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| Original file line number | Diff line number | Diff line change |
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| @@ -1,34 +1,38 @@ | ||
| Expansion Hunter: a tool for estimating repeat sizes | ||
| ---------------------------------------------------- | ||
| # Expansion Hunter: a tool for estimating repeat sizes | ||
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| There are a number of regions in the human genome consisting of repetitions of short unit sequence (commonly a trimer). | ||
| Such repeat regions can expand to a size much larger than the read length and thereby cause a disease. | ||
| There are a number of regions in the human genome consisting of repetitions of | ||
| short unit sequence (commonly a trimer). Such repeat regions can expand to a | ||
| size much larger than the read length and thereby cause a disease. | ||
| [Fragile X Syndrome](https://en.wikipedia.org/wiki/Fragile_X_syndrome), | ||
| [ALS](https://en.wikipedia.org/wiki/Amyotrophic_lateral_sclerosis), and | ||
| [Huntington's Disease](https://en.wikipedia.org/wiki/Huntington%27s_disease) are well known examples. | ||
| [Huntington's Disease](https://en.wikipedia.org/wiki/Huntington%27s_disease) | ||
| are well known examples. | ||
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| Expansion Hunter aims to estimate sizes of such repeats by performing a targeted search through a BAM/CRAM file for | ||
| reads that span, flank, and are fully contained in each repeat. | ||
| Expansion Hunter aims to estimate sizes of such repeats by performing a targeted | ||
| search through a BAM/CRAM file for reads that span, flank, and are fully | ||
| contained in each repeat. | ||
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| Linux and macOS operating systems are currently supported. | ||
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| License | ||
| ------- | ||
|
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| Expansion Hunter is provided under the terms and conditions of the [GPLv3 license](LICENSE.txt). It relies on several | ||
| third party packages provided under other open source licenses, please see [COPYRIGHT.txt](COPYRIGHT.txt) for additional | ||
| details. | ||
| ## License | ||
|
|
||
| Documentation | ||
| ------------- | ||
| Expansion Hunter is provided under the terms and conditions of the | ||
| [GPLv3 license](LICENSE.txt). It relies on several third party packages provided | ||
| under other open source licenses, please see [COPYRIGHT.txt](COPYRIGHT.txt) for | ||
| additional details. | ||
|
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| Installation instructions, usage guide, and description of file formats are contained in the [docs folder](docs/01_Introduction.md). | ||
|
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| ## Documentation | ||
|
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| Method | ||
| ------ | ||
| Installation instructions, usage guide, and description of file formats are | ||
| contained in the [docs folder](docs/01_Introduction.md). | ||
|
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|
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| ## Method | ||
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| The detailed description of the method can be found here: | ||
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| Dolzhenko et al., [Detection of long repeat expansions from PCR-free whole-genome sequence | ||
| data](http://genome.cshlp.org/content/27/11/1895), Genome Research 2017 | ||
| Dolzhenko and others, [Detection of long repeat expansions from PCR-free | ||
| whole-genome sequence data](http://genome.cshlp.org/content/27/11/1895), Genome | ||
| Research 2017 |
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| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // | ||
| // Author: Egor Dolzhenko <edolzhenko@illumina.com> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
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| #include "alignment/AlignmentFilters.hh" | ||
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| #include <list> | ||
| #include <vector> | ||
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| #include "graphalign/GaplessAligner.hh" | ||
| #include "graphalign/GraphAlignmentOperations.hh" | ||
| #include "graphalign/LinearAlignmentOperations.hh" | ||
| #include "graphcore/PathOperations.hh" | ||
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| #include "alignment/GraphAlignmentOperations.hh" | ||
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| using graphtools::GraphAlignment; | ||
| using graphtools::NodeId; | ||
| using graphtools::Path; | ||
| using std::list; | ||
| using std::string; | ||
| using std::vector; | ||
|
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| namespace ehunter | ||
| { | ||
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| bool checkIfLocallyPlacedReadPair( | ||
