CVS changes by file

review to branch (2009-04-07 to 2009-04-14) v204

• src/hg/blastToPsl/blastToPsl.c
  • 1.23 lines changed: 7, context: html, text, full: html, text
    added support for PSI BLAST madness
• src/hg/blastToPsl/tests/expected/blastpPsiTest.bscores
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added support for PSI BLAST madness
• src/hg/blastToPsl/tests/expected/blastpPsiTest.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added support for PSI BLAST madness
• src/hg/blastToPsl/tests/expected/psiBadFormatTest.bscores
  • 1.1 lines changed: 10, context: html, text, full: html, text
    skip bogus blocks in PSI BLAST output
• src/hg/blastToPsl/tests/expected/psiBadFormatTest.err
  • 1.1 lines changed: 5, context: html, text, full: html, text
    skip bogus blocks in PSI BLAST output
• src/hg/blastToPsl/tests/expected/psiBadFormatTest.psl
  • 1.1 lines changed: 9, context: html, text, full: html, text
    skip bogus blocks in PSI BLAST output
• src/hg/blastToPsl/tests/expected/psiNoHitsTest.bscores
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed bug parsing PSI BLAST output with no hits
• src/hg/blastToPsl/tests/expected/psiNoHitsTest.psl
  • 1.1 lines changed: 0, context: html, text, full: html, text
    fixed bug parsing PSI BLAST output with no hits
• src/hg/blastToPsl/tests/input/blastpPsi.blast
  • 1.1 lines changed: 244, context: html, text, full: html, text
    added support for PSI BLAST madness
• src/hg/blastToPsl/tests/input/psiBadFormat.blast
  • 1.1 lines changed: 220, context: html, text, full: html, text
    skip bogus blocks in PSI BLAST output
• src/hg/blastToPsl/tests/input/psiNoHits.blast
  • 1.1 lines changed: 61, context: html, text, full: html, text
    fixed bug parsing PSI BLAST output with no hits
• src/hg/blastToPsl/tests/makefile
  • 1.20 lines changed: 1, context: html, text, full: html, text
    don't pslCheck empty file, writes warning to stderr
  • 1.19 lines changed: 10, context: html, text, full: html, text
    skip bogus blocks in PSI BLAST output
  • 1.18 lines changed: 8, context: html, text, full: html, text
    fixed bug parsing PSI BLAST output with no hits
  • 1.17 lines changed: 9, context: html, text, full: html, text
    added support for PSI BLAST madness
• src/hg/encode/encodeStatus/encodeStatus.pl
  • 1.6 lines changed: 1, context: html, text, full: html, text
    modify qapushq host yet again
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.15 lines changed: 6, context: html, text, full: html, text
    add a generic options field so we can easily add options to views
• src/hg/encode/encodeValidate/config/hg18_chromInfo.txt
  • 1.1 lines changed: 49, context: html, text, full: html, text
    need chromInfo for bigbed
• src/hg/encode/encodeValidate/makefile
  • 1.17 lines changed: 2, context: html, text, full: html, text
    add chromInfo to makefile
• src/hg/encode/encodeValidate/tagAlignSanityCheck.pl
  • 1.2 lines changed: 36, context: html, text, full: html, text
    lots of improvements
  • 1.1 lines changed: 100, context: html, text, full: html, text
    initial checkin
• src/hg/encode/encodeValidate/test/input/methylseq/HudsonAlphaMethylSeq.DDF
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Update test file to include Tier1 cell line
• src/hg/encode/validateFiles/hg18_chromInfo.txt
  • 1.1 lines changed: 49, context: html, text, full: html, text
    chrom info file to send with validateFiles prog
• src/hg/gsid/gsidMember/bio.c
  • 1.2 lines changed: 5, context: html, text, full: html, text
    rearranging to get openssl to compile with gcc4, mainly by eliminating use of common.h and openssl together wherever possible
• src/hg/gsid/gsidMember/bio.h
  • 1.2 lines changed: 2, context: html, text, full: html, text
    rearranging to get openssl to compile with gcc4, mainly by eliminating use of common.h and openssl together wherever possible
• src/hg/gsid/gsidMember/makefile
  • 1.11 lines changed: 2, context: html, text, full: html, text
    rearranging to get openssl to compile with gcc4, mainly by eliminating use of common.h and openssl together wherever possible
• src/hg/gsid/gsidMember/paypalSignEncrypt.c
  • 1.3 lines changed: 17, context: html, text, full: html, text
    rearranging to get openssl to compile with gcc4, mainly by eliminating use of common.h and openssl together wherever possible
• src/hg/gsid/gsidMember/paypalSignEncrypt.h
  • 1.2 lines changed: 18, context: html, text, full: html, text
    rearranging to get openssl to compile with gcc4, mainly by eliminating use of common.h and openssl together wherever possible
• src/hg/hgBlat/hgBlat.c
  • 1.126 lines changed: 9, context: html, text, full: html, text
    fixing chrom name compare function, it was not handling pattern chr99_something
• src/hg/hgGenome/custom.c
  • 1.4 lines changed: 14, context: html, text, full: html, text
    Replaced lookupCt with macro to ctFind() common subroutine
• src/hg/hgGenome/hgGenome.h
  • 1.37 lines changed: 3, context: html, text, full: html, text
    Replaced lookupCt with macro to ctFind() common subroutine
• src/hg/hgTables/bedList.c
  • 1.65 lines changed: 1, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/compositeTrack.c
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Added check for NULL tdb from findTdbForTable.
