[med-svn] [libvcflib] 02/03: Imported Upstream version 1.0.0~rc0
Andreas Tille
tille at debian.org
Sun Dec 6 06:31:40 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libvcflib.
commit d97fda1acfba5bdeda69dd969b180fbb2d60ea72
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 6 07:31:17 2015 +0100
Imported Upstream version 1.0.0~rc0
---
Makefile | 14 +++-----------
bin/bed2region | 2 +-
bin/plot_roc.r | 2 +-
bin/vcf2bed.py | 2 +-
bin/vcf2sqlite.py | 2 +-
bin/vcf_strip_extra_headers | 2 +-
bin/vcfbiallelic | 2 +-
bin/vcfclearid | 2 +-
bin/vcfclearinfo | 2 +-
bin/vcfcomplex | 2 +-
bin/vcffirstheader | 2 +-
bin/vcfindelproximity | 2 +-
bin/vcfindels | 2 +-
bin/vcfmultiallelic | 2 +-
bin/vcfnobiallelicsnps | 2 +-
bin/vcfnoindels | 2 +-
bin/vcfnosnps | 2 +-
bin/vcfnulldotslashdot | 2 +-
bin/vcfplotaltdiscrepancy.r | 2 +-
bin/vcfplotsitediscrepancy.r | 2 +-
bin/vcfprintaltdiscrepancy.r | 2 +-
bin/vcfqualfilter | 2 +-
bin/vcfremovenonATGC | 2 +-
bin/vcfsnps | 2 +-
bin/vcfvarstats | 2 +-
src/Variant.cpp | 2 +-
src/Variant.h | 2 +-
src/vcf2dag.cpp | 2 +-
src/vcf2fasta.cpp | 2 +-
src/vcf2tsv.cpp | 2 +-
src/vcfaddinfo.cpp | 2 +-
src/vcfafpath.cpp | 2 +-
src/vcfallelicprimitives.cpp | 2 +-
src/vcfaltcount.cpp | 2 +-
src/vcfannotate.cpp | 2 +-
src/vcfannotategenotypes.cpp | 2 +-
src/vcfbreakmulti.cpp | 2 +-
src/vcfcat.cpp | 2 +-
src/vcfcheck.cpp | 2 +-
src/vcfclassify.cpp | 2 +-
src/vcfcleancomplex.cpp | 2 +-
src/vcfcombine.cpp | 2 +-
src/vcfcommonsamples.cpp | 2 +-
src/vcfcountalleles.cpp | 2 +-
src/vcfcreatemulti.cpp | 2 +-
src/vcfdistance.cpp | 2 +-
src/vcfecho.cpp | 2 +-
src/vcfentropy.cpp | 2 +-
src/vcfevenregions.cpp | 2 +-
src/vcffilter.cpp | 2 +-
src/vcffixup.cpp | 2 +-
src/vcfflatten.cpp | 2 +-
src/vcfgeno2alleles.cpp | 2 +-
src/vcfgeno2haplo.cpp | 2 +-
src/vcfgenosamplenames.cpp | 2 +-
src/vcfgenosummarize.cpp | 2 +-
src/vcfgenotypecompare.cpp | 2 +-
src/vcfgenotypes.cpp | 2 +-
src/vcfglbound.cpp | 2 +-
src/vcfglxgt.cpp | 2 +-
src/vcfhetcount.cpp | 2 +-
src/vcfhethomratio.cpp | 2 +-
src/vcfindex.cpp | 2 +-
src/vcfinfo2qual.cpp | 2 +-
src/vcfinfosummarize.cpp | 2 +-
src/vcfintersect.cpp | 2 +-
src/vcfkeepgeno.cpp | 2 +-
src/vcfkeepinfo.cpp | 2 +-
src/vcfkeepsamples.cpp | 2 +-
src/vcfleftalign.cpp | 2 +-
src/vcflength.cpp | 2 +-
src/vcfnumalt.cpp | 2 +-
src/vcfoverlay.cpp | 2 +-
src/vcfparsealts.cpp | 2 +-
src/vcfprimers.cpp | 2 +-
src/vcfqual2info.cpp | 2 +-
src/vcfrandom.cpp | 2 +-
src/vcfrandomsample.cpp | 2 +-
src/vcfremap.cpp | 2 +-
src/vcfremoveaberrantgenotypes.cpp | 2 +-
src/vcfremovesamples.cpp | 2 +-
src/vcfroc.cpp | 2 +-
src/vcfsample2info.cpp | 2 +-
src/vcfsamplediff.cpp | 2 +-
src/vcfsamplenames.cpp | 2 +-
src/vcfsamplestats.cpp | 2 +-
src/vcfsitesummarize.cpp | 2 +-
src/vcfsom.cpp | 2 +-
src/vcfstats.cpp | 2 +-
src/vcfstreamsort.cpp | 2 +-
src/vcfuniq.cpp | 2 +-
src/vcfuniqalleles.cpp | 2 +-
92 files changed, 94 insertions(+), 102 deletions(-)
diff --git a/Makefile b/Makefile
index 5a45987..d818f2b 100644
