Commit d97fda1a authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 1.0.0~rc0

parent 47d88078
......@@ -81,25 +81,17 @@ BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
TABIX = tabixpp/tabix.o
FASTAHACK = fastahack/Fasta.o
SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
REPEATS = smithwaterman/Repeats.o
INDELALLELE = smithwaterman/IndelAllele.o
DISORDER = smithwaterman/disorder.o
LEFTALIGN = smithwaterman/LeftAlign.o
FSOM = fsom/fsom.o
FILEVERCMP = filevercmp/filevercmp.o
INCLUDES = -I. -L. -Ltabixpp/
LDFLAGS = -lvcflib -ltabix -lz -lm
INCLUDES = -I. -Itabixpp/htslib/ -L. -Ltabixpp/ -Ltabixpp/htslib/
LDFLAGS = -lvcflib -ltabix -lhts -lpthread -lz -lm
all: $(OBJECTS) $(BINS)
......@@ -156,7 +148,7 @@ $(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(D
$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX)
ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX) tabixpp/bgzf.o tabixpp/index.o tabixpp/knetfile.o tabixpp/kstring.o
ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
test: $(BINS)
......
#!/usr/bin/perl
#!/usr/bin/env perl
while (<STDIN>) {
$_ =~ /^(.+?)\s(.+?)\s(.+)\s*/;
......
#!/usr/bin/Rscript
#!/usr/bin/env Rscript
......
#!/usr/bin/python
#!/usr/bin/env python
import sys
......
#!/usr/bin/python
#!/usr/bin/env python
import sys
import re
......
#!/usr/bin/perl
#!/usr/bin/env perl
my $seen_non_header = 0;
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/python
#!/usr/bin/env python
#
import sys
......
#!/usr/bin/python
#!/usr/bin/env python
#
import sys
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/python
#!/usr/bin/env python
import sys
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/python
#!/usr/bin/env python
import sys
import math
......
#!/usr/bin/Rscript
#!/usr/bin/env Rscript
# helper functions
......
#!/usr/bin/Rscript --vanilla --slave
#!/usr/bin/env Rscript --vanilla --slave
# get the input VCF tabular format, assert that sites must have AC > 0
vcf <- subset(read.table(pipe('cat /dev/stdin'), header=T), AC > 0)
......
#!/usr/bin/Rscript --vanilla --slave
#!/usr/bin/env Rscript --vanilla --slave
# get the input VCF tabular format, assert that sites must have AC > 0
vcf <- subset(read.table(pipe('cat /dev/stdin'), header=T), AC > 0)
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
#
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
while (<STDIN>) {
......
#!/usr/bin/perl
#!/usr/bin/env perl
#
use IPC::Open2;
......
#include "Variant.h"
#include <utility>
namespace vcf {
namespace vcflib {
void Variant::parse(string& line, bool parseSamples) {
......
......@@ -27,7 +27,7 @@ extern "C" {
using namespace std;
namespace vcf {
namespace vcflib {
class Variant;
......
......@@ -8,7 +8,7 @@
#include <set>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
......
......@@ -9,7 +9,7 @@
#include <fstream>
using namespace std;
using namespace vcf;
using namespace vcflib;
#define ALLELE_NULL -1
......
......@@ -2,7 +2,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [-n null_string] [-g]" << " [vcf file]" << endl
......
......@@ -5,7 +5,7 @@
#include <set>
using namespace std;
using namespace vcf;
using namespace vcflib;
// adds non-overlapping info fields from varB to varA
void addInfo(Variant& varA, Variant& varB) {
......
......@@ -4,7 +4,7 @@
#include <map>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -6,7 +6,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
#define ALLELE_NULL -1
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -3,7 +3,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
......
......@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
void annotateWithBlankGenotypes(Variant& var, string& annotationTag) {
......
......@@ -4,7 +4,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
double convertStrDbl(const string& s) {
......
#include "Variant.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -4,7 +4,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
......@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
bool isTransition(string& ref, string& alt) {
if (((ref == "A" && alt == "G") || (ref == "G" && alt == "A")) ||
......
......@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -4,7 +4,7 @@
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [vcf file] [vcf file] ..." << endl
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
template<class T>
vector<T> intersection(vector<T>& a, vector<T>& b) {
......
#include "Variant.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -5,7 +5,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
double convertStrDbl(const string& s) {
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
#include "Variant.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -4,7 +4,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
......@@ -5,7 +5,7 @@
#include <cmath>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
......@@ -3,7 +3,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
......@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int countAlts(Variant& var, int alleleIndex) {
int alts = 0;
......
......@@ -2,7 +2,7 @@
#include "convert.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
double convertStrDbl(const string& s) {
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -6,7 +6,7 @@
#include <set>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
......
#include "Variant.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -6,7 +6,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -5,7 +5,7 @@
#include <sstream>
using namespace std;
using namespace vcf;
using namespace vcflib;
// TODO fix this for multi-allelic!!!!
string genotypeSpec(map<int, int>& genotype) {
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -3,7 +3,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
......@@ -3,7 +3,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -3,7 +3,7 @@
#include <vector>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
#include "Variant.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -6,7 +6,7 @@
#include <numeric>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
......@@ -8,7 +8,7 @@
#include <set>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
......
......@@ -5,7 +5,7 @@
#include <set>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -5,7 +5,7 @@
#include <set>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -9,7 +9,7 @@
#include <cmath>
using namespace std;
using namespace vcf;
using namespace vcflib;
// Attempts to left-realign all the indels represented by the alignment cigar.
......
......@@ -3,7 +3,7 @@
#include <vector>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -2,7 +2,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
......
#include "Variant.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -4,7 +4,7 @@
#include <getopt.h>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
cerr << "usage: " << argv[0] << " [options] <vcf file>" << endl
......
#include "Variant.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -5,7 +5,7 @@
#include <cmath>
using namespace std;
using namespace vcf;
using namespace vcflib;
int main(int argc, char** argv) {
......
......@@ -7,7 +7,7 @@
#include "convert.h"
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
......
......@@ -8,7 +8,7 @@
#include <set>
using namespace std;
using namespace vcf;
using namespace vcflib;
void printSummary(char** argv) {
......
......@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;
void stripAberrant(Variant& var) {
map<string, map<string, vector<string> > >::iterator s = var.samples.begin();
......
......@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
using namespace vcf;
using namespace vcflib;