  • 1.14 lines changed: 25, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/correlate.c
  • 1.76 lines changed: 2, context: html, text, full: html, text
    Added check for NULL tdb from findTdbForTable.
  • 1.75 lines changed: 2, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/custom.c
  • 1.40 lines changed: 14, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/filterFields.c
  • 1.72 lines changed: 2, context: html, text, full: html, text
    Added check for NULL tdb from findTdbForTable.
  • 1.71 lines changed: 7, context: html, text, full: html, text
    Added numeric filed validation by javascript
  • 1.70 lines changed: 131, context: html, text, full: html, text
    Added numeric filed validation by javascript
  • 1.69 lines changed: 9, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/hgTables.c
  • 1.183 lines changed: 2, context: html, text, full: html, text
    Added check for NULL tdb from findTdbForTable.
  • 1.182 lines changed: 6, context: html, text, full: html, text
    Added isSqlIntType so that integer fileds can be validated as such
  • 1.181 lines changed: 43, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/hgTables.h
  • 1.136 lines changed: 1, context: html, text, full: html, text
    Added check for NULL tdb from findTdbForTable.
  • 1.135 lines changed: 3, context: html, text, full: html, text
    Added isSqlIntType so that integer fileds can be validated as such
  • 1.134 lines changed: 12, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/intersect.c
  • 1.50 lines changed: 15, context: html, text, full: html, text
    anyIntersection() was forgetting to check whether the primary table is positional.
  • 1.49 lines changed: 20, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/mainPage.c
  • 1.142 lines changed: 1, context: html, text, full: html, text
    Clumsy check in
  • 1.141 lines changed: 2, context: html, text, full: html, text
    Fix bug where db was not selected
  • 1.140 lines changed: 14, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/microarrayTables.c
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Added error Ann suggested when intersection is turned on.
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/rangeHistogram.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/schema.c
  • 1.59 lines changed: 4, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/seqOut.c
  • 1.21 lines changed: 4, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/sumStats.c
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgTables/wiggle.c
  • 1.72 lines changed: 35, context: html, text, full: html, text
    Fix many instances of using composite tdb when subtrack tdb is needed
• src/hg/hgc/hgc.c
  • 1.1525 lines changed: 2, context: html, text, full: html, text
    allow mirror sites to add their own RNA secondary structure tracks by adding rnaSecStr to the table name
• src/hg/inc/customTrack.h
  • 1.55 lines changed: 3, context: html, text, full: html, text
    Added ctFind support routine
• src/hg/inc/hgMaf.h
  • 1.22 lines changed: 8, context: html, text, full: html, text
    Added consWiggleFind support routine
• src/hg/inc/jksql.h
  • 1.82 lines changed: 7, context: html, text, full: html, text
    added function to determine if a mysql server appears to be remote; ignore SQL_TAB_FILE_ON_SERVER if server is remote
• src/hg/inc/trackDb.h
  • 1.46 lines changed: 6, context: html, text, full: html, text
    Added subTdbFind() and tdbFindOrCreate() support routines
• src/hg/inc/versionInfo.h
  • 1.144 lines changed: 1, context: html, text, full: html, text
    "New version number v204"
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.26 lines changed: 120, context: html, text, full: html, text
    Added grouping for clinical features
• src/hg/instinct/bioInt2/bioIntUI.c
  • 1.15 lines changed: 6, context: html, text, full: html, text
    changed codes (again)
• src/hg/js/hgTracks.js
  • 1.26 lines changed: 1, context: html, text, full: html, text
    And if the link has no form to submit, better just follow it
  • 1.25 lines changed: 2, context: html, text, full: html, text
    More tightening of the postTheForm screws
• src/hg/lib/bedCart.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Closest to home
