9b1d1612efa7f321c5d3c500ce799c804c977135 markd Tue May 12 14:23:51 2026 -0700 Add to .gitignore update LICENSE to remove htslib just note old htslib directory, not require removal diff --git LICENSE LICENSE index 23a87e656e8..4857cbc83cb 100644 --- LICENSE +++ LICENSE @@ -15,58 +15,51 @@ All other UCSC Genome Browser command-line tools and their required libraries are released under the MIT License. This includes our various file format converters, such as bedToBigBed and wigToBigWig, and any tools to create files needed for track hubs. They can be redistributed in any way necessary. The following sections list all licenses and which directories are covered by which one. FREE Licenses: 1. As described above, the default is the MIT license (attached below) - this includes, for example, all code to read and write the Genome Browser file formats, such as bigBed and bigWig, and the command line tools for these, bedToBigBed, wigToBigWig and the tagStorm tools and the parasol job scheduler. - - also, third-party code for reading BAM files bundled for convenience, - in src/htslib (MIT) -2. A modified BSD license for src/htslib/cram/, see src/htslib/LICENSE. - Copyright (C) 2012-2014 Genome Research Ltd. -3. A public domain "with attribution" license for sorting bigWig files, +2. A public domain "with attribution" license for sorting bigWig files, see src/optimalLeaf/LICENSE NON-COMMERCIAL licenses: 4. A non-commercial license from UC for the genome browser interactive web code in the following subdirectories of src/hg/ (see the LICENSE files in these directories): cgilib hgApi hgCollection hgFileSearch hgFileUi hgGateway hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near visiGene liftOver 5. A non-commercial license from Kent Informatics for the BLAT and isPCR code in src/blat/, src/isPcr and src/jkOwnLib/, for more information see https://genome.ucsc.edu/license/ and http://www.kentinformatics.com/ See https://genome.ucsc.edu/license/ for more details and on how to obtain a license for commercial use for the case (4) and (5): Commercial users interested in the interactive Genome Browser web software listed under (4) should contact genomebrowser@ucsc.edu. Those interested in BLAT, so any code listed under (5), should contact kent@soe.ucsc.edu. -The code in src/htslib is distributed under a dual license as noted in the LICENSE -file in that directory. - Mandatory acknowledgements for third party open source libraries that are used but not distributed as part of this source tree are provided at https://genome.ucsc.edu/license/ ---- MIT License Copyright (C) 2001 UC Regents Permission is hereby granted, free of charge, to any person or non-commercial entity obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: