CVS changes by file

branch to review (2009-07-21 to 2009-07-27) v211

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.70 lines changed: 2, context: html, text, full: html, text
    remove underscore for natrMaga0
  • 1.69 lines changed: 13, context: html, text, full: html, text
    remove short contigs from natrMaga0
• src/hg/archaeStuff/scripts/archaeBrowser/Track.pm
  • 1.12 lines changed: 7, context: html, text, full: html, text
    use alt .hg.conf when not on archdev and other .hg.conf exists
• src/hg/encode/DAFs/CshlLongRnaSeq.daf
  • 1.3 lines changed: 2, context: html, text, full: html, text
    shortening name
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.69 lines changed: 1, context: html, text, full: html, text
    change releaseLogUrl to use ../..
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.121 lines changed: 16, context: html, text, full: html, text
    temporarily add U87 and BE2_C to get some HudonAlpha data loaded
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.188 lines changed: 2, context: html, text, full: html, text
    use $submitPath instead of $submitDir when determining the encode pipeline instance
• src/hg/encode/hgEncodeSubmit/config/database.yml.beta
  • 1.2 lines changed: 77, context: html, text, full: html, text
    cleanup
• src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
  • 1.4 lines changed: 14, context: html, text, full: html, text
    adding more info to the commandline and removing some debug output from log
• src/hg/encode/validateFiles/validateFiles.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    free the dna
  • 1.19 lines changed: 130, context: html, text, full: html, text
    check sequence or seq1/seq2 match the genome for tagAlign and pairedTagAlign files
• src/hg/gsid/pbGsid/pbGsid.c
  • 1.10 lines changed: 4, context: html, text, full: html, text
    Added "target=_blank" for PDF and PS links per GSID's request.
• src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Updated for new blastTab tables.
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Updated for new blastTab tables.
• src/hg/hgGene/hgGeneData/Human/hg18/otherOrgs.ra
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Updated for new blastTab tables.
• src/hg/hgGene/hgGeneData/Mouse/mm9/otherOrgs.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Updated for new blastTab tables.
• src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Updated for new blastTab tables.
• src/hg/hgTracks/bamTrack.c
  • 1.4 lines changed: 27, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
  • 1.3 lines changed: 177, context: html, text, full: html, text
    Added option (trackDb setting pairEndsByName) to join separate BAM records for paired ends into linkedFeaturesSeries paired-end items.
• src/hg/hgTracks/hgTracks.h
  • 1.186 lines changed: 5, context: html, text, full: html, text
    Added option (trackDb setting pairEndsByName) to join separate BAM records for paired ends into linkedFeaturesSeries paired-end items.
• src/hg/hgTracks/simpleTracks.c
  • 1.94 lines changed: 1, context: html, text, full: html, text
    Added option (trackDb setting pairEndsByName) to join separate BAM records for paired ends into linkedFeaturesSeries paired-end items.
  • 1.93 lines changed: 50, context: html, text, full: html, text
    Fix for B0b's toggle problem, but ifdef'd out since I am leaving on vacation. Look for TOGGLE_SUBTRACKS
• src/hg/hgc/hgc.c
  • 1.1561 lines changed: 6, context: html, text, full: html, text
    When htmStart'ing in a subdirectory of trash (showSomeAlignment), call htmStartDirDepth with depth=2 so that htmlWarnBox will generate a correct relative path to images.
