Third Party Software Notices

ABSEIL

                                 Apache License
                           Version 2.0, January 2004
                        https://www.apache.org/licenses/

   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

   1. Definitions.

      "License" shall mean the terms and conditions for use, reproduction,
      and distribution as defined by Sections 1 through 9 of this document.

      "Licensor" shall mean the copyright owner or entity authorized by
      the copyright owner that is granting the License.

      "Legal Entity" shall mean the union of the acting entity and all
      other entities that control, are controlled by, or are under common
      control with that entity. For the purposes of this definition,
      "control" means (i) the power, direct or indirect, to cause the
      direction or management of such entity, whether by contract or
      otherwise, or (ii) ownership of fifty percent (50%) or more of the
      outstanding shares, or (iii) beneficial ownership of such entity.

      "You" (or "Your") shall mean an individual or Legal Entity
      exercising permissions granted by this License.

      "Source" form shall mean the preferred form for making modifications,
      including but not limited to software source code, documentation
      source, and configuration files.

      "Object" form shall mean any form resulting from mechanical
      transformation or translation of a Source form, including but
      not limited to compiled object code, generated documentation,
      and conversions to other media types.

      "Work" shall mean the work of authorship, whether in Source or
      Object form, made available under the License, as indicated by a
      copyright notice that is included in or attached to the work
      (an example is provided in the Appendix below).

      "Derivative Works" shall mean any work, whether in Source or Object
      form, that is based on (or derived from) the Work and for which the
      editorial revisions, annotations, elaborations, or other modifications
      represent, as a whole, an original work of authorship. For the purposes
      of this License, Derivative Works shall not include works that remain
      separable from, or merely link (or bind by name) to the interfaces of,
      the Work and Derivative Works thereof.

      "Contribution" shall mean any work of authorship, including
      the original version of the Work and any modifications or additions
      to that Work or Derivative Works thereof, that is intentionally
      submitted to Licensor for inclusion in the Work by the copyright owner
      or by an individual or Legal Entity authorized to submit on behalf of
      the copyright owner. For the purposes of this definition, "submitted"
      means any form of electronic, verbal, or written communication sent
      to the Licensor or its representatives, including but not limited to
      communication on electronic mailing lists, source code control systems,
      and issue tracking systems that are managed by, or on behalf of, the
      Licensor for the purpose of discussing and improving the Work, but
      excluding communication that is conspicuously marked or otherwise
      designated in writing by the copyright owner as "Not a Contribution."

      "Contributor" shall mean Licensor and any individual or Legal Entity
      on behalf of whom a Contribution has been received by Licensor and
      subsequently incorporated within the Work.

   2. Grant of Copyright License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      copyright license to reproduce, prepare Derivative Works of,
      publicly display, publicly perform, sublicense, and distribute the
      Work and such Derivative Works in Source or Object form.

   3. Grant of Patent License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      (except as stated in this section) patent license to make, have made,
      use, offer to sell, sell, import, and otherwise transfer the Work,
      where such license applies only to those patent claims licensable
      by such Contributor that are necessarily infringed by their
      Contribution(s) alone or by combination of their Contribution(s)
      with the Work to which such Contribution(s) was submitted. If You
      institute patent litigation against any entity (including a
      cross-claim or counterclaim in a lawsuit) alleging that the Work
      or a Contribution incorporated within the Work constitutes direct
      or contributory patent infringement, then any patent licenses
      granted to You under this License for that Work shall terminate
      as of the date such litigation is filed.

   4. Redistribution. You may reproduce and distribute copies of the
      Work or Derivative Works thereof in any medium, with or without
      modifications, and in Source or Object form, provided that You
      meet the following conditions:

      (a) You must give any other recipients of the Work or
          Derivative Works a copy of this License; and

      (b) You must cause any modified files to carry prominent notices
          stating that You changed the files; and

      (c) You must retain, in the Source form of any Derivative Works
          that You distribute, all copyright, patent, trademark, and
          attribution notices from the Source form of the Work,
          excluding those notices that do not pertain to any part of
          the Derivative Works; and

      (d) If the Work includes a "NOTICE" text file as part of its
          distribution, then any Derivative Works that You distribute must
          include a readable copy of the attribution notices contained
          within such NOTICE file, excluding those notices that do not
          pertain to any part of the Derivative Works, in at least one
          of the following places: within a NOTICE text file distributed
          as part of the Derivative Works; within the Source form or
          documentation, if provided along with the Derivative Works; or,
          within a display generated by the Derivative Works, if and
          wherever such third-party notices normally appear. The contents
          of the NOTICE file are for informational purposes only and
          do not modify the License. You may add Your own attribution
          notices within Derivative Works that You distribute, alongside
          or as an addendum to the NOTICE text from the Work, provided
          that such additional attribution notices cannot be construed
          as modifying the License.

      You may add Your own copyright statement to Your modifications and
      may provide additional or different license terms and conditions
      for use, reproduction, or distribution of Your modifications, or
      for any such Derivative Works as a whole, provided Your use,
      reproduction, and distribution of the Work otherwise complies with
      the conditions stated in this License.

   5. Submission of Contributions. Unless You explicitly state otherwise,
      any Contribution intentionally submitted for inclusion in the Work
      by You to the Licensor shall be under the terms and conditions of
      this License, without any additional terms or conditions.
      Notwithstanding the above, nothing herein shall supersede or modify
      the terms of any separate license agreement you may have executed
      with Licensor regarding such Contributions.

   6. Trademarks. This License does not grant permission to use the trade
      names, trademarks, service marks, or product names of the Licensor,
      except as required for reasonable and customary use in describing the
      origin of the Work and reproducing the content of the NOTICE file.

   7. Disclaimer of Warranty. Unless required by applicable law or
      agreed to in writing, Licensor provides the Work (and each
      Contributor provides its Contributions) on an "AS IS" BASIS,
      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
      implied, including, without limitation, any warranties or conditions
      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
      PARTICULAR PURPOSE. You are solely responsible for determining the
      appropriateness of using or redistributing the Work and assume any
      risks associated with Your exercise of permissions under this License.

   8. Limitation of Liability. In no event and under no legal theory,
      whether in tort (including negligence), contract, or otherwise,
      unless required by applicable law (such as deliberate and grossly
      negligent acts) or agreed to in writing, shall any Contributor be
      liable to You for damages, including any direct, indirect, special,
      incidental, or consequential damages of any character arising as a
      result of this License or out of the use or inability to use the
      Work (including but not limited to damages for loss of goodwill,
      work stoppage, computer failure or malfunction, or any and all
      other commercial damages or losses), even if such Contributor
      has been advised of the possibility of such damages.

   9. Accepting Warranty or Additional Liability. While redistributing
      the Work or Derivative Works thereof, You may choose to offer,
      and charge a fee for, acceptance of support, warranty, indemnity,
      or other liability obligations and/or rights consistent with this
      License. However, in accepting such obligations, You may act only
      on Your own behalf and on Your sole responsibility, not on behalf
      of any other Contributor, and only if You agree to indemnify,
      defend, and hold each Contributor harmless for any liability
      incurred by, or claims asserted against, such Contributor by reason
      of your accepting any such warranty or additional liability.

   END OF TERMS AND CONDITIONS

   APPENDIX: How to apply the Apache License to your work.

      To apply the Apache License to your work, attach the following
      boilerplate notice, with the fields enclosed by brackets "[]"
      replaced with your own identifying information. (Don't include
      the brackets!)  The text should be enclosed in the appropriate
      comment syntax for the file format. We also recommend that a
      file or class name and description of purpose be included on the
      same "printed page" as the copyright notice for easier
      identification within third-party archives.

   Copyright [yyyy] [name of copyright owner]

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       https://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.

BWA

Apache License

Version 2.0, January 2004

http://www.apache.org/licenses/

TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

1. Definitions.

   "License" shall mean the terms and conditions for use, reproduction, and
   distribution as defined by Sections 1 through 9 of this document.

   "Licensor" shall mean the copyright owner or entity authorized by the
   copyright owner that is granting the License.