• src/hg/lib/customTrack.c
  • 1.176 lines changed: 10, context: html, text, full: html, text
    Added ctFind support routine
• src/hg/lib/hgMaf.c
  • 1.13 lines changed: 13, context: html, text, full: html, text
    Added consWiggleFind support routine
• src/hg/lib/jksql.c
  • 1.129 lines changed: 10, context: html, text, full: html, text
    added function to determine if a mysql server appears to be remote; ignore SQL_TAB_FILE_ON_SERVER if server is remote
• src/hg/lib/trackDbCustom.c
  • 1.62 lines changed: 5, context: html, text, full: html, text
    In tdbFindOrCreate, call hMaybeTrackInfo instead of hTrackDbForTrack so if db is non-genome, we don't get an errAbort due to the lack of trackDb table. NULL was already an OK return value from this.
  • 1.61 lines changed: 33, context: html, text, full: html, text
    Added subTdbFind() and tdbFindOrCreate() support routines
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.111 lines changed: 3, context: html, text, full: html, text
    added to-do item
• src/hg/makeDb/genbank/etc/dbload
  • 1.23 lines changed: 5, context: html, text, full: html, text
    set env var for hgsqlbeta
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.97 lines changed: 1, context: html, text, full: html, text
    Adding hg19.
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • 1.23 lines changed: 1, context: html, text, full: html, text
    added tests for hgwbeta using hgsqlbeta
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.40 lines changed: 49, context: html, text, full: html, text
    use new hgsql programs instead of mysql directly
  • 1.39 lines changed: 5, context: html, text, full: html, text
    added tests for hgwbeta using hgsqlbeta
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • 1.68 lines changed: 6, context: html, text, full: html, text
    fix problem where fillInScore field might contain only -1 values which is the equivalent of a NULL in the not-null field
• src/hg/makeDb/schema/all.joiner
  • 1.703 lines changed: 1, context: html, text, full: html, text
    added Hg19 to chain list
  • 1.702 lines changed: 1, context: html, text, full: html, text
    Added hg19 to hg set.
• src/hg/makeDb/trackDb/hiv/vax003PosSel.html
  • 1.13 lines changed: 3, context: html, text, full: html, text
    yet more work on this page...
  • 1.12 lines changed: 26, context: html, text, full: html, text
    mostly edited subtype and A/E
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Added "Each positive selection site is labeled by the corresponding amino acid of the consensus sequence." in the Description section.
  • 1.10 lines changed: 2, context: html, text, full: html, text
    changed -blank to _blank
• src/hg/makeDb/trackDb/hiv/vax004PosSelLoc.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Added "Each positive selection site is labeled by the corresponding amino acid of the consensus sequence." in the Description section.
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changed -blank to _blank
• src/hg/makeDb/trackDb/hiv/vax004PosSelRace.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Added "Each positive selection site is labeled by the corresponding amino acid of the consensus sequence." in the Description section.
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changed -blank to _blank
• src/hg/makeDb/trackDb/hiv/vax004PosSelVac.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Added "Each positive selection site is labeled by the corresponding amino acid of the consensus sequence." in the Description section.
  • 1.5 lines changed: 2, context: html, text, full: html, text
    changed -blank to _blank
• src/hg/makeDb/trackDb/human/chainSelf.html
  • 1.14 lines changed: 4, context: html, text, full: html, text
    added description for new chain coloring options
• src/hg/makeDb/trackDb/human/fox2ClipSeqComp.html
  • 1.5 lines changed: 21, context: html, text, full: html, text
    Added to the FOX2 track's description.
• src/hg/makeDb/trackDb/human/hg16/chainSelf.html
  • 1.1 lines changed: 90, context: html, text, full: html, text
    moved this down from the /human level, as hg16 is the only human assembly that will not use the new coloring feature for Self Chains.
