hg/lib/chainCart.c
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
• src/hg/lib/encode/broadPeak.as
  • 1.4 lines changed: 1, context: html, text, full: html, text
    The Q-value is log after all
• src/hg/lib/encode/encodePeak.as
  • 1.6 lines changed: 1, context: html, text, full: html, text
    The Q-value is log after all
• src/hg/lib/encode/narrowPeak.as
  • 1.4 lines changed: 1, context: html, text, full: html, text
    The Q-value is log after all
• src/hg/lib/hdb.c
  • 1.398 lines changed: 24, context: html, text, full: html, text
    Remember answers to hDbIsActive and hgDbExists, was being called thousands of times during a simple refresh
  • 1.397 lines changed: 3, context: html, text, full: html, text
    Making hFindBed12FieldsAndBinWithConn static. Initializing empty strings a place where it might have been missed, and would certainly do no harm to add.
• src/hg/lib/hui.c
  • 1.176 lines changed: 62, context: html, text, full: html, text
    allow net tracks to color by gray scale, and fixing chain tracks Ui options
  • 1.175 lines changed: 1, context: html, text, full: html, text
    Presort to set priorites in trackDb now defaults to 10000 and above, allowing new subtracks to appear after subtracks known to cart.
  • 1.174 lines changed: 18, context: html, text, full: html, text
    Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs
  • 1.173 lines changed: 6, context: html, text, full: html, text
    Fixup the naming of the chain track variables in the multi-view composite
  • 1.172 lines changed: 30, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
  • 1.171 lines changed: 2, context: html, text, full: html, text
    Revert last change -- we need to wait till the RNA data submissions quiet down first
  • 1.170 lines changed: 4, context: html, text, full: html, text
    Move ENCODE downloads down a directory level
  • 1.169 lines changed: 1, context: html, text, full: html, text
    The Q-value is log after all
• src/hg/lib/trackDbCustom.c
  • 1.60 lines changed: 1, context: html, text, full: html, text
    Fixup the naming of the chain track variables in the multi-view composite
  • 1.59 lines changed: 7, context: html, text, full: html, text
    Fixup chain and net trackUi so they will work in multi-views
• src/hg/lib/web.c
  • 1.159 lines changed: 2, context: html, text, full: html, text
    Disable TB for CGB servers.
• src/hg/lib/wigDataStream.c
  • 1.85 lines changed: 82, context: html, text, full: html, text
    Adding wigCompareFromString and wigCompareValFilter.
• src/hg/makeDb/doc/droMoj2.txt
  • 1.4 lines changed: 11, context: html, text, full: html, text
    LiftOver to dm3 for genome list q.
• src/hg/makeDb/doc/galGal3.txt
  • 1.27 lines changed: 28, context: html, text, full: html, text
    added galGal3 N-SCAN
• src/hg/makeDb/doc/hg17.txt
  • 1.120 lines changed: 9, context: html, text, full: html, text
    Updated DGV (v7).
• src/hg/makeDb/doc/hg18.txt
  • 1.358 lines changed: 16, context: html, text, full: html, text
    liftOver to hg19 done
  • 1.357 lines changed: 30, context: html, text, full: html, text
    Vega genes update.
  • 1.356 lines changed: 21, context: html, text, full: html, text
    Fixed coords of hgdpHzyBantu and reloaded.
  • 1.355 lines changed: 11, context: html, text, full: html, text
    Updated DGV (v7).
  • 1.354 lines changed: 110, context: html, text, full: html, text
    Adding sections for Genome Variants subtracks loaded by Belinda.
• src/hg/makeDb/doc/hg19.txt
  • 1.3 lines changed: 150, context: html, text, full: html, text
    cpgIslands done, genbank run done, blatServers assigned
• src/hg/makeDb/doc/ucscGenes/hg18.ucscGenes11.csh
  • 1.18 lines changed: 21, context: html, text, full: html, text
    Updated to reflect the KG related tables update. The working directory is at /hive/data/genomes/gs.19/build36/bed/ucsc.11/update2.
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.95 lines changed: 1, context: html, text, full: html, text
    Added hg19 - Human - GRCh37
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.332 lines changed: 1, context: html, text, full: html, text
    Going to try non-split tables for hg19
  • 1.331 lines changed: 1, context: html, text, full: html, text
    incorrect path for hg19 unbridged lift file
  • 1.330 lines changed: 2, context: html, text, full: html, text
    added hg19.lift and hg19.hapRegions
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.100 lines changed: 1, context: html, text, full: html, text
    Added hg19 - Human - GRCh37
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • 1.67 lines changed: 14, context: html, text, full: html, text
    Restoring option -allowStartEqualEnd which I shouldn't have removed in 1.52 (thanks Kate). SNPs and other tracks with valid 0-length items like insertion points will have to use -allowStartEqualEnd, but most tracks will get the appropriate level of checking b y default.
• src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
  • 1.34 lines changed: 54, context: html, text, full: html, text
    Sort output by target coords unless -noSort is specified. Thanks MarkD for the idea to pipe output to sort!
