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Merge pull request #36 from ComparativeGenomicsToolkit/chop
Add dupe remover and name munger
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| /* | ||
| * Copyright (C) 2016 by Glenn Hickey ([email protected]) | ||
| * | ||
| * Released under the MIT license, see LICENSE.txt | ||
| */ | ||
|
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| // This file was created by merging hal2sg.cpp and sg2vg.cpp with | ||
| // a small amount of glue for the interface. | ||
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| //#define debug | ||
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| #include <cstdlib> | ||
| #include <iostream> | ||
| #include <cassert> | ||
| #include <fstream> | ||
| #include <deque> | ||
| #include <unordered_map> | ||
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| #include "hal.h" | ||
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| using namespace std; | ||
| using namespace hal; | ||
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| static void initParser(CLParser* optionsParser) { | ||
| optionsParser->addArgument("halFile", "input hal file"); | ||
| optionsParser->addArgument("genome", "remove all paralogy edges from this genome"); | ||
| optionsParser->setDescription("Remove paralogy edges from given genome (in place)"); | ||
| } | ||
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| int main(int argc, char** argv) { | ||
| CLParser optionsParser(WRITE_ACCESS); | ||
| initParser(&optionsParser); | ||
| string halPath; | ||
| string genomeName; | ||
| try { | ||
| optionsParser.parseOptions(argc, argv); | ||
| halPath = optionsParser.getArgument<string>("halFile"); | ||
| genomeName = optionsParser.getArgument<string>("genome"); | ||
| } | ||
| catch(exception& e) { | ||
| cerr << e.what() << endl; | ||
| optionsParser.printUsage(cerr); | ||
| exit(1); | ||
| } | ||
| try { | ||
| AlignmentPtr alignment(openHalAlignment(halPath, &optionsParser, READ_ACCESS | WRITE_ACCESS)); | ||
| if (alignment->getNumGenomes() == 0) { | ||
| throw hal_exception("input hal alignmenet is empty"); | ||
| } | ||
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| Genome* genome = alignment->openGenome(genomeName); | ||
| if (genome == NULL) { | ||
| throw hal_exception("Genome " + genomeName + " not found in alignment"); | ||
| } | ||
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| if (genomeName == alignment->getRootName()) { | ||
| throw hal_exception("Cannot run on root"); | ||
| } | ||
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| TopSegmentIteratorPtr topIt = genome->getTopSegmentIterator(); | ||
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| size_t total_length = 0; | ||
| size_t total_edges = 0; | ||
| for (; not topIt->atEnd(); topIt->toRight()) { | ||
| TopSegment* topSeg = topIt->tseg(); | ||
| if (topSeg->hasNextParalogy()) { | ||
| topSeg->setNextParalogyIndex(NULL_INDEX); | ||
| total_length += topSeg->getLength(); | ||
| ++total_edges; | ||
| } | ||
| } | ||
|
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| if (total_length > 0) { | ||
| cerr << "[halRemoveDupes]: " << total_edges << " paralogy edges removed from " << genomeName | ||
| << " with total length " << total_length << endl; | ||
| } else { | ||
| cerr << "[halRemoveDupes] : No paralogy edges found in " << genomeName << endl; | ||
| } | ||
| } | ||
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| catch(exception& e) { | ||
| cerr << e.what() << endl; | ||
| exit(1); | ||
| } | ||
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| return 0; | ||
| } |