CVS changes by file

review to branch (2009-07-27 to 2009-08-04) v212

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.72 lines changed: 56, context: html, text, full: html, text
    add methVulc0, methInfe0, methFerv0
  • 1.71 lines changed: 13, context: html, text, full: html, text
    add natrMaga0 to multiz of all halophiles
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.20 lines changed: 3, context: html, text, full: html, text
    add index for target field in blast Hits table
  • 1.19 lines changed: 2, context: html, text, full: html, text
    replace die with PrintErrorAndExit
  • 1.18 lines changed: 356, context: html, text, full: html, text
    add igenics and blastx tracks
  • 1.17 lines changed: 1, context: html, text, full: html, text
    turn off spectum for self blastz by Todd
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.17 lines changed: 6, context: html, text, full: html, text
    add support to old version of genePred
  • 1.16 lines changed: 1, context: html, text, full: html, text
    fix bug in parsing cds
  • 1.15 lines changed: 9, context: html, text, full: html, text
    replace die with PrintErrorAndExit
  • 1.14 lines changed: 135, context: html, text, full: html, text
    add igenics and blastx tracks
  • 1.13 lines changed: 15, context: html, text, full: html, text
    take precomputed .gp and .xra for TIGR genomes if files exist
• src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm
  • 1.8 lines changed: 13, context: html, text, full: html, text
    add igenics and blastx tracks
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.38 lines changed: 93, context: html, text, full: html, text
    add --cleanblast to delete private genomes from blastp and blastx hits
  • 1.37 lines changed: 95, context: html, text, full: html, text
    Started work on --generefs track load google Scholar publication hits. Also fixed problem with loading description page for isolation papers with authors that have a single quote in their name (those French!)
• src/hg/archaeStuff/scripts/archaeBrowser/Track.pm
  • 1.13 lines changed: 4, context: html, text, full: html, text
    put N/A to description field of table html if value doesn't exist
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.44 lines changed: 4, context: html, text, full: html, text
    add --cleanblast to delete private genomes from blastp and blastx hits
  • 1.43 lines changed: 10, context: html, text, full: html, text
    add igenics and blastx tracks
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.18 lines changed: 3, context: html, text, full: html, text
    show only the encode dir, not full hive path
• src/hg/encode/encodeValidate/tagAlignSanityCheck.pl
  • 1.3 lines changed: 10, context: html, text, full: html, text
    tweaks
• src/hg/encode/validateFiles/validateFiles.c
  • 1.21 lines changed: 6, context: html, text, full: html, text
    adding coords to error message
• src/hg/gsid/gsidTable/gsidTableData/columnDb.ra.v3B
  • 1.1 lines changed: 295, context: html, text, full: html, text
    Created for V3 with new immuno data.
• src/hg/hgTracks/bamTrack.c
  • 1.5 lines changed: 15, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
• src/hg/hgTracks/makefile
  • 1.86 lines changed: 1, context: html, text, full: html, text
    allow more flexability in find SAMTools
• src/hg/hgTracks/simpleTracks.c
  • 1.95 lines changed: 6, context: html, text, full: html, text
    Added a track handler for the vegaGeneComposite track so that it uses vegaMethods(). Updated a sprintf to safef in vegaGeneName() as suggested by Hiram.
• src/hg/hgc/bamClick.c
  • 1.2 lines changed: 44, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
  • 1.1 lines changed: 137, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
• src/hg/hgc/hgc.c
  • 1.1563 lines changed: 4, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
  • 1.1562 lines changed: 20, context: html, text, full: html, text
    Added stuff for first cut of the UW Southerns track.
• src/hg/hgc/hgc.h
  • 1.47 lines changed: 3, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
• src/hg/hgc/makefile
  • 1.63 lines changed: 1, context: html, text, full: html, text
    allow more flexability in find SAMTools
  • 1.62 lines changed: 4, context: html, text, full: html, text
    Added rudimentary click handler for bam tracks (Heng Li's alignment format).
• src/hg/inc/bamFile.h
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Oops, silly flag-testing bug (& comment clarification) in bamGetQuerySequence.
  • 1.2 lines changed: 28, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
• src/hg/inc/hui.h
  • 1.136 lines changed: 4, context: html, text, full: html, text
    Added stuff for first cut of the UW Southerns track.
• src/hg/inc/versionInfo.h
  • 1.152 lines changed: 1, context: html, text, full: html, text
    "New version number v212"
• src/hg/instinct/instinctMember/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    I do not think the lssl part is needed since they are not using paypal liked gsidMember does
• src/hg/instinct/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Removed instinctMember from makefile to avoid ssl lib conflict.
• src/hg/lib/bamFile.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Oops, silly flag-testing bug (& comment clarification) in bamGetQuerySequence.
  • 1.2 lines changed: 65, context: html, text, full: html, text
    Libified more commonly used BAM code from hgc and hgTracks.
• src/hg/lib/customFactory.c
  • 1.98 lines changed: 31, context: html, text, full: html, text
    work-around for collision of two uses of dataUrl
• src/hg/lib/makefile
  • 1.393 lines changed: 5, context: html, text, full: html, text
    allow more flexability in find SAMTools
• src/hg/makeDb/doc/ce6.txt
  • 1.17 lines changed: 14, context: html, text, full: html, text
    5-way alignments done on ce7 and ce8, liftOvers done for ce6 to ce7 and ce7 to ce8
• src/hg/makeDb/doc/ce7.txt
  • 1.3 lines changed: 171, context: html, text, full: html, text
    5-way alignments done on ce7 and ce8, liftOvers done for ce6 to ce7 and ce7 to ce8
• src/hg/makeDb/doc/ce8.txt
  • 1.2 lines changed: 357, context: html, text, full: html, text
    5-way alignments done on ce7 and ce8, liftOvers done for ce6 to ce7 and ce7 to ce8
• src/hg/makeDb/doc/hg18.txt
  • 1.375 lines changed: 45, context: html, text, full: html, text
    Updated Vega Genes track to build 35 to bring it up to the current release.
  • 1.374 lines changed: 18, context: html, text, full: html, text
    added RNA Binding proteins track
  • 1.373 lines changed: 4, context: html, text, full: html, text
    Fix to previous two Agilent Arrays track load. Faked two extra columns to make it bed 6.
  • 1.372 lines changed: 9, context: html, text, full: html, text
    Added a couple more Agilent arrays to that composite track.
• src/hg/makeDb/doc/hg19.txt
  • 1.34 lines changed: 14, context: html, text, full: html, text
    Added note about chrM sequence for next build.
  • 1.33 lines changed: 31, context: html, text, full: html, text
    Added lifted version of Agilent Probes track to hg19.
• src/hg/makeDb/doc/mm9.txt
  • 1.104 lines changed: 8, context: html, text, full: html, text
    Added note about code addition for this track.
  • 1.103 lines changed: 45, context: html, text, full: html, text
    Updated Vega Genes track to Build 35 from March 2009.
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.345 lines changed: 2, context: html, text, full: html, text
    enabled automatic generation of upstream fa files for download server
  • 1.344 lines changed: 2, context: html, text, full: html, text
    Added a couple lines for genbank zip-file creation on hgdownload.
• src/hg/makeDb/genbank/etc/hgdownload-copy
  • 1.4 lines changed: 1, context: html, text, full: html, text
    added support for two hgdownload servers
• src/hg/makeDb/genbank/etc/hgdownload.crontab
  • 1.19 lines changed: 6, context: html, text, full: html, text
    make hgdownload contrab solaris comapatible
• src/hg/makeDb/genbank/src/copy/gbCopyDownload
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added support for two hgdownload servers
• src/hg/makeDb/genbank/src/copy/gbMakeDownload
  • 1.21 lines changed: 25, context: html, text, full: html, text
    fixed time overflow check
  • 1.20 lines changed: 24, context: html, text, full: html, text
    added debugging for download build problem
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.47 lines changed: 3, context: html, text, full: html, text
    added support for two hgdownload servers
• src/hg/makeDb/schema/all.joiner
  • 1.728 lines changed: 2, context: html, text, full: html, text
    Added a couple rules for Agilent arrays.
• src/hg/makeDb/trackDb/affyExonTissues.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    One last minor edit.
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Forgot to uncomment changes in last commit.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Updated reference.