   "Legal Entity" shall mean the union of the acting entity and all other
   entities that control, are controlled by, or are under common control with
   that entity.  For the purposes of this definition, "control" means (i) the
   power, direct or indirect, to cause the direction or management of such
   entity, whether by contract or otherwise, or (ii) ownership of fifty percent
   (50%) or more of the outstanding shares, or (iii) beneficial ownership of
   such entity.

   "You" (or "Your") shall mean an individual or Legal Entity exercising
   permissions granted by this License.

   "Source" form shall mean the preferred form for making modifications,
   including but not limited to software source code, documentation source, and
   configuration files.

   "Object" form shall mean any form resulting from mechanical transformation
   or translation of a Source form, including but not limited to compiled
   object code, generated documentation, and conversions to other media types.

   "Work" shall mean the work of authorship, whether in Source or Object form,
   made available under the License, as indicated by a copyright notice that is
   included in or attached to the work (an example is provided in the Appendix
   below).

   "Derivative Works" shall mean any work, whether in Source or Object form,
   that is based on (or derived from) the Work and for which the editorial
   revisions, annotations, elaborations, or other modifications represent, as a
   whole, an original work of authorship. For the purposes of this License,
   Derivative Works shall not include works that remain separable from, or
   merely link (or bind by name) to the interfaces of, the Work and Derivative
   Works thereof.

   "Contribution" shall mean any work of authorship, including the original
   version of the Work and any modifications or additions to that Work or
   Derivative Works thereof, that is intentionally submitted to Licensor for
   inclusion in the Work by the copyright owner or by an individual or Legal
   Entity authorized to submit on behalf of the copyright owner. For the
   purposes of this definition, "submitted" means any form of electronic,
   verbal, or written communication sent to the Licensor or its
   representatives, including but not limited to communication on electronic
   mailing lists, source code control systems, and issue tracking systems that
   are managed by, or on behalf of, the Licensor for the purpose of discussing
   and improving the Work, but excluding communication that is conspicuously
   marked or otherwise designated in writing by the copyright owner as "Not a
   Contribution."

   "Contributor" shall mean Licensor and any individual or Legal Entity on
   behalf of whom a Contribution has been received by Licensor and subsequently
   incorporated within the Work.

2. Grant of Copyright License. Subject to the terms and conditions of this
   License, each Contributor hereby grants to You a perpetual, worldwide,
   non-exclusive, no-charge, royalty-free, irrevocable copyright license to
   reproduce, prepare Derivative Works of, publicly display, publicly perform,
   sublicense, and distribute the Work and such Derivative Works in Source or
   Object form.

3. Grant of Patent License. Subject to the terms and conditions of this
   License, each Contributor hereby grants to You a perpetual, worldwide,
   non-exclusive, no-charge, royalty-free, irrevocable (except as stated in
   this section) patent license to make, have made, use, offer to sell, sell,
   import, and otherwise transfer the Work, where such license applies only to
   those patent claims licensable by such Contributor that are necessarily
   infringed by their Contribution(s) alone or by combination of their
   Contribution(s) with the Work to which such Contribution(s) was submitted.
   If You institute patent litigation against any entity (including a
   cross-claim or counterclaim in a lawsuit) alleging that the Work or a
   Contribution incorporated within the Work constitutes direct or contributory
   patent infringement, then any patent licenses granted to You under this
   License for that Work shall terminate as of the date such litigation is
   filed.

4. Redistribution. You may reproduce and distribute copies of the Work or
   Derivative Works thereof in any medium, with or without modifications, and
   in Source or Object form, provided that You meet the following conditions:

   (a) You must give any other recipients of the Work or Derivative Works a
       copy of this License; and
   
   (b) You must cause any modified files to carry prominent notices stating
       that You changed the files; and
   
   (c) You must retain,in the Source form of any Derivative Works that You
       distribute, all copyright, patent, trademark, and attribution notices
       from the Source form of the Work, excluding those notices that do not
       pertain to any part of the Derivative Works; and
   
   (d) If the Work includes a "NOTICE" text file as part of its distribution,
       then any Derivative Works that You distribute must include a readable
       copy of the attribution notices contained within such NOTICE file,
       excluding those notices that do not pertain to any part of the
       Derivative Works, in at least one of the following places: within a
       NOTICE text file distributed as part of the Derivative Works; within the
       Source form or documentation, if provided along with the Derivative
       Works; or, within a display generated by the Derivative Works, if and
       wherever such third-party notices normally appear. The contents of the
       NOTICE file are for informational purposes only and do not modify the
       License. You may add Your own attribution notices within Derivative
       Works that You distribute, alongside or as an addendum to the NOTICE
       text from the Work, provided that such additional attribution notices
       cannot be construed as modifying the License. 

