v301
- v301 Preview 1 - 26 May 2014
- v301 Preview 2 - 2 June 2014
- v301 Final - 9 June 2014
Code changes:
- Altered makefiles to gracefully make the hgwdev-demoN machines without tripping on permissions. Tim
- Added support for RetroFinder gene ids without parent gene version numbers. Rachel
- Added copyright notices to several source files. Jim
- Worked on "fq.c" library routine for fastq files. Jim, Chris
- Made prototype Tukay plotter and bar grapher for GTEx project and added some prototype programs to oneShot. Jim
- Created a BAM filtering program and added to bamFile.c library. Jim
- Created a convertor program: BAM to fastq. Chris
- Added support for new data formats and new organisms (drosophila, worm) to ENCODE Data Warehouse. Jim, Chin, Galt.
- UI improvements to Encode Data Warehouse submit and browse CGIs. Kate
- Added support for details page of in-progress DNase Combined Sites track. Extension of generic code to display a list of IDs in a BED 'extra field', to display a list of names based on lookup of name by ID in a joined table. Kate
- Created tool hgBedSources, to generate a bed file with id list and an id+name map file from input file of bed items + list of names. Kate
- Changed ENCODE peaks display to be full height when no peak summit ('point source') is defined (when there is peak summit, the peak is full height and the remainder of the item is half height). This affects all ENCODE broadPeak format tracks, and all narrowPeak tracks with peak summit undefined (#13305). Kate
- Added support for Watson/Crick mode (i.e. negative values wiggle data types) (#11630). Brian
- Make-over for Track Hub Portal to make it more user-friendly (#8974). Brian
- Fixed bug in border-case drawing problem with snake tracks (HAL data type) (#10637). Brian
- Added support for mafDot in trackDb to show "." if a base is identical to maf reference (#13299). Brian
- Fixed some bugs in splitFileByColumn (#13297). Brian
- Enabled searching for tracks with Track Hubs (#11633). Brian
- Compiled source code on Mac OSX Mavericks and fixed issues (#12209). Hiram, Angie
- Edited htmlCheck so that it now tolerates missing HIDDEN and CHECKBOX input types (#13212). Angie
- Added back missing dense mode left labels to pgSNP tracks (#13344). Angie
- Fixed VAI so it ignores "variants" with no observed variation (#13310). Angie
- Fixed VAI so that it stops trying to find a chrom that is not in the input file (#13343). Angie
- Added support for assemblies with many sequences (> 100) to checkTableCoords.c. Angie
Data changes:
- Minor changes to the TFBS Clusters input table (wgEncodeRegTfbsClusteredInputsV3) - the source column of 4 rows were updated to uniquely identify experiments. Kate
- Updated Gene Reviews track for hg38 (#13281). Chin
- Automated Gene Reviews tracks for hg18, hg19, hg38 (#5522). Chin
- Started working on minimal browsers for D. melanogaster genome release 6 (dm6) (#4049). Chin
- Ongoing work on farm animal QTL tracks (#10954). Pauline
- Ongoing work on Facebase microarray track, hg19 (#12606). Pauline
- Completed 13-way conservation track for rat, rn5 (#8212). Pauline
- Created liftOver from rheMac2 to mm10 (#13319). Hiram
- Added more species to master phylogenetic tree - now at 131 organisms (#10272). Hiram
- Added several chain/net tracks (#10272). Hiram
- Completed 7-way conservation track for human, hg38 (#13300). Hiram
- Update to Locus Reference Genomic (LRG) track for hg19, and new LRG track for hg38 (#13359). Angie