Commit e3768d23 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.01-wu1-3+dfsg

parent 6328b642

.gitignore

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*.o

.gitmodules

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[submodule "samtools"]

	path = samtools

	url = https://github.com/samtools/samtools.git

DInDel.cpp

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@@ -24,7 +24,7 @@ 
#include <boost/math/special_functions/digamma.hpp>

#include <seqan/align.h>

#include <seqan/graph_align.h>

#include "foreach.hpp"

#include <boost/foreach.hpp>

#include "bam.h"

#include "DInDel.hpp"

#include "Haplotype.hpp"

Faster.cpp

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@@ -35,7 +35,7 @@ 
#include "Haplotype.hpp"

#include "Faster.hpp"

#include "Utils.hpp"

#include "foreach.hpp"

#include <boost/foreach.hpp>

using namespace std;

const int DEBUGS=0;

GetCandidates.cpp

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@@ -22,7 +22,7 @@ 
#include <fstream>

#include <string>

#include "MyBam.hpp"

#include "foreach.hpp"

#include <boost/foreach.hpp>

#include "ObservationModelSeqAn.hpp"

#include "GetCandidates.hpp"

#include "Variant.hpp"
@@ -32,7 +32,6 @@ 
#include "Fasta.hpp"

#include "StringHash.hpp"

#include <set>

#include "foreach.hpp"

using namespace std;



int GetCandidatesFromCIGAR::getIndelFromCIGARFetchFunc(const bam1_t *b, void *data)