   You may add Your own copyright statement to Your modifications and may
   provide additional or different license terms and conditions for use,
   reproduction, or distribution of Your modifications, or for any such
   Derivative Works as a whole, provided Your use, reproduction, and
   distribution of the Work otherwise complies with the conditions stated in
   this License.

5. Submission of Contributions. Unless You explicitly state otherwise, any
   Contribution intentionally submitted for inclusion in the Work by You to the
   Licensor shall be under the terms and conditions of this License, without
   any additional terms or conditions. Notwithstanding the above, nothing
   herein shall supersede or modify the terms of any separate license agreement
   you may have executed with Licensor regarding such Contributions.

6. Trademarks. This License does not grant permission to use the trade names,
   trademarks, service marks, or product names of the Licensor, except as
   required for reasonable and customary use in describing the origin of the
   Work and reproducing the content of the NOTICE file.

7. Disclaimer of Warranty. Unless required by applicable law or agreed to in
   writing, Licensor provides the Work (and each Contributor provides its
   Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
   KIND, either express or implied, including, without limitation, any
   warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or
   FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining
   the appropriateness of using or redistributing the Work and assume any risks
   associated with Your exercise of permissions under this License.

8. Limitation of Liability. In no event and under no legal theory, whether in
   tort (including negligence), contract, or otherwise, unless required by
   applicable law (such as deliberate and grossly negligent acts) or agreed to
   in writing, shall any Contributor be liable to You for damages, including
   any direct, indirect, special, incidental, or consequential damages of any
   character arising as a result of this License or out of the use or inability
   to use the Work (including but not limited to damages for loss of goodwill,
   work stoppage, computer failure or malfunction, or any and all other
   commercial damages or losses), even if such Contributor has been advised of
   the possibility of such damages.

9. Accepting Warranty or Additional Liability. While redistributing the Work or
   Derivative Works thereof, You may choose to offer, and charge a fee for,
   acceptance of support, warranty, indemnity, or other liability obligations
   and/or rights consistent with this License. However, in accepting such
   obligations, You may act only on Your own behalf and on Your sole
   responsibility, not on behalf of any other Contributor, and only if You
   agree to indemnify, defend, and hold each Contributor harmless for any
   liability incurred by, or claims asserted against, such Contributor by
   reason of your accepting any such warranty or additional liability.

END OF TERMS AND CONDITIONS

DEEPVARIANT

Copyright 2020 Google LLC.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors
   may be used to endorse or promote products derived from this software without
   specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

GATK

Copyright (c) 2009-2020, Broad Institute, Inc. All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
  list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
  this list of conditions and the following disclaimer in the documentation
  and/or other materials provided with the distribution.

* Neither the name Broad Institute, Inc. nor the names of its
  contributors may be used to endorse or promote products derived from
  this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

HTSLIB

[Files in this distribution outwith the cram/ subdirectory are distributed
according to the terms of the following MIT/Expat license.]

The MIT/Expat License

Copyright (C) 2012-2020 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person 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:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.


[Files within the cram/ subdirectory in this distribution are distributed
according to the terms of the following Modified 3-Clause BSD license.]

The Modified-BSD License

Copyright (C) 2012-2020 Genome Research Ltd.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute
   nor the names of its contributors may be used to endorse or promote products
   derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


[The use of a range of years within a copyright notice in this distribution
should be interpreted as being equivalent to a list of years including the
first and last year specified and all consecutive years between them.

For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
2011-2012" should be interpreted as being identical to a notice that reads
"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
that reads "Copyright (C) 2005-2012" should be interpreted as being identical
to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
2011, 2012".]

ISA-L

  Copyright(c) 2011-2017 Intel Corporation All rights reserved.