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.39 lines changed: 1, context: html, text, full: html, text
    removed release alpha
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    removed release alpha
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.32 lines changed: 1, context: html, text, full: html, text
    removed release alpha
• src/hg/makeDb/trackDb/human/agilentProbes.html
  • 1.7 lines changed: 21, context: html, text, full: html, text
    Added a couple more Agilent arrays to that composite track.
• src/hg/makeDb/trackDb/human/hg18/agilentProbes.html
  • 1.1 lines changed: 150, context: html, text, full: html, text
    Added hg19 lifted version of Agilent Probes track.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.408 lines changed: 3, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.476 lines changed: 2, context: html, text, full: html, text
    shortened short labels
  • 1.475 lines changed: 1, context: html, text, full: html, text
    no autoscale, limit 1-20
  • 1.474 lines changed: 75, context: html, text, full: html, text
    removed release alphas from ENCODE UW DNaseI HS subtrack blocks
  • 1.473 lines changed: 6, context: html, text, full: html, text
    fix up wig limits for Broad TFBS tracks
  • 1.472 lines changed: 31, context: html, text, full: html, text
    Backing out previous change -- those tables are on hgwbeta after all, oops.
  • 1.471 lines changed: 31, context: html, text, full: html, text
    Workaround for appearance of extra column on hgwbeta which is missing some tables: add "release alpha" to the subtrack defs for hgwdev-only tables and the complete composite track def, and add a "release beta" composite track def which omits the subGroup item for the hgwdev-only tables.
  • 1.470 lines changed: 1, context: html, text, full: html, text
    removed release alpha
  • 1.469 lines changed: 1, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
  • 1.468 lines changed: 2, context: html, text, full: html, text
    getting ready for beta
  • 1.467 lines changed: 2, context: html, text, full: html, text
    removing prostate cellType
  • 1.466 lines changed: 56, context: html, text, full: html, text
    enabling RikenCage alpha release
  • 1.465 lines changed: 1, context: html, text, full: html, text
    changed full+ to full on RawSignal visibilityViewDefaults so that the configuration menu does not display by default
  • 1.464 lines changed: 13, context: html, text, full: html, text
    Added stuff for first cut of the UW Southerns track.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLoRnaSeq.html
  • 1.11 lines changed: 1, context: html, text, full: html, text
    extra angle
  • 1.10 lines changed: 5, context: html, text, full: html, text
    fixed contacts
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Fixed contact name.
  • 1.8 lines changed: 28, context: html, text, full: html, text
    Mostly wording and punctuation changes.
  • 1.7 lines changed: 1, context: html, text, full: html, text
    tweak the text
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.html
  • 1.12 lines changed: 6, context: html, text, full: html, text
    added strand info
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    a wee bit of text.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.16 lines changed: 4, context: html, text, full: html, text
    added link for color space
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
  • 1.9 lines changed: 11, context: html, text, full: html, text
    Minor edits to Methods, Verification and References sections
• src/hg/makeDb/trackDb/human/hg19/agilentProbes.html
  • 1.1 lines changed: 158, context: html, text, full: html, text
    Added lifted version of Agilent Probes track to hg19. track override for group. HTML has an extra methods section explaining the lift along with a downloads link.
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.13 lines changed: 11, context: html, text, full: html, text
    Added a note about incorrect chrM sequence.
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Added two periods.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.45 lines changed: 7, context: html, text, full: html, text
    loxAfr2 has become loxAfr3
  • 1.44 lines changed: 1, context: html, text, full: html, text
    dropped s from Primate chain/net track short label
  • 1.43 lines changed: 8, context: html, text, full: html, text
    turned on some tracks be default so it's not blank when users want to see it. changed lonagLabl slightly
  • 1.42 lines changed: 3, context: html, text, full: html, text
    fixed Capitalization on long labels for chain/net tracks
  • 1.41 lines changed: 3, context: html, text, full: html, text
    Added lifted version of Agilent Probes track to hg19. track override for group. HTML has an extra methods section explaining the lift along with a downloads link.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.467 lines changed: 1, context: html, text, full: html, text
    Added lifted version of Agilent Probes track to hg19.
  • 1.466 lines changed: 26, context: html, text, full: html, text
    Added a couple more Agilent arrays to that composite track.