| boost::optional<GraphAlignment> readAlignment, boost::optional<GraphAlignment> mateAlignment, | ||
| int kMinNonRepeatAlignmentScore) | ||
| { | ||
| int nonRepeatAlignmentScore = 0; | ||
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| if (readAlignment) | ||
| { | ||
| nonRepeatAlignmentScore += scoreAlignmentToNonloopNodes(*readAlignment); | ||
| } | ||
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| if (mateAlignment) | ||
| { | ||
| nonRepeatAlignmentScore += scoreAlignmentToNonloopNodes(*mateAlignment); | ||
| } | ||
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| if (nonRepeatAlignmentScore < kMinNonRepeatAlignmentScore) | ||
| { | ||
| return false; | ||
| } | ||
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| return true; | ||
| } | ||
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| bool checkIfUpstreamAlignmentIsGood(NodeId nodeId, GraphAlignment alignment) | ||
| { | ||
| const list<int> repeatNodeIndexes = alignment.getIndexesOfNode(nodeId); | ||
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| if (repeatNodeIndexes.empty()) | ||
| { | ||
| return false; | ||
| } | ||
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| const int firstRepeatNodeIndex = repeatNodeIndexes.front(); | ||
| int score = 0; | ||
| LinearAlignmentParameters parameters; | ||
| for (int nodeIndex = 0; nodeIndex != firstRepeatNodeIndex; ++nodeIndex) | ||
| { | ||
| score += scoreAlignment( | ||
| alignment[nodeIndex], parameters.matchScore, parameters.mismatchScore, parameters.gapOpenScore); | ||
| } | ||
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| const int kScoreCutoff = parameters.matchScore * 8; | ||
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| return score >= kScoreCutoff; | ||
| } | ||
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| bool checkIfDownstreamAlignmentIsGood(NodeId nodeId, GraphAlignment alignment) | ||
| { | ||
| const list<int> repeatNodeIndexes = alignment.getIndexesOfNode(nodeId); | ||
|
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| if (repeatNodeIndexes.empty()) | ||
| { | ||
| return false; | ||
| } | ||
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| const int lastRepeatNodeIndex = repeatNodeIndexes.back(); | ||
| int score = 0; | ||
| LinearAlignmentParameters parameters; | ||
| for (int nodeIndex = lastRepeatNodeIndex + 1; nodeIndex != static_cast<int>(alignment.size()); ++nodeIndex) | ||
| { | ||
| score += scoreAlignment( | ||
| alignment[nodeIndex], parameters.matchScore, parameters.mismatchScore, parameters.gapOpenScore); | ||
| } | ||
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| const int kScoreCutoff = parameters.matchScore * 8; | ||
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| return score >= kScoreCutoff; | ||
| } | ||
|
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| } |
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| // | ||
| // Expansion Hunter | ||
| // Copyright (c) 2018 Illumina, Inc. | ||
| // | ||
| // Author: Egor Dolzhenko <edolzhenko@illumina.com> | ||
| // | ||
| // 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 <http://www.gnu.org/licenses/>. | ||
| // | ||
|
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| #pragma once | ||
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| #include <string> | ||
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| #include <boost/optional.hpp> | ||
|
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| #include "graphalign/GraphAlignment.hh" | ||
|
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| namespace ehunter | ||
| { | ||
|
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| /** | ||
| * Checks if a read pair is likely to have originated in the alignment region | ||
| * | ||
| * The check is performed by verifying that the alignment score to non-repeat nodes (combined for both mates) is | ||
| * sufficiently high. | ||
| * | ||
| * @param readAlignment: Alignment of a read | ||
| * @param mateAlignment: Alignment of read's mate | ||
| * @param kMinNonRepeatAlignmentScore: Score threshold | ||
| * @return true if the alignment score to non-repeat nodes exceeds the threshold | ||
| */ | ||
| bool checkIfLocallyPlacedReadPair( | ||
| boost::optional<graphtools::GraphAlignment> readAlignment, | ||
| boost::optional<graphtools::GraphAlignment> mateAlignment, int kMinNonRepeatAlignmentScore); | ||
|
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| // Checks if alignment upstream of a given node is high quality | ||
| bool checkIfUpstreamAlignmentIsGood(graphtools::NodeId nodeId, graphtools::GraphAlignment alignment); | ||
|
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| // Checks if alignment downstream of a given node is high quality | ||
| bool checkIfDownstreamAlignmentIsGood(graphtools::NodeId nodeId, graphtools::GraphAlignment alignment); | ||
|
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| } |
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