All File Changes

v275_preview2 to v275_base (2012-10-23 to 2012-10-30) v275

• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    Bumping blat version.
  • lines changed 2, context: html, text, full: html, text
    Resolving conflicts in blat version bump.
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    Correcting link to narrowPeak, RM#9428
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 5, context: html, text, full: html, text
    Additional code needed for Contacts link. Thanks Brooke. #9328
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 11, context: html, text, full: html, text
    Fixing supertrack children's support for 'parent' setting. With this, superfluous code was removed. Galt has reviewed this code already.
• src/hg/hgc/hgc.c
  • lines changed 47, context: html, text, full: html, text
    VCF details: if name looks like a dbSNP or dbVar ID, add a link.Also a fix to how we encode HTML (<>) in allele names, and
    refactoring of hardcoded links to dbSNP rs report (now hardcoded
    in only one place instead of half dozen).
    
• src/hg/hgc/hgc.h
  • lines changed 7, context: html, text, full: html, text
    VCF details: if name looks like a dbSNP or dbVar ID, add a link.Also a fix to how we encode HTML (<>) in allele names, and
    refactoring of hardcoded links to dbSNP rs report (now hardcoded
    in only one place instead of half dozen).
    
• src/hg/hgc/vcfClick.c
  • lines changed 34, context: html, text, full: html, text
    VCF details: if name looks like a dbSNP or dbVar ID, add a link.Also a fix to how we encode HTML (<>) in allele names, and
    refactoring of hardcoded links to dbSNP rs report (now hardcoded
    in only one place instead of half dozen).
    
• src/hg/htdocs/ENCODE/index.html
  • lines changed 2, context: html, text, full: html, text
    Cosmetics. As part of #9316 (Y5Q4 Pubs page update)
  • lines changed 8, context: html, text, full: html, text
    Correct outreach info based on current status of materials. Negotiations with OpenHelix are underware to restore free access to the ENCODE tutorials
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 17, context: html, text, full: html, text
    Cosmetics. As part of #9316 (Y5Q4 Pubs page update)
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 8, context: html, text, full: html, text
    Cosmetics. As part of #9316 (Y5Q4 Pubs page update)
  • lines changed 90, context: html, text, full: html, text
    Made changes suggested by Mike Pazin (redmine #9316)
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 15, context: html, text, full: html, text
    links to the new Track Hub trackDb doc
  • lines changed 7, context: html, text, full: html, text
    Ack. Fixing links to go to the correct doc (Track Hub doc, not Generic doc)
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 2, context: html, text, full: html, text
    added link to new Hub Track Database Definitiondoc
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 28, context: html, text, full: html, text
    Checking in Donna's first pass. A few minor edits by me are also included and a merge conflict was resolved.
  • lines changed 4, context: html, text, full: html, text
    Removing all trace of bamWig type tracks. This was an experimental track type which Brian was trying out and has certainly not been released.
  • lines changed 1, context: html, text, full: html, text
    Get rid of 'self-assembly' self-promotion of the table of contents.
  • lines changed 1, context: html, text, full: html, text
    Oops. Minor oversite of missing [+] toggle for bamSkipPrintQualScore. Without it, the details are never seen.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 2, context: html, text, full: html, text
    Get rid of 'self-assembly' self-promotion of the table of contents.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 20, context: html, text, full: html, text
    Checking in Donna's first pass. A few minor edits by me are also included and a merge conflict was resolved.
  • lines changed 4, context: html, text, full: html, text
    Removing all trace of bamWig type tracks. This was an experimental track type which Brian was trying out and has certainly not been released.
  • lines changed 8, context: html, text, full: html, text
    Since trackDbHub doc is going forward, I made separate intro and 'type' setting blurbs that are hub specific.
  • lines changed 19, context: html, text, full: html, text
    One more round before Donna picks this up again. These changes are almost all to clarify the hub version as distinct from the general version. There were also a couple of mistakes and omissions that have been rectified and affect both documents.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 927, context: html, text, full: html, text
    Checking in Donna's first pass. A few minor edits by me are also included and a merge conflict was resolved.
  • lines changed 19, context: html, text, full: html, text
    Removing all trace of bamWig type tracks. This was an experimental track type which Brian was trying out and has certainly not been released.
  • lines changed 62, context: html, text, full: html, text
    Since trackDbHub doc is going forward, I made separate intro and 'type' setting blurbs that are hub specific.
  • lines changed 3, context: html, text, full: html, text
    Fixed 1 corrupted end paragraph tag and 2 hr tags. Thanks Ann for finding this.
