-
Notifications
You must be signed in to change notification settings - Fork 51
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #45 from Illumina/develop
ExpansionHunter-v3.0.0-rc3
- Loading branch information
Showing
269 changed files
with
5,940 additions
and
5,849 deletions.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #include "alignment/AlignmentFilters.hh" | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #pragma once | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #include "alignment/AlignmentTweakers.hh" | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #pragma once | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #include "alignment/GraphAlignmentOperations.hh" | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #pragma once | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #include "alignment/GreedyAlignmentIntersector.hh" | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #pragma once | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #include "alignment/HighQualityBaseRunFinder.hh" | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #pragma once | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,22 @@ | ||
| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // Copyright 2016-2019 Illumina, Inc. | ||
| // All rights reserved. | ||
| // | ||
| // Author: Egor Dolzhenko <[email protected]> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
|
||
| #include "alignment/SoftclippingAligner.hh" | ||
|
|
||
Oops, something went wrong.