• src/hg/makeDb/trackDb/human/hg18/description.html
  • 1.21 lines changed: 7, context: html, text, full: html, text
    Rearranged PAR section so it's easier to see. Thanks, b0b.
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Adjusted chromStart for the second chrX PAR region by one. The off-by-one was found by a user.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.243 lines changed: 36, context: html, text, full: html, text
    first version of Helicos
  • 1.242 lines changed: 37, context: html, text, full: html, text
    first version of gDNA data
  • 1.241 lines changed: 21, context: html, text, full: html, text
    Added tRNAs and polyAs to ENCODE GENCODE track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.9 lines changed: 5, context: html, text, full: html, text
    fixes suggested by Rachel
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fixes per suggestions from Rachel
• src/hg/makeDb/trackDb/human/hg18/wgEncodeNhgriBip.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Added Mary Yang to the credits
• src/hg/makeDb/trackDb/human/hg19/gap.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Katrina and I removed the 'Fragment' type from the list of types
• src/hg/makeDb/trackDb/human/omimGene.html
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Small edits to disclaimer section.
  • 1.17 lines changed: 5, context: html, text, full: html, text
    added border around disclaimer
  • 1.16 lines changed: 9, context: html, text, full: html, text
    added more warnings. Thanks, Katrina
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.449 lines changed: 1, context: html, text, full: html, text
    Changed a shortLabel.
  • 1.448 lines changed: 12, context: html, text, full: html, text
    Added FOX2 cluster subtrack to composite track.
• src/hg/utils/automation/Encode.pm
  • 1.39 lines changed: 1, context: html, text, full: html, text
    Correct path for ENCODE downloads
• src/inc/blastParse.h
  • 1.6 lines changed: 2, context: html, text, full: html, text
    added support for PSI BLAST madness
• src/inc/cheapcgi.h
  • 1.62 lines changed: 3, context: html, text, full: html, text
    Added new flavor of Text input box using standard class and declarable width
• src/inc/common.h
  • 1.149 lines changed: 0, context: html, text, full: html, text
    Adding cmpStringsWithEmbeddedNumbers.
  • 1.148 lines changed: 13, context: html, text, full: html, text
    Adding cmpStringsWithEmbeddedNumbers.
• src/lib/blastParse.c
  • 1.24 lines changed: 133, context: html, text, full: html, text
    skip bogus blocks in PSI BLAST output
  • 1.23 lines changed: 38, context: html, text, full: html, text
    fixed bug parsing PSI BLAST output with no hits
  • 1.22 lines changed: 40, context: html, text, full: html, text
    added support for PSI BLAST madness
• src/lib/cheapcgi.c
  • 1.117 lines changed: 17, context: html, text, full: html, text
    Added new flavor of Text input box using standard class and declarable width
• src/utils/qa/GS1.csh
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/PB.csh
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/activeGenbank.csh
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/alertBqueue.csh
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/allowTraffic.csh
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/backupCentral.csh
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/bigPush.csh
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/blatPing.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/browserUsage.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/catchBot.csh
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/chain.csh
  • 1.23 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/chain2.csh
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/chainNetTrio.csh
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkAllStaticLinks.csh
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkBOT.csh
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkCoverage.csh
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkEncodeRegions.csh
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkGbdb.csh
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkGbdbDiffs.csh
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkHitter.csh
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkMachineName.csh
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkMetaAday.csh
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkMetaData.csh
  • 1.17 lines changed: 3, context: html, text, full: html, text
    fixed bug where genomeClade comparison breaks because original tables not sorted
  • 1.16 lines changed: 4, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkOffend.csh
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkScaffoldGaps.csh
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
• src/utils/qa/checkStaticLinks.csh
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• src/utils/qa/checkStoreUnits.csh
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• src/utils/qa/checkSync.csh
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• src/utils/qa/checkSyncAll.csh
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• src/utils/qa/checkTableStatus.csh
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• src/utils/qa/checkTrackUiLinks.csh
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• src/utils/qa/check_grp.csh
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• src/utils/qa/chromInfo_file_test.csh
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• src/utils/qa/compareHgFindSpecAll.csh
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• src/utils/qa/compareHgFindSpecFast.csh
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• src/utils/qa/compareHgFindSpecs.csh
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• src/utils/qa/compareTableLists.csh
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• src/utils/qa/compareTrackDbAll.csh
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• src/utils/qa/compareTrackDbFast.csh
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• src/utils/qa/compareTrackDbs.csh
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• src/utils/qa/compareWholeColumn.csh
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• src/utils/qa/compareWholeTable.csh
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• src/utils/qa/copyExtSeqRows.csh
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• src/utils/qa/countPerChrom.csh
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• src/utils/qa/countRows.csh
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• src/utils/qa/cronLinks.csh
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• src/utils/qa/databaseAday.csh
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• src/utils/qa/dbUpdateTimes.csh
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• src/utils/qa/doGenbankTests
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    Forgot to specify entire path to a file.