• src/hg/hgcentralTidy/hgcentralTidy.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    better err reporting
  • 1.4 lines changed: 2, context: html, text, full: html, text
    better err reporting
  • 1.3 lines changed: 1, context: html, text, full: html, text
    minor typo
• src/hg/inc/bamFile.h
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
• src/hg/instinct/bioInt2/bioController.c
  • 1.12 lines changed: 1, context: html, text, full: html, text
    shortened table name prefixes, oops forgot one
  • 1.11 lines changed: 9, context: html, text, full: html, text
    shortened table name prefixes
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Added geneset for balagurunathan dataset
• src/hg/lib/bamFile.c
  • 1.1 lines changed: 52, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
• src/hg/lib/hdb.c
  • 1.407 lines changed: 27, context: html, text, full: html, text
    reintroduced silent truncation of chromosome part of split table names as other code relies on the buggy behavior
• src/hg/lib/hui.c
  • 1.227 lines changed: 6, context: html, text, full: html, text
    Removing the unused combination logic from bedUi
• src/hg/lib/liftOver.c
  • 1.45 lines changed: 1, context: html, text, full: html, text
    Restore a chainFree() to eliminate a memory leak
• src/hg/lib/makefile
  • 1.392 lines changed: 4, context: html, text, full: html, text
    Libified the code that interfaces directly with libbam to open, fetch, close.
• src/hg/makeDb/doc/anoCar1.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/bosTau4.txt
  • 1.17 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/caeJap2.txt
  • 1.2 lines changed: 189, context: html, text, full: html, text
    Now running genbank
  • 1.1 lines changed: 163, context: html, text, full: html, text
    Initial sequence through masking
• src/hg/makeDb/doc/calJac1.txt
  • 1.19 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/canFam2.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/cavPor3.txt
  • 1.19 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/ce7.txt
  • 1.2 lines changed: 151, context: html, text, full: html, text
    lastz runs done for caePb2, caeRem3, cb3, caeJap2
  • 1.1 lines changed: 217, context: html, text, full: html, text
    Through genome build and first lastz of caePb2
• src/hg/makeDb/doc/ce8.txt
  • 1.1 lines changed: 167, context: html, text, full: html, text
    Initial build through repeat masking and kluster scratch data populating
• src/hg/makeDb/doc/danRer5.txt
  • 1.16 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/danRer6.txt
  • 1.5 lines changed: 1, context: html, text, full: html, text
    minor correction, thanks Hiram
• src/hg/makeDb/doc/dasNov1.txt
  • 1.7 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/echTel1.txt
  • 1.6 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/equCab2.txt
  • 1.27 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/felCat3.txt
  • 1.54 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/fr2.txt
  • 1.23 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/galGal3.txt
  • 1.29 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/gasAcu1.txt
  • 1.37 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/hg18.txt
  • 1.371 lines changed: 98, context: html, text, full: html, text
    44way phyloP update from Adam Siepel
  • 1.370 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/hg19.txt
  • 1.32 lines changed: 1, context: html, text, full: html, text
    testing commit from outside UCSC
  • 1.31 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/loxAfr1.txt
  • 1.8 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/loxAfr3.txt
  • 1.3 lines changed: 20, context: html, text, full: html, text
    added human proteins track
  • 1.2 lines changed: 163, context: html, text, full: html, text
    start human proteins track
  • 1.1 lines changed: 143, context: html, text, full: html, text
    Initial file, through genbank run
• src/hg/makeDb/doc/mm9.txt
  • 1.102 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/monDom5.txt
  • 1.13 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/ornAna1.txt
  • 1.26 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/oryCun1.txt
  • 1.9 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/oryLat2.txt
  • 1.13 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/otoGar1.txt
  • 1.9 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/panTro2.txt
  • 1.15 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/petMar1.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/ponAbe2.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/rheMac2.txt
  • 1.17 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/rn4.txt
  • 1.33 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/sacCer2.txt
  • 1.14 lines changed: 10, context: html, text, full: html, text
    Add indexes for chrM_gold and chrM_gap
• src/hg/makeDb/doc/taeGut1.txt
  • 1.18 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/tetNig1.txt
  • 1.19 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/xenTro2.txt
  • 1.14 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.98 lines changed: 1, context: html, text, full: html, text
    Added loxAfr3 - Loxodonta africana
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.343 lines changed: 19, context: html, text, full: html, text
    Added caeJap2
  • 1.342 lines changed: 17, context: html, text, full: html, text
    Adding loxAfr3
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.103 lines changed: 1, context: html, text, full: html, text
    Added loxAfr3 - Loxodonta africana
• src/hg/makeDb/trackDb/README
  • 1.85 lines changed: 3, context: html, text, full: html, text
    Adding a little documentation about the bedFilter flag
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • 1.36 lines changed: 2, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.38 lines changed: 18, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.20 lines changed: 25, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/drosophila/bdtnpChipper.html
  • 1.5 lines changed: 3, context: html, text, full: html, text
    fixed citation
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Added link to just-published article (not yet in pubmed, but it's open-access).