• src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloSali1/trackDb.ra
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/haloVolc1/trackDb.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    add natrMaga0 to multiz
• src/hg/makeDb/trackDb/lowelab/haloWals1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/methJann1/trackDb.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    add methVulc0, methInfe0, methFerv0 to multiz
• src/hg/makeDb/trackDb/lowelab/natrPhar1/trackDb.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.80 lines changed: 12, context: html, text, full: html, text
    add igenics track; rename igenics microarray track to igenicsMicroarray
  • 1.79 lines changed: 12, context: html, text, full: html, text
    add BlastX_Related
• src/hg/makeDb/trackDb/mouse/mm4/trackDb.ra
  • 1.25 lines changed: 1, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.56 lines changed: 2, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.55 lines changed: 1, context: html, text, full: html, text
    removed release alpha
• src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Add links to Broad FTP site, and photo dimensions
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.38 lines changed: 1, context: html, text, full: html, text
    removed release alpha
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.45 lines changed: 1, context: html, text, full: html, text
    removed release alpha
  • 1.44 lines changed: 2, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.523 lines changed: 10, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
• src/hg/makeDb/trackDb/treeShrew/tupBel1/description.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Correct comment about sequencing center
• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
  • 1.36 lines changed: 3, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • 1.12 lines changed: 3, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • 1.37 lines changed: 5, context: html, text, full: html, text
    fixed some capitalization on chain/net composites
  • 1.36 lines changed: 126, context: html, text, full: html, text
    Combining chains and nets into single composite tracks
• src/hg/maskOutFa/maskOutFa.c
  • 1.10 lines changed: 39, context: html, text, full: html, text
    add option to specify mask input format when reading from stdin. check command line options
• src/hg/mouseStuff/netFilter/netFilter.c
  • 1.23 lines changed: 17, context: html, text, full: html, text
    made several hard-coded parameters into command line options
  • 1.22 lines changed: 4, context: html, text, full: html, text
    added comment about how syntenic filtering works
• src/hg/overlapSelect/chromAnn.c
  • 1.15 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/chromAnnMap.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/coordCols.c
  • 1.3 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    clean up executable
• src/hg/overlapSelect/overlapSelect.c
  • 1.42 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/rowReader.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/selectTable.c
  • 1.31 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/tests/expected/xenoGpPslStatsStrandTest.stats
  • 1.1 lines changed: 7, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/expected/xenoPslGpStatsStrandTest.stats
  • 1.1 lines changed: 7, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/expected/xenoPslStatsStrandTest.stats
  • 1.1 lines changed: 7, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/expected/xenoPslStatsTest.stats
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/input/xenoEst1.gp
  • 1.1 lines changed: 5, context: html, text, full: html, text
    forgot test file
• src/hg/overlapSelect/tests/input/xenoEst1.psl
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/makefile
  • 1.34 lines changed: 1, context: html, text, full: html, text
    added new valgrid defs
  • 1.33 lines changed: 25, context: html, text, full: html, text
    added some test cases around strand
• src/hg/protein/lib/doStamps.c
  • 1.8 lines changed: 14, context: html, text, full: html, text
    Updated help links for GSID stamps.
• src/hg/protein/lib/doTracks.c
  • 1.21 lines changed: 7, context: html, text, full: html, text
    Updated PB help links for GSID.
  • 1.20 lines changed: 7, context: html, text, full: html, text
    Updated link to Explanation ...
• src/hg/pslCDnaFilter/makefile
  • 1.12 lines changed: 2, context: html, text, full: html, text
    removing unneeded dependency
• src/hg/pslPseudo/checkExp/checkExp.c
  • 1.6 lines changed: 4, context: html, text, full: html, text
    type checking and add -l ssl
• src/hg/pslPseudo/checkExp/makefile
  • 1.11 lines changed: 1, context: html, text, full: html, text
    type checking and add -l ssl
• src/hg/ratStuff/mafSplitPos/mafSplitPos.c
  • 1.7 lines changed: 8, context: html, text, full: html, text
    allow disabling gap or repeat spliting, fixed bug creating duplicate output, make -minRepeat actually work
• src/hg/utils/automation/makeDownloads.pl
  • 1.24 lines changed: 1, context: html, text, full: html, text
    No need to explicitly mention liftOver binary in makeDownloads README business, and better warning messages in makePushQSql.pl and move one genbank to optional list
  • 1.23 lines changed: 17, context: html, text, full: html, text
    Add 2bit file to bigZips, and checking bed/repeatMasker/ directory for the fa.out file
• src/hg/utils/automation/makePushQSql.pl
  • 1.26 lines changed: 13, context: html, text, full: html, text
    No need to explicitly mention liftOver binary in makeDownloads README business, and better warning messages in makePushQSql.pl and move one genbank to optional list
• src/inc/bbiFile.h
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Including cirTree.h to avoid compiler error in bedToBigBed.