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    Added a date stamp at the end. Put cd in a subshell.
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    Initial file. Script to run genePredCheck/pslCheck, joinerCheck, gbSanity, and featureBits on GenBank tables.
• src/utils/qa/doRLUpdate.csh
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• src/utils/qa/dropUserTables.csh
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• src/utils/qa/dumpEmpty.csh
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• src/utils/qa/field_null_none_range_checker.csh
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• src/utils/qa/findBigFiles.csh
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• src/utils/qa/findBlatServer.csh
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• src/utils/qa/findColumn.csh
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• src/utils/qa/findDbPartners.csh
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• src/utils/qa/findLevel.csh
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• src/utils/qa/findMtNets.csh
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• src/utils/qa/findNewTables.csh
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• src/utils/qa/findOrg.csh
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• src/utils/qa/findPushQLocks.csh
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• src/utils/qa/full_joinerCheck.csh
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• src/utils/qa/genbankRun.csh
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• src/utils/qa/generic_range_check.csh
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• src/utils/qa/getAssemblies.csh
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• src/utils/qa/getChromFieldName.csh
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• src/utils/qa/getChromlist.csh
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• src/utils/qa/getConservation.csh
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• src/utils/qa/getDbSize.csh
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• src/utils/qa/getField.csh
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• src/utils/qa/getGbdbBeta.csh
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• src/utils/qa/getLastMonth.csh
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• src/utils/qa/getLiftOver.csh
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• src/utils/qa/getMatrixLines.csh
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• src/utils/qa/getMonthLastYear.csh
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• src/utils/qa/getOrderKey.csh
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• src/utils/qa/getRRdatabases.csh
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• src/utils/qa/getRRdumpfile.csh
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• src/utils/qa/getRRtableStatus.csh
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• src/utils/qa/getRRtables.csh
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• src/utils/qa/getSplit.csh
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• src/utils/qa/getTableSize.csh
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• src/utils/qa/getTableStatus.csh
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• src/utils/qa/getTrackName.csh
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• src/utils/qa/getVersion.csh
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• src/utils/qa/getYield.csh
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• src/utils/qa/hgFindSpecGlobal.csh
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• src/utils/qa/host.csh
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• src/utils/qa/igtc.csh
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• src/utils/qa/makefile
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    Added doGenbankTests.
• src/utils/qa/net.csh
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• src/utils/qa/proteins.csh
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• src/utils/qa/qaConfig.bash
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    Initial checkin. qaConfig.csh and qaConfig.bash are configuration files for the remaining scripts.
• src/utils/qa/qaConfig.csh
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    Initial checkin. qaConfig.csh and qaConfig.bash are configuration files for the remaining scripts.
• src/utils/qa/qaEnsGenes.csh
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• src/utils/qa/realTime.csh
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• src/utils/qa/retirePushQ.csh
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• src/utils/qa/runBits.csh
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• src/utils/qa/runJoiner.csh
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• src/utils/qa/sessionStats.csh
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• src/utils/qa/showProcesslist.csh
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• src/utils/qa/showTracks
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• src/utils/qa/syncAday.csh
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• src/utils/qa/tableDumpDates.csh
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• src/utils/qa/trackDbGlobal.csh
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• src/utils/qa/trackDb_compare.csh
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• src/utils/qa/trackDb_compare_visibility.csh
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• src/utils/qa/track_Db_compare_priority.csh
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• src/utils/qa/updateTimes.csh
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• src/utils/qa/updateTimesDb.csh
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• src/utils/qa/weeklybld/buildEnv.csh
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    v204 final build
• src/utils/qa/whoMadeIt.csh
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• lines changed: 2536
• files changed: 199