  • lines changed 148, context: html, text, full: html, text
    One more round before Donna picks this up again. These changes are almost all to clarify the hub version as distinct from the general version. There were also a couple of mistakes and omissions that have been rectified and affect both documents.
  • lines changed 106, context: html, text, full: html, text
    Did a quick editing pass through remainder of file.
  • lines changed 47, context: html, text, full: html, text
    Insignificnat changes. Corrected word-wrap bad formatting, which is invisible in use. Fixed one tiny typo and hid one TODO that was meant to be hidden. Also tried to answer one of Donna's questions.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    changed ref to point to open-source full text version
• src/hg/inc/trackDb.h
  • lines changed 7, context: html, text, full: html, text
    Fixing supertrack children's support for 'parent' setting. With this, superfluous code was removed. Galt has reviewed this code already.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v275
• src/hg/lib/trackDbCustom.c
  • lines changed 104, context: html, text, full: html, text
    Fixing supertrack children's support for 'parent' setting. With this, superfluous code was removed. Galt has reviewed this code already.
• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 4, context: html, text, full: html, text
    blat servers assigned
  • lines changed 44, context: html, text, full: html, text
    lastz done hg19 and mm10 to cerSim1
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 65, context: html, text, full: html, text
    done with lastz for chicken lamprey
• src/hg/makeDb/doc/hetGla1.txt
  • lines changed 22, context: html, text, full: html, text
    fixup labels on naked mole rat lastz
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, context: html, text, full: html, text
    lastz done hg19 and mm10 to cerSim1
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 22, context: html, text, full: html, text
    duplicate lastz entry for mm10
• src/hg/makeDb/doc/mm10.txt
  • lines changed 66, context: html, text, full: html, text
    lastz mm10 petMar2 done
  • lines changed 60, context: html, text, full: html, text
    lastz done hg19 and mm10 to cerSim1
  • lines changed 4, context: html, text, full: html, text
    fixup some comment names in lastz sections
  • lines changed 3, context: html, text, full: html, text
    fixup labels on naked mole rat lastz
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 64, context: html, text, full: html, text
    lastz done to petMar2
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 22, context: html, text, full: html, text
    lastz for mm10 swap procedure included here
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 22, context: html, text, full: html, text
    lastz mm10 petMar2 done
  • lines changed 8, context: html, text, full: html, text
    default position set and in the pushQ
  • lines changed 3, context: html, text, full: html, text
    blat servers assigned
  • lines changed 46, context: html, text, full: html, text
    lastz done for monDom5 and oryLat2
  • lines changed 19, context: html, text, full: html, text
    done with lastz for chicken lamprey
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added papAnu2.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    adding papAnu2 Papio anubis
  • lines changed 31, context: html, text, full: html, text
    add xenoMrna track to assemblies that already have it. Had to do this since I changed the default to not load it.
  • lines changed 1, context: html, text, full: html, text
    use correct version of CCDS on hg19
  • lines changed 2, context: html, text, full: html, text
    ooops... need the fr* to have xenoMrna too!
  • lines changed 1, context: html, text, full: html, text
    use CCDS 103.0 for hg19
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added papAnu2.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding definition for papAnulNames
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    not petMar2 on the proteinAccession identifier
  • lines changed 9, context: html, text, full: html, text
    adding braFlo2
• src/hg/makeDb/trackDb/README
  • lines changed 1, context: html, text, full: html, text
    changed reference to 'hgN' to make it more generic
  • lines changed 1, context: html, text, full: html, text
    changed reference to 'hg7' to make it more relevant (it talks about 'mouse' just above that)
  • lines changed 1197, context: html, text, full: html, text
    removed all of the trackDb documentation that is now covered in the new trackDb doc (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html)
  • lines changed 3, context: html, text, full: html, text
    added link to the new trackDb doc (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html
• src/hg/makeDb/trackDb/baboon/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/cat/felCat3/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated photo links; fixed improperly formatted link in felCat4
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated photo links; fixed improperly formatted link in felCat4
• src/hg/makeDb/trackDb/cat/felCat5/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links; fixed improperly formatted link in felCat4
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
  • lines changed 21, context: html, text, full: html, text
    Updated journal links
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Adding santa cruz number to BAF155 and ATF3, and correcting lot info for ATF2 based on validation doc
  • lines changed 1, context: html, text, full: html, text
    Adding lot number for BAF170 according to validation doc for antibody
  • lines changed 1, context: html, text, full: html, text
    Removing line I forgot to take away when adding new line to antibody sc-66884 RM# 9428
  • lines changed 2, context: html, text, full: html, text
    Deprecating 2 antibodies after approval from Chuck Epstien and Mike Pazin
  • lines changed 11, context: html, text, full: html, text
    Adding the names of the validation submitters to the lab list
  • lines changed 7, context: html, text, full: html, text
    Beginning the merge of two antibodies that have different term names but are the same, sc-150. Also removed the 1) from ELAV for better access to the host information
  • lines changed 25, context: html, text, full: html, text
    Cleaning up lots: Removing missing or unknown lines, removing commas, removing odd information if it is clear somewhere else
  • lines changed 26, context: html, text, full: html, text
    Trying to remove the phrases that are part of the vendor advertisement. The Reccommened for use with phrase was a clear plagerism and often the information is for purchasing and not for understanding the antibody.