--- a/Makefile
+++ b/Makefile
@@ -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)
diff --git a/bin/bed2region b/bin/bed2region
index ffa40ef..9f0a003 100755
--- a/bin/bed2region
+++ b/bin/bed2region
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
while (<STDIN>) {
$_ =~ /^(.+?)\s(.+?)\s(.+)\s*/;
diff --git a/bin/plot_roc.r b/bin/plot_roc.r
index 5a99615..ca1f86d 100755
--- a/bin/plot_roc.r
+++ b/bin/plot_roc.r
@@ -1,4 +1,4 @@
-#!/usr/bin/Rscript
+#!/usr/bin/env Rscript
diff --git a/bin/vcf2bed.py b/bin/vcf2bed.py
index c04cb60..95a2e88 100755
--- a/bin/vcf2bed.py
+++ b/bin/vcf2bed.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
import sys
diff --git a/bin/vcf2sqlite.py b/bin/vcf2sqlite.py
index f0170b0..cdbc720 100755
--- a/bin/vcf2sqlite.py
+++ b/bin/vcf2sqlite.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
import sys
import re
diff --git a/bin/vcf_strip_extra_headers b/bin/vcf_strip_extra_headers
index c8b05e6..179ff64 100755
--- a/bin/vcf_strip_extra_headers
+++ b/bin/vcf_strip_extra_headers
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
my $seen_non_header = 0;
diff --git a/bin/vcfbiallelic b/bin/vcfbiallelic
index 7761fec..7945e39 100755
--- a/bin/vcfbiallelic
+++ b/bin/vcfbiallelic
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfclearid b/bin/vcfclearid
index f428682..10641b6 100755
--- a/bin/vcfclearid
+++ b/bin/vcfclearid
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
#
import sys
diff --git a/bin/vcfclearinfo b/bin/vcfclearinfo
index a0512fd..210d19e 100755
--- a/bin/vcfclearinfo
+++ b/bin/vcfclearinfo
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
#
import sys
diff --git a/bin/vcfcomplex b/bin/vcfcomplex
index 9c2b188..00ae090 100755
--- a/bin/vcfcomplex
+++ b/bin/vcfcomplex
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcffirstheader b/bin/vcffirstheader
index 2e77c2e..d37bb87 100755
--- a/bin/vcffirstheader
+++ b/bin/vcffirstheader
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
import sys
diff --git a/bin/vcfindelproximity b/bin/vcfindelproximity
index 982ba81..5098857 100755
--- a/bin/vcfindelproximity
+++ b/bin/vcfindelproximity
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
diff --git a/bin/vcfindels b/bin/vcfindels
index 1b92a45..f78db36 100755
--- a/bin/vcfindels
+++ b/bin/vcfindels
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfmultiallelic b/bin/vcfmultiallelic
index 47f3dce..d9539b8 100755
--- a/bin/vcfmultiallelic
+++ b/bin/vcfmultiallelic
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfnobiallelicsnps b/bin/vcfnobiallelicsnps
index 2433eee..d4f61ed 100755
--- a/bin/vcfnobiallelicsnps
+++ b/bin/vcfnobiallelicsnps
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfnoindels b/bin/vcfnoindels
index c2051ac..90b10ee 100755
--- a/bin/vcfnoindels
+++ b/bin/vcfnoindels
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfnosnps b/bin/vcfnosnps
index 19ee084..a5cd256 100755
--- a/bin/vcfnosnps