• src/inc/common.mk
  • 1.66 lines changed: 4, context: html, text, full: html, text
    Fixed our local samtools installation so it's always in samtools/x86_64 (no exception for x86_64) -- thanks Mark.
  • 1.65 lines changed: 10, context: html, text, full: html, text
    allow more flexability in find SAMTools
• src/inc/haval.h
  • 1.2 lines changed: 89, context: html, text, full: html, text
    Removing these unused modules. Can get them off the web again if need be.
• src/lib/haval.c
  • 1.3 lines changed: 751, context: html, text, full: html, text
    Removing these unused modules. Can get them off the web again if need be.
• src/lib/makefile
  • 1.153 lines changed: 1, context: html, text, full: html, text
    Removing these unused modules. Can get them off the web again if need be.
• src/lib/pslGenoShow.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    making pslShow and pslGenoShow use the same maxSkip==8 for small block merging that hgBlat htcUserAli uses
  • 1.6 lines changed: 3, context: html, text, full: html, text
    changing 60 column display to 50
  • 1.5 lines changed: 15, context: html, text, full: html, text
    fixing padded display coordinate offset and negative strand issues, adjusting pslGenoShow.c to be like fixed pslShow.c
• src/lib/pslShow.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    making pslShow and pslGenoShow use the same maxSkip==8 for small block merging that hgBlat htcUserAli uses
  • 1.8 lines changed: 3, context: html, text, full: html, text
    changing 60 column display to 50
  • 1.7 lines changed: 15, context: html, text, full: html, text
    fixing padded display coordinate offset and negative strand issues, adjusting pslGenoShow.c to be like fixed pslShow.c
• src/utils/faCount/faCount.c
  • 1.8 lines changed: 99, context: html, text, full: html, text
    Add options for counting di-nucleotide frequencies and looking at both strands of the input sequences. (from stanford)
• src/utils/qa/chainNetTrio.csh
  • 1.10 lines changed: 4, context: html, text, full: html, text
    added a little prtective logic for when the otherOrg does not have an assembly (chromInfo)
• src/utils/qa/checkPushedFiles.csh
  • 1.1 lines changed: 55, context: html, text, full: html, text
    this script checks to see if the file push got to its correct destination
• src/utils/qa/makefile
  • 1.112 lines changed: 1, context: html, text, full: html, text
    new script
  • 1.111 lines changed: 2, context: html, text, full: html, text
    can't alphabetize!
  • 1.110 lines changed: 1, context: html, text, full: html, text
    added new qaEncodeTracks script
• src/utils/qa/qaEncodeTracks.csh
  • 1.3 lines changed: 3, context: html, text, full: html, text
    fixed logic error
  • 1.2 lines changed: 1, context: html, text, full: html, text
    added line for qaConfig script
  • 1.1 lines changed: 137, context: html, text, full: html, text
    initial quick version of script for uor use QAing Encode tracks
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.70 lines changed: 5, context: html, text, full: html, text
    v212 final build
• src/utils/qa/weeklybld/doZip.csh
  • 1.9 lines changed: 9, context: html, text, full: html, text
    moved the download
• src/utils/userApps/mkREADME.sh
  • 1.3 lines changed: 8, context: html, text, full: html, text
    removed first part of FOOTER file, as we now have proper help files (that are mentioned instead in the README)
• src/webBlat/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    stay clean
• src/webBlat/webBlat.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    changing 60 column display to 50

• lines changed: 4609
• files changed: 117