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
- 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
- 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
- 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
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
- 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
- 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
- src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
- 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