  • lines changed 1, context: html, text, full: html, text
    Shortening URL length, Code Review 9424/9369
  • lines changed 39, context: html, text, full: html, text
    Commenting out controls that are not used
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 186, context: html, text, full: html, text
    moving beta to public, this is mostly work on the validation naming
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.html
  • lines changed 26, context: html, text, full: html, text
    Updating contact information for hg18 to have primary contact for Encode BU Orchid
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/human/hg19/hg19mammalChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 191, context: html, text, full: html, text
    added accessions for HAIB RRBS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 2, context: html, text, full: html, text
    made note of a corrupted file in HAIB methyl seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 229, context: html, text, full: html, text
    added accessions numbers for UW Dnase and UW Tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 157, context: html, text, full: html, text
    added accessions numbers for UW Dnase and UW Tfbs
  • lines changed 17, context: html, text, full: html, text
    added the Rep3s that got overlooekd previously
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 229, context: html, text, full: html, text
    Adding GEO Accession numbers to tracks UW DNase and UW TranFactorBindingSites RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
  • lines changed 157, context: html, text, full: html, text
    Adding GEO Accession numbers to tracks UW DNase and UW TranFactorBindingSites RM#9359
  • lines changed 17, context: html, text, full: html, text
    Adding GEO Accession numbers to UW TransFactorBindingSites RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 229, context: html, text, full: html, text
    Adding GEO Accession numbers to tracks UW DNase and UW TranFactorBindingSites RM#9359
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwTfbs.ra
  • lines changed 157, context: html, text, full: html, text
    Adding GEO Accession numbers to tracks UW DNase and UW TranFactorBindingSites RM#9359
  • lines changed 17, context: html, text, full: html, text
    Adding GEO Accession numbers to UW TransFactorBindingSites RM#9359
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
  • lines changed 23, context: html, text, full: html, text
    Track #7964 (1000 Genomes Variant Calls): added a few more links tomore info, and a very brief overview, to the Methods section.
    The process involved lots of work at lots of different institutions
    using lots of different tools, and if I start going into details,
    I won't know where to stop.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.html
  • lines changed 26, context: html, text, full: html, text
    Making Tom Tullius primary contact, santizing emails for contacts for wgEncodeBuOrchid contacts section
  • lines changed 8, context: html, text, full: html, text
    Making contact line more visible, per Kate's feedback
  • lines changed 23, context: html, text, full: html, text
    Pulling links to individual emails in contacts section of Encode BU Orchid per Kate's input.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
  • lines changed 23, context: html, text, full: html, text
    Fixing a bad search and replace
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    overrides for Mm10 chainNet
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Removed semicolon in reference to match http://www.ncbi.nlm.nih.gov/pubmed/11928468?dopt=Abstract.
• src/hg/makeDb/trackDb/mouseLemur/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Added override section for micMur1<->gorGor3 matrix
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.chainNet.ra
  • lines changed 10, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/tarsier/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 156, context: html, text, full: html, text
    adding petMar2 braFlo2 and cerSim1
  • lines changed 306, context: html, text, full: html, text
    adding sections for Dolphin, Alpaca, Pig, Coelacanth, Atlantic cod
  • lines changed 51, context: html, text, full: html, text
    addind in Atlantic Cod gadMor1
  • lines changed 2, context: html, text, full: html, text
    Added/modified appropriate override sections so that chain/net information displays properly
• src/hg/near/hgNear/customColumn.c
  • lines changed 4, context: html, text, full: html, text
    fixing minor security issue with hgNear - make it verify that it really is a URL, otherwise our low-level library allows it to use relative and absolute filenames.
• src/hg/oneShot/testSearch/makefile
  • lines changed 14, context: html, text, full: html, text
    Moving testSearch out of oneShot and renaming it to trixSearch to be more specific.
• src/hg/oneShot/testSearch/testSearch.c
  • lines changed 23, context: html, text, full: html, text
    Improving output and adding command line option.