• src/hg/makeDb/trackDb/drosophila/droSim1/description.html
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to WUSTL.
• src/hg/makeDb/trackDb/genscan.html
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Updated link to reference. Changed credit to reflect the fact that we run Genscan locally.
• src/hg/makeDb/trackDb/human/hg18/fantomCageGraphTop.html
  • 1.2 lines changed: 16, context: html, text, full: html, text
    Adding some methods documentation from fantom 4
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.407 lines changed: 1, context: html, text, full: html, text
    bamNA12878: adding stripPrefix so we don't hardcode stripping of chr from chromName for bam tracks.
  • 1.406 lines changed: 1, context: html, text, full: html, text
    Added setting pairEndsByName.
  • 1.405 lines changed: 1, context: html, text, full: html, text
    Hide snp129 by default now that snp130 is released.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.463 lines changed: 3, context: html, text, full: html, text
    Removed release alphas for CSHL Long RNA-seq (Jul-09).
  • 1.462 lines changed: 60, context: html, text, full: html, text
    took out views, and added replicate in matrix for HA Methyl tracks
  • 1.461 lines changed: 30, context: html, text, full: html, text
    some rearrangements and track suppression for HA Methyl tracks
  • 1.460 lines changed: 1, context: html, text, full: html, text
    change default visibility on HudsonalphaCNV track
  • 1.459 lines changed: 38, context: html, text, full: html, text
    add wiggles to the CNV track
  • 1.458 lines changed: 154, context: html, text, full: html, text
    Changes to coloring, hotspot shortLabels, and "DNase-Seq" -> "Digital DNaseI" longLabel changes in UW DNase track that Kate put in and I clobbered later.
  • 1.457 lines changed: 2, context: html, text, full: html, text
    removed release alpha line to push table to beta
  • 1.456 lines changed: 49, context: html, text, full: html, text
    fixed HudsonAlpha CNV track
  • 1.455 lines changed: 255, context: html, text, full: html, text
    added new Hudsonalpha cell types and factors for ChIP-seq track
  • 1.454 lines changed: 2, context: html, text, full: html, text
    configurable tracks
  • 1.453 lines changed: 2, context: html, text, full: html, text
    fixing GM colorByStrand on GisPet
  • 1.452 lines changed: 2, context: html, text, full: html, text
    color by strand
  • 1.451 lines changed: 1, context: html, text, full: html, text
    Set default wig config for CSHL Long RNA
  • 1.450 lines changed: 10, context: html, text, full: html, text
    removed unused subgroups to get rid of trackDb warning
  • 1.449 lines changed: 7, context: html, text, full: html, text
    removed some "release alpha" lines
  • 1.448 lines changed: 10, context: html, text, full: html, text
    Remove superfluous matrix from several Transcriptome tracks
  • 1.447 lines changed: 4, context: html, text, full: html, text
    Removing release alphas to stage on track on beta.
