diff --git a/LICENSE.txt b/LICENSE.txt
index 94a9ed0..d645695 100644
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -1,674 +1,202 @@
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-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-
- Copyright (C)
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
+
+ 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
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+ "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.
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+ including but not limited to software source code, documentation
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+
+ "Object" form shall mean any form resulting from mechanical
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+ 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
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+ 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,
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+ Work and such Derivative Works in Source or Object form.
+
+ 3. Grant of Patent License. Subject to the terms and conditions of
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+ worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+ (except as stated in this section) patent license to make, have made,
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+ 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
+
+ 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.
diff --git a/alignment/AlignmentFilters.cpp b/alignment/AlignmentFilters.cpp
index df5d177..2e02915 100644
--- a/alignment/AlignmentFilters.cpp
+++ b/alignment/AlignmentFilters.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/AlignmentFilters.hh"
diff --git a/alignment/AlignmentFilters.hh b/alignment/AlignmentFilters.hh
index 26373af..4d94631 100644
--- a/alignment/AlignmentFilters.hh
+++ b/alignment/AlignmentFilters.hh
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#pragma once
diff --git a/alignment/AlignmentTweakers.cpp b/alignment/AlignmentTweakers.cpp
index 136318d..fd839da 100644
--- a/alignment/AlignmentTweakers.cpp
+++ b/alignment/AlignmentTweakers.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/AlignmentTweakers.hh"
diff --git a/alignment/AlignmentTweakers.hh b/alignment/AlignmentTweakers.hh
index d703daf..8797935 100644
--- a/alignment/AlignmentTweakers.hh
+++ b/alignment/AlignmentTweakers.hh
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#pragma once
diff --git a/alignment/GraphAlignmentOperations.cpp b/alignment/GraphAlignmentOperations.cpp
index 26f06d1..86e79c1 100644
--- a/alignment/GraphAlignmentOperations.cpp
+++ b/alignment/GraphAlignmentOperations.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/GraphAlignmentOperations.hh"
diff --git a/alignment/GraphAlignmentOperations.hh b/alignment/GraphAlignmentOperations.hh
index 1a98e31..333a6a0 100644
--- a/alignment/GraphAlignmentOperations.hh
+++ b/alignment/GraphAlignmentOperations.hh
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#pragma once
diff --git a/alignment/GreedyAlignmentIntersector.cpp b/alignment/GreedyAlignmentIntersector.cpp
index 4f399d6..aebffa1 100644
--- a/alignment/GreedyAlignmentIntersector.cpp
+++ b/alignment/GreedyAlignmentIntersector.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/GreedyAlignmentIntersector.hh"
diff --git a/alignment/GreedyAlignmentIntersector.hh b/alignment/GreedyAlignmentIntersector.hh
index 5450040..bddf025 100644
--- a/alignment/GreedyAlignmentIntersector.hh
+++ b/alignment/GreedyAlignmentIntersector.hh
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#pragma once
diff --git a/alignment/HighQualityBaseRunFinder.cpp b/alignment/HighQualityBaseRunFinder.cpp
index 4d1afac..ae8245c 100644
--- a/alignment/HighQualityBaseRunFinder.cpp
+++ b/alignment/HighQualityBaseRunFinder.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/HighQualityBaseRunFinder.hh"
diff --git a/alignment/HighQualityBaseRunFinder.hh b/alignment/HighQualityBaseRunFinder.hh
index 721441c..7fc5849 100644
--- a/alignment/HighQualityBaseRunFinder.hh
+++ b/alignment/HighQualityBaseRunFinder.hh
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#pragma once
diff --git a/alignment/SoftclippingAligner.cpp b/alignment/SoftclippingAligner.cpp
index 7436f6b..b419ed5 100644
--- a/alignment/SoftclippingAligner.cpp
+++ b/alignment/SoftclippingAligner.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/SoftclippingAligner.hh"
diff --git a/alignment/SoftclippingAligner.hh b/alignment/SoftclippingAligner.hh
index a2d4179..af77ce2 100644
--- a/alignment/SoftclippingAligner.hh
+++ b/alignment/SoftclippingAligner.hh
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#pragma once
diff --git a/alignment/tests/AlignmentTweakersTest.cpp b/alignment/tests/AlignmentTweakersTest.cpp
index 29ac73d..a5df47f 100644
--- a/alignment/tests/AlignmentTweakersTest.cpp
+++ b/alignment/tests/AlignmentTweakersTest.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/AlignmentTweakers.hh"
diff --git a/alignment/tests/GraphAlignmentOperationsTest.cpp b/alignment/tests/GraphAlignmentOperationsTest.cpp
index be4cb98..767af56 100644
--- a/alignment/tests/GraphAlignmentOperationsTest.cpp
+++ b/alignment/tests/GraphAlignmentOperationsTest.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/GraphAlignmentOperations.hh"
diff --git a/alignment/tests/GreedyAlignmentIntersectorTest.cpp b/alignment/tests/GreedyAlignmentIntersectorTest.cpp
index 0ed0187..7fc624f 100644
--- a/alignment/tests/GreedyAlignmentIntersectorTest.cpp
+++ b/alignment/tests/GreedyAlignmentIntersectorTest.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/GreedyAlignmentIntersector.hh"
diff --git a/alignment/tests/HighQualityBaseRunFinderTest.cpp b/alignment/tests/HighQualityBaseRunFinderTest.cpp
index 73605e7..28275eb 100644
--- a/alignment/tests/HighQualityBaseRunFinderTest.cpp
+++ b/alignment/tests/HighQualityBaseRunFinderTest.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/HighQualityBaseRunFinder.hh"
diff --git a/alignment/tests/SoftclippingAlignerTest.cpp b/alignment/tests/SoftclippingAlignerTest.cpp
index 5c03818..145eef5 100644
--- a/alignment/tests/SoftclippingAlignerTest.cpp
+++ b/alignment/tests/SoftclippingAlignerTest.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2018 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include "alignment/SoftclippingAligner.hh"
@@ -89,4 +90,4 @@ TEST_P(AligningReads, RealReadEndingInManyLowQualityBases_Aligned)
INSTANTIATE_TEST_CASE_P(
AlignerTestsInst, AligningReads, ::testing::Values(std::string("path-aligner"), std::string("dag-aligner")), );
-*/
\ No newline at end of file
+*/
diff --git a/classification/AlignmentClassifier.cpp b/classification/AlignmentClassifier.cpp
index 13301fd..70a91dd 100644
--- a/classification/AlignmentClassifier.cpp
+++ b/classification/AlignmentClassifier.cpp
@@ -1,21 +1,22 @@
//
// Expansion Hunter
-// Copyright (c) 2016 Illumina, Inc.
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
//
// Author: Egor Dolzhenko
//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// at your option) any later version.
+// 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
//
-// This program is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-// GNU General Public License for more details.
+// 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.
//
-// You should have received a copy of the GNU General Public License
-// along with this program. If not, see .
//
#include