  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions
  are met:
    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
    * Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in
      the documentation and/or other materials provided with the
      distribution.
    * Neither the name of Intel Corporation nor the names of its
      contributors may be used to endorse or promote products derived
      from this software without specific prior written permission.

  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
  "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
  LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
  A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
  OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
  LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
  THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NUCLEUS

Files:  all except for vendor/message_module.cc


                                 Apache License
                           Version 2.0, January 2004
                        http://www.apache.org/licenses/

   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

   1. Definitions.

      "License" shall mean the terms and conditions for use, reproduction,
      and distribution as defined by Sections 1 through 9 of this document.

      "Licensor" shall mean the copyright owner or entity authorized by
      the copyright owner that is granting the License.

      "Legal Entity" shall mean the union of the acting entity and all
      other entities that control, are controlled by, or are under common
      control with that entity. For the purposes of this definition,
      "control" means (i) the power, direct or indirect, to cause the
      direction or management of such entity, whether by contract or
      otherwise, or (ii) ownership of fifty percent (50%) or more of the
      outstanding shares, or (iii) beneficial ownership of such entity.

      "You" (or "Your") shall mean an individual or Legal Entity
      exercising permissions granted by this License.

      "Source" form shall mean the preferred form for making modifications,
      including but not limited to software source code, documentation
      source, and configuration files.

      "Object" form shall mean any form resulting from mechanical
      transformation or translation of a Source form, including but
      not limited to compiled object code, generated documentation,
      and conversions to other media types.

      "Work" shall mean the work of authorship, whether in Source or
      Object form, made available under the License, as indicated by a
      copyright notice that is included in or attached to the work
      (an example is provided in the Appendix below).

      "Derivative Works" shall mean any work, whether in Source or Object
      form, that is based on (or derived from) the Work and for which the
      editorial revisions, annotations, elaborations, or other modifications
      represent, as a whole, an original work of authorship. For the purposes
      of this License, Derivative Works shall not include works that remain
      separable from, or merely link (or bind by name) to the interfaces of,
      the Work and Derivative Works thereof.

      "Contribution" shall mean any work of authorship, including
      the original version of the Work and any modifications or additions
      to that Work or Derivative Works thereof, that is intentionally
      submitted to Licensor for inclusion in the Work by the copyright owner
      or by an individual or Legal Entity authorized to submit on behalf of
      the copyright owner. For the purposes of this definition, "submitted"
      means any form of electronic, verbal, or written communication sent
      to the Licensor or its representatives, including but not limited to
      communication on electronic mailing lists, source code control systems,
      and issue tracking systems that are managed by, or on behalf of, the
      Licensor for the purpose of discussing and improving the Work, but
      excluding communication that is conspicuously marked or otherwise
      designated in writing by the copyright owner as "Not a Contribution."

      "Contributor" shall mean Licensor and any individual or Legal Entity
      on behalf of whom a Contribution has been received by Licensor and
      subsequently incorporated within the Work.

   2. Grant of Copyright License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      copyright license to reproduce, prepare Derivative Works of,
      publicly display, publicly perform, sublicense, and distribute the
      Work and such Derivative Works in Source or Object form.

   3. Grant of Patent License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      (except as stated in this section) patent license to make, have made,
      use, offer to sell, sell, import, and otherwise transfer the Work,
      where such license applies only to those patent claims licensable
      by such Contributor that are necessarily infringed by their
      Contribution(s) alone or by combination of their Contribution(s)
      with the Work to which such Contribution(s) was submitted. If You
      institute patent litigation against any entity (including a
      cross-claim or counterclaim in a lawsuit) alleging that the Work
      or a Contribution incorporated within the Work constitutes direct
      or contributory patent infringement, then any patent licenses
      granted to You under this License for that Work shall terminate
      as of the date such litigation is filed.