  • 1.446 lines changed: 2, context: html, text, full: html, text
    short label was too long for the Encode Helicos RNA-Seq subtracks and so I shortened them
  • 1.445 lines changed: 12, context: html, text, full: html, text
    Label and sort ordering changes to CSHL RNA-seq for consistency
  • 1.444 lines changed: 2, context: html, text, full: html, text
    adding ranges for CSHL Long RNASEQ wiggles
  • 1.443 lines changed: 5, context: html, text, full: html, text
    fixing up controlled vocab so clickable link works in config box
  • 1.442 lines changed: 2, context: html, text, full: html, text
    user-friendly names in subgroup
  • 1.441 lines changed: 6, context: html, text, full: html, text
    metadata missing from Helicos
  • 1.440 lines changed: 26, context: html, text, full: html, text
    adding Plus/Minus Raw Signal Views
  • 1.439 lines changed: 3, context: html, text, full: html, text
    Tweak labels on Helicos track so it's easier to interpret in dense
  • 1.438 lines changed: 1, context: html, text, full: html, text
    Removed release alpha from wgEncodeUncFAIREseqPeaksHelas3 subtrack. Data contributor noticed it was missing from RR.
  • 1.437 lines changed: 110, context: html, text, full: html, text
    added HudsonAlpha ChIP-seq celltypes U87 and BE2_C vs NRSF
  • 1.436 lines changed: 40, context: html, text, full: html, text
    Yale resubmitted 8 signal tracks as V2s
  • 1.435 lines changed: 136, context: html, text, full: html, text
    HudsonAlpha GM12878 TAF-II PU.1 Pbx3 Oct-2
  • 1.434 lines changed: 54, context: html, text, full: html, text
    HudsonAlpha ChIP-sec PFSK-1 NRSF
  • 1.433 lines changed: 46, context: html, text, full: html, text
    HudsonAlpha ChIPsec HeLa-S3 Pol2
  • 1.432 lines changed: 55, context: html, text, full: html, text
    added HudsonAlpha ChIP-seq SK-N-SH_RA vs. NRSF
  • 1.431 lines changed: 54, context: html, text, full: html, text
    added Hudsonalpha ChIP PANC-1 vs NRSF
  • 1.430 lines changed: 53, context: html, text, full: html, text
    removing GIS PET Tags views
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLoRnaSeq.html
  • 1.6 lines changed: 11, context: html, text, full: html, text
    Explain views
  • 1.5 lines changed: 7, context: html, text, full: html, text
    added contacts
  • 1.4 lines changed: 2, context: html, text, full: html, text
    adding Plus/Minus Raw Signal Views
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    removing GIS PET Tags views
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    added warning about link
  • 1.10 lines changed: 1, context: html, text, full: html, text
    fixed minor formatting
  • 1.9 lines changed: 3, context: html, text, full: html, text
    link to source data on Helicos
  • 1.8 lines changed: 4, context: html, text, full: html, text
    Add some ENCODE links. Updaet signal view description for CSHL long rna track
  • 1.7 lines changed: 14, context: html, text, full: html, text
    Minor edits to Helicos page
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • 1.8 lines changed: 6, context: html, text, full: html, text
    add Rami as contact
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • 1.8 lines changed: 5, context: html, text, full: html, text
    add Rami as contact
• src/hg/makeDb/trackDb/human/hg18/wgEncodeNhgriNre.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Corrected ref format.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Add some ENCODE links. Updaet signal view description for CSHL long rna track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Add some ENCODE links. Updaet signal view description for CSHL long rna track
• src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html
  • 1.3 lines changed: 9, context: html, text, full: html, text
    added disclaimer about chain/nets to assemblies without browsers
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.40 lines changed: 50, context: html, text, full: html, text
    reordered placental chain/nets and added to the long label: Non-primate mammals and non-mammal verts
  • 1.39 lines changed: 1, context: html, text, full: html, text
    turned off confg boxes for view controls
  • 1.38 lines changed: 100, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/human/mrna.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    adjusted grammar
• src/hg/makeDb/trackDb/lowelab/glimmer.html
  • 1.1 lines changed: 32, context: html, text, full: html, text
    Adding glimmer web page
• src/hg/makeDb/trackDb/makefile
  • 1.273 lines changed: 1, context: html, text, full: html, text
    Adding ce8 to the build
  • 1.272 lines changed: 2, context: html, text, full: html, text
    Adding caeJap2 to the build
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.3 lines changed: 16, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/orangutan/trackDb.ra
  • 1.3 lines changed: 23, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/rhesus/priority.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.43 lines changed: 12, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • 1.11 lines changed: 2, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
  • 1.18 lines changed: 1, context: html, text, full: html, text
    Fixed link.
• src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed link.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.522 lines changed: 21, context: html, text, full: html, text
    mods for hg19.primateChainNet and reverse tracks on chimp, orang, rhesus and marmoset
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • 1.35 lines changed: 43, context: html, text, full: html, text
    Adding chainNet composite for caePb2
  • 1.34 lines changed: 38, context: html, text, full: html, text
    Adding ce7ChainNet
• src/hg/overlapSelect/chromAnn.c
  • 1.14 lines changed: 36, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/overlapSelect.c
  • 1.41 lines changed: 1, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/expected/orthoStrandTest.stats
  • 1.1 lines changed: 2, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/input/orthoIn.gp
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/input/orthoSel.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/makefile
  • 1.32 lines changed: 6, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/ratStuff/mafSpeciesList/mafSpeciesList.c
  • 1.2 lines changed: 7, context: html, text, full: html, text
    fixed memoryleak. remove chrom name from component names (from stanford)
• src/hg/ratStuff/mafsInRegion/mafsInRegion.c
  • 1.7 lines changed: 5, context: html, text, full: html, text
    added option to keep initial/training gaps in alignment'
  • 1.6 lines changed: 17, context: html, text, full: html, text
    fixed major memory leak (from stanford)
• src/inc/bbiFile.h
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Added include needed by .c's that include this .h only, which should be OK.
  • 1.10 lines changed: 46, context: html, text, full: html, text
    Refactoring bedGraphToBigWig to put more code in libraries for reuse and to clean up some.
• src/inc/haval.h
  • 1.1 lines changed: 89, context: html, text, full: html, text
    Adding haval, an md5 alternative.
• src/inc/htmshell.h
  • 1.21 lines changed: 7, context: html, text, full: html, text
    Added htmStartDirDepth, so htmlWarnBox can generate a relative path to images with the correct number of ../'s depending on where the HTML comes from (used only in hgc's alignment index/ and body/ files now). Cleaned up code a bit.
• src/lib/bbiWrite.c
  • 1.3 lines changed: 135, context: html, text, full: html, text
    Refactoring bedGraphToBigWig to put more code in libraries for reuse and to clean up some.
• src/lib/bwgCreate.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Refactoring bedGraphToBigWig to put more code in libraries for reuse and to clean up some.
• src/lib/haval.c
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Fixing compiler warnings.
  • 1.1 lines changed: 750, context: html, text, full: html, text
    Adding haval, an md5 alternative.
• src/lib/htmshell.c
  • 1.60 lines changed: 71, context: html, text, full: html, text
    Added htmStartDirDepth, so htmlWarnBox can generate a relative path to images with the correct number of ../'s depending on where the HTML comes from (used only in hgc's alignment index/ and body/ files now). Cleaned up code a bit.
• src/lib/maf.c
  • 1.40 lines changed: 0, context: html, text, full: html, text
    fixed broken indent
  • 1.39 lines changed: 4, context: html, text, full: html, text
    fixed null pointer derefernces on i and e lines (from stanford); fix broken formatting
• src/lib/makefile
  • 1.152 lines changed: 1, context: html, text, full: html, text
    Adding haval, an md5 alternative.
• src/lib/obscure.c
  • 1.47 lines changed: 2, context: html, text, full: html, text
    changed shuffleArrayOfPointer to produce a truly uniform random permutation of the input elements (from stanford)
• src/parasol/paraHub/paraHub.c
  • 1.130 lines changed: 1, context: html, text, full: html, text
    host names should be treated as case-insensitive (fix from stanford)
• src/utils/makefile
  • 1.73 lines changed: 2, context: html, text, full: html, text
    add to build fastqToFa and faToFastq

• lines changed: 5223
• files changed: 119