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#ifndef ALIGN_STATUS_H |
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#define ALIGN_STATUS_H |
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|
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#ifdef HAVE_CONFIG_H |
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#include <config.h> |
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#endif |
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|
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#include <stdint.h> |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string> |
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#include <map> |
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#include <vector> |
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#include <cassert> |
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#include <cstring> |
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#include <seqan/sequence.h> |
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#include <bam/sam.h> |
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#include "common.h" |
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|
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#include "bwt_map.h" |
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#include "junctions.h" |
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#include "insertions.h" |
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#include "deletions.h" |
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#include "fusions.h" |
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|
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using namespace std; |
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|
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class Coverage; |
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|
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/** |
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*/ |
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struct AlignStatus |
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{ |
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public: |
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/** |
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* Is there an alignment? |
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*/ |
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int _alignment_score; |
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|
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public: |
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AlignStatus(); |
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AlignStatus(const BowtieHit& bh, |
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const JunctionSet& gtf_junctions, |
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const JunctionSet& junctions, |
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const InsertionSet& insertions, |
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const DeletionSet& deletions, |
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const FusionSet& fusions, |
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const Coverage& coverage); |
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|
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bool operator<(const AlignStatus& rhs) const; |
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bool operator==(const AlignStatus& rhs) const; |
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bool operator!=(const AlignStatus& rhs) const; |
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}; |
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|
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#endif |