   4. Redistribution. You may reproduce and distribute copies of the
      Work or Derivative Works thereof in any medium, with or without
      modifications, and in Source or Object form, provided that You
      meet the following conditions:

      (a) You must give any other recipients of the Work or
          Derivative Works a copy of this License; and

      (b) You must cause any modified files to carry prominent notices
          stating that You changed the files; and

      (c) You must retain, in the Source form of any Derivative Works
          that You distribute, all copyright, patent, trademark, and
          attribution notices from the Source form of the Work,
          excluding those notices that do not pertain to any part of
          the Derivative Works; and

      (d) If the Work includes a "NOTICE" text file as part of its
          distribution, then any Derivative Works that You distribute must
          include a readable copy of the attribution notices contained
          within such NOTICE file, excluding those notices that do not
          pertain to any part of the Derivative Works, in at least one
          of the following places: within a NOTICE text file distributed
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          of the NOTICE file are for informational purposes only and
          do not modify the License. You may add Your own attribution
          notices within Derivative Works that You distribute, alongside
          or as an addendum to the NOTICE text from the Work, provided
          that such additional attribution notices cannot be construed
          as modifying the License.

      You may add Your own copyright statement to Your modifications and
      may provide additional or different license terms and conditions
      for use, reproduction, or distribution of Your modifications, or
      for any such Derivative Works as a whole, provided Your use,
      reproduction, and distribution of the Work otherwise complies with
      the conditions stated in this License.

   5. Submission of Contributions. Unless You explicitly state otherwise,
      any Contribution intentionally submitted for inclusion in the Work
      by You to the Licensor shall be under the terms and conditions of
      this License, without any additional terms or conditions.
      Notwithstanding the above, nothing herein shall supersede or modify
      the terms of any separate license agreement you may have executed
      with Licensor regarding such Contributions.

   6. Trademarks. This License does not grant permission to use the trade
      names, trademarks, service marks, or product names of the Licensor,
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   7. Disclaimer of Warranty. Unless required by applicable law or
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      PARTICULAR PURPOSE. You are solely responsible for determining the
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   8. Limitation of Liability. In no event and under no legal theory,
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      unless required by applicable law (such as deliberate and grossly
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   9. Accepting Warranty or Additional Liability. While redistributing
      the Work or Derivative Works thereof, You may choose to offer,
      and charge a fee for, acceptance of support, warranty, indemnity,
      or other liability obligations and/or rights consistent with this
      License. However, in accepting such obligations, You may act only
      on Your own behalf and on Your sole responsibility, not on behalf
      of any other Contributor, and only if You agree to indemnify,
      defend, and hold each Contributor harmless for any liability
      incurred by, or claims asserted against, such Contributor by reason
      of your accepting any such warranty or additional liability.

   END OF TERMS AND CONDITIONS

   APPENDIX: How to apply the Apache License to your work.

      To apply the Apache License to your work, attach the following
      boilerplate notice, with the fields enclosed by brackets "[]"
      replaced with your own identifying information. (Don't include
      the brackets!)  The text should be enclosed in the appropriate
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   Copyright [yyyy] [name of copyright owner]

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
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------------------

Files: vendor/message_module.cc

Copyright <YEAR> <COPYRIGHT HOLDER>

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

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3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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SAMTOOLS

The MIT/Expat License

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Permission is hereby granted, free of charge, to any person obtaining a copy
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The above copyright notice and this permission notice shall be included in
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.


[The use of a range of years within a copyright notice in this distribution
should be interpreted as being equivalent to a list of years including the
first and last year specified and all consecutive years between them.

For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
2011-2012" should be interpreted as being identical to a notice that reads
"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
that reads "Copyright (C) 2005-2012" should be interpreted as being identical
to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
2011, 2012".]

STAR

MIT License

Copyright (c) 2019 Alexander Dobin

Permission is hereby granted, free of charge, to any person 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:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

STAR-FUSION

Copyright (c) 2015, STAR-Fusion, Broad Institute
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
  list of conditions and the following disclaimer.

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* Neither the name of the Broad Institute nor the names of its
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

TCMALLOC


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      defend, and hold each Contributor harmless for any liability
      incurred by, or claims asserted against, such Contributor by reason
      of your accepting any such warranty or additional liability.

   END OF TERMS AND CONDITIONS

   APPENDIX: How to apply the Apache License to your work.

      To apply the Apache License to your work, attach the following
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      replaced with your own identifying information. (Don't include
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   limitations under the License.