• src/hg/makeDb/schema/all.joiner
  • 1.700 lines changed: 6, context: html, text, full: html, text
    Added Genome Variants tables to tablesIgnored.
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • 1.7 lines changed: 8, context: html, text, full: html, text
    added galGal3 N-SCAN
• src/hg/makeDb/trackDb/human/hg17/encodeMavidAlign.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to lior pachter group.
• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to lior pachter group.
• src/hg/makeDb/trackDb/human/hg17/hapmapSnps.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Added missing <P>.
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • 1.7 lines changed: 56, context: html, text, full: html, text
    Split off the unreleaseable subtracks of pgSnp (Genome Variants) into a new composite track, pgSnpHgwdev. More polishing of pgSnp.html in preparation for release.
• src/hg/makeDb/trackDb/human/hg18/pgSnpHgwdev.html
  • 1.1 lines changed: 61, context: html, text, full: html, text
    Split off the unreleaseable subtracks of pgSnp (Genome Variants) into a new composite track, pgSnpHgwdev. More polishing of pgSnp.html in preparation for release.
• src/hg/makeDb/trackDb/human/hg18/rnaGene.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    lower-cased mt-tRNA for mitochondrial
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.384 lines changed: 1, context: html, text, full: html, text
    fixing tpyo
  • 1.383 lines changed: 79, context: html, text, full: html, text
    Keep configuration panel on by default for SUNY track
  • 1.382 lines changed: 22, context: html, text, full: html, text
    Split off the unreleaseable subtracks of pgSnp (Genome Variants) into a new composite track, pgSnpHgwdev. More polishing of pgSnp.html in preparation for release.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.213 lines changed: 376, context: html, text, full: html, text
    removing GIS RNA PET Project while I reload it
  • 1.212 lines changed: 1, context: html, text, full: html, text
    Add settings config for SUNY track
  • 1.211 lines changed: 30, context: html, text, full: html, text
    HeLa-S3/Input for Duke UTA
  • 1.210 lines changed: 4, context: html, text, full: html, text
    Adjust SUNY track labels and subtrack config for usability
  • 1.209 lines changed: 17, context: html, text, full: html, text
    fixing problem with CSHL where this track should be short rna not shortDeplRrna
  • 1.208 lines changed: 4, context: html, text, full: html, text
    Expand cell type in label, at request of Peggy Farnham
  • 1.207 lines changed: 275, context: html, text, full: html, text
    tracks finally loaded
  • 1.206 lines changed: 39, context: html, text, full: html, text
    Turn on K562 experiments by default, to beef up track
  • 1.205 lines changed: 7, context: html, text, full: html, text
    Darken color for Hek cell line a bit, at Q/A request
  • 1.204 lines changed: 43, context: html, text, full: html, text
    Added HepG2 Input for Duke/Terry Furey
  • 1.203 lines changed: 84, context: html, text, full: html, text
    Added HepG2 DNase for Duke/Terry Furey
  • 1.202 lines changed: 14, context: html, text, full: html, text
    Updated labels for Encode Gencode February Freeze
  • 1.201 lines changed: 185, context: html, text, full: html, text
    last of the affy freeze
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html
  • 1.4 lines changed: 31, context: html, text, full: html, text
    adding standard blurbs to CSHL
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.5 lines changed: 51, context: html, text, full: html, text
    adding standard blurbs
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Change Type to Class in the table of colors
  • 1.7 lines changed: 19, context: html, text, full: html, text
    Updated labels for Encode Gencode February Freeze
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html
  • 1.10 lines changed: 39, context: html, text, full: html, text
    Edited for clarity
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
  • 1.35 lines changed: 4, context: html, text, full: html, text
    Moved more periods outside of links.
  • 1.34 lines changed: 1, context: html, text, full: html, text
    moved period outside of link (thanks Brooke)
  • 1.33 lines changed: 1, context: html, text, full: html, text
    Removed a comma in refs.
  • 1.32 lines changed: 2, context: html, text, full: html, text
    Capitalization.
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Updated descriptions to be close to final versions
  • 1.2 lines changed: 183, context: html, text, full: html, text
    Much more closer to a final description
• src/hg/makeDb/trackDb/human/hg19/gap.html
  • 1.2 lines changed: 67, context: html, text, full: html, text
    Updated descriptions to be close to final versions
• src/hg/makeDb/trackDb/human/hg19/gold.html
  • 1.2 lines changed: 36, context: html, text, full: html, text
    Updated descriptions to be close to final versions
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.7 lines changed: 1, context: html, text, full: html, text
    No need for chainColor setting
  • 1.6 lines changed: 3, context: html, text, full: html, text
    The haplotype mapping to reference is now bed 12
  • 1.5 lines changed: 65, context: html, text, full: html, text
    Fixup the haplotype multi-view
  • 1.4 lines changed: 152, context: html, text, full: html, text
    An attempt at a multi-view chain and net situation
  • 1.3 lines changed: 157, context: html, text, full: html, text
    Haplotype chains and nets added
• src/hg/makeDb/trackDb/human/hgdpIhs.html
  • 1.4 lines changed: 11, context: html, text, full: html, text
    Added more descriptive info from ref's and added links to source code tars from Joe Pickrell.
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
  • 1.3 lines changed: 9, context: html, text, full: html, text
    Added more descriptive info from ref's and added links to source code tars from Joe Pickrell.
• src/hg/makeDb/trackDb/human/kiddEichlerDisc.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    fixed typo
  • 1.9 lines changed: 5, context: html, text, full: html, text
    added title of project higher up in text so the acronym in the track name, HGSV, is more clear
• src/hg/makeDb/trackDb/human/kiddEichlerValid.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added title of project higher up in text so the acronym in the track name, HGSV, is more clear
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.442 lines changed: 1, context: html, text, full: html, text
    Removed the alpha from hgdpHzyBantu -- coords adjusted, looks good now.
  • 1.441 lines changed: 3, context: html, text, full: html, text
    Added release alpha setting to subtrack hgdpHzyBantu because it seems to be in a different format than the others. Updated DGV's dataVersion to v7.
• src/hg/makeDb/trackDb/lowelab/pyrAer1/trackDb.ra
  • 1.51 lines changed: 8, context: html, text, full: html, text
    comment out RNase P track
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.500 lines changed: 22, context: html, text, full: html, text
    
• src/hg/makefile
  • 1.149 lines changed: 1, context: html, text, full: html, text
    hgEncodeVocab needed to be built with the BROWSER_BINS
• src/hg/oneShot/freen/freen.c
  • 1.87 lines changed: 29, context: html, text, full: html, text
    Testing bedAsDef.
• src/hg/qa/apacheMonitor.c
  • 1.15 lines changed: 4, context: html, text, full: html, text
    Always show up to 20 most recent error 500's.
• src/hg/utils/automation/HgAutomate.pm
  • 1.24 lines changed: 4, context: html, text, full: html, text
    eliminate the duplicate hiveDataGenomes specification, been fixed elsewhere
• src/hg/utils/automation/SafePipe.pm
  • 1.5 lines changed: 6, context: html, text, full: html, text
    change exec to handle cases where /data/tmp doesn't exist
  • 1.4 lines changed: 2, context: html, text, full: html, text
    these error files get too large for /tmp so put them in /data/tmp where the rest of the tmp files go
• src/hg/utils/automation/doBlastzChainNet.pl
  • 1.27 lines changed: 17, context: html, text, full: html, text
    New option -inclHap to pass along to the net stage, and properly find at least some kind of db name from the path
• src/hg/utils/automation/doCpgIslands.pl
  • 1.2 lines changed: 6, context: html, text, full: html, text
    eliminate the duplicate hiveDataGenomes specification, been fixed elsewhere
• src/hg/utils/automation/doWindowMasker.pl
  • 1.8 lines changed: 6, context: html, text, full: html, text
    eliminate the duplicate hiveDataGenomes specification, been fixed elsewhere
• src/inc/bbiFile.h
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/inc/bigBed.h
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Adding bigBedItemCount
  • 1.10 lines changed: 4, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
  • 1.9 lines changed: 6, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/inc/cheapcgi.h
  • 1.60 lines changed: 4, context: html, text, full: html, text
    Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs
• src/inc/common.h
  • 1.147 lines changed: 1, context: html, text, full: html, text
    Adding BIGDOUBLE constant.
• src/inc/common.mk
  • 1.59 lines changed: 2, context: html, text, full: html, text
    oops do not want debug symbols on by default
• src/inc/psl.h
  • 1.41 lines changed: 1, context: html, text, full: html, text
    fixed typo in comment
• src/inc/udc.h
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Adding udcReadStringAndZero
• src/lib/bbiRead.c
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/lib/bigBed.c
  • 1.13 lines changed: 9, context: html, text, full: html, text
    Adding bigBedItemCount
  • 1.12 lines changed: 16, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
  • 1.11 lines changed: 49, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/lib/cheapcgi.c
  • 1.111 lines changed: 22, context: html, text, full: html, text
    Add support for enable/disabling checkboxes by having 4 state boolShad hidden inputs
• src/lib/common.c
  • 1.128 lines changed: 1, context: html, text, full: html, text
    making it easier to find .ra bugs
• src/lib/udc.c
  • 1.15 lines changed: 28, context: html, text, full: html, text
    Adding udcReadStringAndZero
• src/oneShot/testCache/makefile
  • 1.3 lines changed: 0, context: html, text, full: html, text
    remove one stray space
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Adding -as option.
• src/utils/bigBedSummary/bigBedSummary.c
  • 1.4 lines changed: 41, context: html, text, full: html, text
    Adding fields flag.
• src/utils/bigBedToBed/bigBedToBed.c
  • 1.5 lines changed: 17, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
• src/utils/qa/checkBOT.csh
  • 1.11 lines changed: 2, context: html, text, full: html, text
    changed description of output slightly
• src/utils/qa/syncAday.csh
  • 1.6 lines changed: 4, context: html, text, full: html, text
    put hgw7 back in
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.18 lines changed: 2, context: html, text, full: html, text
    adding a link to the history
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.51 lines changed: 2, context: html, text, full: html, text
    v203 preview

• lines changed: 6000
• files changed: 130