  • lines changed 76, context: html, text, full: html, text
    Moving testSearch out of oneShot and renaming it to trixSearch to be more specific.
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 1, context: html, text, full: html, text
    removing ; from ;: situation in an article reference, redmine 8887 note 64
  • lines changed 1, context: html, text, full: html, text
    remove stray paren, redmine 8887 note 66
  • lines changed 4, context: html, text, full: html, text
    fixup md5sum of axtNet when single file in there, redmine 8887 note 70
• src/hg/utils/automation/extractRepeats
  • lines changed 73, context: html, text, full: html, text
    copy from bin/scripts from March 2006
• src/hg/utils/phyloTrees/64way.dissect.txt
  • lines changed 889, context: html, text, full: html, text
    need 64 way dissect tree
• src/hg/utils/phyloTrees/64way.nh
  • lines changed 27, context: html, text, full: html, text
    brought up to 64-way species
• src/hg/utils/phyloTrees/64wayChainNet.pl
  • lines changed 136, context: html, text, full: html, text
    brought up to 64-way species
• src/hg/utils/phyloTrees/65way.dissect.txt
  • lines changed 903, context: html, text, full: html, text
    adding chiLan1 Chinchilla
• src/hg/utils/phyloTrees/65way.nh
  • lines changed 28, context: html, text, full: html, text
    adding chiLan1 Chinchilla
• src/hg/utils/phyloTrees/chainNet.pl
  • lines changed 28, context: html, text, full: html, text
    brought up to 64-way species
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    Bumping blat version.
• src/index/trixSearch/makefile
  • lines changed 14, context: html, text, full: html, text
    Moving testSearch out of oneShot and renaming it to trixSearch to be more specific.
• src/index/trixSearch/trixSearch.c
  • lines changed 76, context: html, text, full: html, text
    Moving testSearch out of oneShot and renaming it to trixSearch to be more specific.
• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 887, context: html, text, full: html, text
    Renaming and otherwise refactoring alphaChain program into alphaAsm. Making it hold reads in a list for multiple passes.
  • lines changed 107, context: html, text, full: html, text
    Starting to do orphan beginning/end processing.
  • lines changed 183, context: html, text, full: html, text
    Adding missing types based on reads.
  • lines changed 147, context: html, text, full: html, text
    Integrating orphans (things that are only at beginning or end of any read) by adding fake reads.
  • lines changed 4, context: html, text, full: html, text
    Rearranging order so integrateOrphans gets called before markovChains are made.
  • lines changed 89, context: html, text, full: html, text
    Making it use lower order model once higher order model has reached outTarget. Improving top level comment.
  • lines changed 33, context: html, text, full: html, text
    Adding pseudoCount.
  • lines changed 32, context: html, text, full: html, text
    Polishing code and comments without changing meaning at all.
  • lines changed 7, context: html, text, full: html, text
    Improving readability.
• src/kehayden/alphaAsm/doIt
  • lines changed 2, context: html, text, full: html, text
    Renaming and otherwise refactoring alphaChain program into alphaAsm. Making it hold reads in a list for multiple passes.
  • lines changed 2, context: html, text, full: html, text
    Making testing framework fit usual conventions more.
• src/kehayden/alphaAsm/makefile
  • lines changed 18, context: html, text, full: html, text
    Renaming and otherwise refactoring alphaChain program into alphaAsm. Making it hold reads in a list for multiple passes.
  • lines changed 4, context: html, text, full: html, text
    Making testing framework fit usual conventions more.
• src/kehayden/alphaAsm/yReads.txt
  • lines changed 966, context: html, text, full: html, text
    Making testing framework fit usual conventions more.
• src/kehayden/alphaAsm/yTypeOrder.txt
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    Making testing framework fit usual conventions more.
• src/kehayden/alphaChain/doIt
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    Making testing framework fit usual conventions more.
• src/kehayden/alphaChain/makefile
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    Making testing framework fit usual conventions more.
• src/kehayden/alphaChain/sampleIt
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    Removing old unused one line script.
• src/lib/https.c
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    Fix for strict gcc warning "format not a string literal and no format arguments".
• src/lib/regexHelper.c
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    If regexMatch is called on NULL string, return FALSE (instead of possible segv).
• src/parasol/paraHub/paraHub.c
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    Updating comment to reflect how code actually works these days.
• src/product/README.trackDb
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    added link to new trackDb doc
• src/utils/qa/qaGbTracks
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    Added an exception for an empty table list. Thanks, Pauline.
• src/utils/qa/weeklybld/buildEnv.csh
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    v275 final build

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• files changed: 164