TENSORFLOW

                                 Apache License
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   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

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      "License" shall mean the terms and conditions for use, reproduction,
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      other entities that control, are controlled by, or are under common
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      direction or management of such entity, whether by contract or
      otherwise, or (ii) ownership of fifty percent (50%) or more of the
      outstanding shares, or (iii) beneficial ownership of such entity.

      "You" (or "Your") shall mean an individual or Legal Entity
      exercising permissions granted by this License.

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      including but not limited to software source code, documentation
      source, and configuration files.

      "Object" form shall mean any form resulting from mechanical
      transformation or translation of a Source form, including but
      not limited to compiled object code, generated documentation,
      and conversions to other media types.

      "Work" shall mean the work of authorship, whether in Source or
      Object form, made available under the License, as indicated by a
      copyright notice that is included in or attached to the work
      (an example is provided in the Appendix below).

      "Derivative Works" shall mean any work, whether in Source or Object
      form, that is based on (or derived from) the Work and for which the
      editorial revisions, annotations, elaborations, or other modifications
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      of this License, Derivative Works shall not include works that remain
      separable from, or merely link (or bind by name) to the interfaces of,
      the Work and Derivative Works thereof.

      "Contribution" shall mean any work of authorship, including
      the original version of the Work and any modifications or additions
      to that Work or Derivative Works thereof, that is intentionally
      submitted to Licensor for inclusion in the Work by the copyright owner
      or by an individual or Legal Entity authorized to submit on behalf of
      the copyright owner. For the purposes of this definition, "submitted"
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      designated in writing by the copyright owner as "Not a Contribution."

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      subsequently incorporated within the Work.

   2. Grant of Copyright License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
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      publicly display, publicly perform, sublicense, and distribute the
      Work and such Derivative Works in Source or Object form.

   3. Grant of Patent License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
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      meet the following conditions:

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          Derivative Works a copy of this License; and

      (b) You must cause any modified files to carry prominent notices
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      (c) You must retain, in the Source form of any Derivative Works
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          the Derivative Works; and

      (d) If the Work includes a "NOTICE" text file as part of its
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      this License, without any additional terms or conditions.
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      with Licensor regarding such Contributions.

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      Contributor provides its Contributions) on an "AS IS" BASIS,
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      risks associated with Your exercise of permissions under this License.

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      whether in tort (including negligence), contract, or otherwise,
      unless required by applicable law (such as deliberate and grossly
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      liable to You for damages, including any direct, indirect, special,
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      work stoppage, computer failure or malfunction, or any and all
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   9. Accepting Warranty or Additional Liability. While redistributing
      the Work or Derivative Works thereof, You may choose to offer,
      and charge a fee for, acceptance of support, warranty, indemnity,
      or other liability obligations and/or rights consistent with this
      License. However, in accepting such obligations, You may act only
      on Your own behalf and on Your sole responsibility, not on behalf
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      defend, and hold each Contributor harmless for any liability
      incurred by, or claims asserted against, such Contributor by reason
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   END OF TERMS AND CONDITIONS

   APPENDIX: How to apply the Apache License to your work.

      To apply the Apache License to your work, attach the following
      boilerplate notice, with the fields enclosed by brackets "[]"
      replaced with your own identifying information. (Don't include
      the brackets!)  The text should be enclosed in the appropriate
      comment syntax for the file format. We also recommend that a
      file or class name and description of purpose be included on the
      same "printed page" as the copyright notice for easier
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   Copyright [yyyy] [name of copyright owner]

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.

## Some of TensorFlow's code is derived from Caffe, which is subject to the following copyright notice:

COPYRIGHT

All contributions by the University of California:

Copyright (c) 2014, The Regents of the University of California (Regents)
All rights reserved.

All other contributions:

Copyright (c) 2014, the respective contributors
All rights reserved.

Caffe uses a shared copyright model: each contributor holds copyright over
their contributions to Caffe. The project versioning records all such
contribution and copyright details. If a contributor wants to further mark
their specific copyright on a particular contribution, they should indicate
their copyright solely in the commit message of the change when it is
committed.

LICENSE

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
   ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
   WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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