+++ b/bin/vcfnosnps
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfnulldotslashdot b/bin/vcfnulldotslashdot
index 9951a34..9e124b6 100755
--- a/bin/vcfnulldotslashdot
+++ b/bin/vcfnulldotslashdot
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
import sys
import math
diff --git a/bin/vcfplotaltdiscrepancy.r b/bin/vcfplotaltdiscrepancy.r
index 8717987..78bedf9 100755
--- a/bin/vcfplotaltdiscrepancy.r
+++ b/bin/vcfplotaltdiscrepancy.r
@@ -1,4 +1,4 @@
-#!/usr/bin/Rscript
+#!/usr/bin/env Rscript
# helper functions
diff --git a/bin/vcfplotsitediscrepancy.r b/bin/vcfplotsitediscrepancy.r
index d4f4ecb..323d9b0 100755
--- a/bin/vcfplotsitediscrepancy.r
+++ b/bin/vcfplotsitediscrepancy.r
@@ -1,4 +1,4 @@
-#!/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)
diff --git a/bin/vcfprintaltdiscrepancy.r b/bin/vcfprintaltdiscrepancy.r
index ef33502..e677ad9 100755
--- a/bin/vcfprintaltdiscrepancy.r
+++ b/bin/vcfprintaltdiscrepancy.r
@@ -1,4 +1,4 @@
-#!/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)
diff --git a/bin/vcfqualfilter b/bin/vcfqualfilter
index 8fe970f..6c73774 100755
--- a/bin/vcfqualfilter
+++ b/bin/vcfqualfilter
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
#
diff --git a/bin/vcfremovenonATGC b/bin/vcfremovenonATGC
index 7418843..95ba28b 100755
--- a/bin/vcfremovenonATGC
+++ b/bin/vcfremovenonATGC
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfsnps b/bin/vcfsnps
index b2b8b79..43f335e 100755
--- a/bin/vcfsnps
+++ b/bin/vcfsnps
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
while (<STDIN>) {
diff --git a/bin/vcfvarstats b/bin/vcfvarstats
index 1f645f7..e122b1a 100755
--- a/bin/vcfvarstats
+++ b/bin/vcfvarstats
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
#
use IPC::Open2;
diff --git a/src/Variant.cpp b/src/Variant.cpp
index d6f4a92..57cb53f 100644
--- a/src/Variant.cpp
+++ b/src/Variant.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
#include <utility>
-namespace vcf {
+namespace vcflib {
void Variant::parse(string& line, bool parseSamples) {
diff --git a/src/Variant.h b/src/Variant.h
index 307ca84..8422675 100644
--- a/src/Variant.h
+++ b/src/Variant.h
@@ -27,7 +27,7 @@ extern "C" {
using namespace std;
-namespace vcf {
+namespace vcflib {
class Variant;
diff --git a/src/vcf2dag.cpp b/src/vcf2dag.cpp
index 1257cd0..1c56791 100644
--- a/src/vcf2dag.cpp
+++ b/src/vcf2dag.cpp
@@ -8,7 +8,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcf2fasta.cpp b/src/vcf2fasta.cpp
index 88de80a..d1120d2 100644
--- a/src/vcf2fasta.cpp
+++ b/src/vcf2fasta.cpp
@@ -9,7 +9,7 @@
#include <fstream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
#define ALLELE_NULL -1
diff --git a/src/vcf2tsv.cpp b/src/vcf2tsv.cpp
index 9a1e2dd..cea2eae 100644
--- a/src/vcf2tsv.cpp
+++ b/src/vcf2tsv.cpp
@@ -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
diff --git a/src/vcfaddinfo.cpp b/src/vcfaddinfo.cpp
index cff66d6..5690f40 100644
--- a/src/vcfaddinfo.cpp
+++ b/src/vcfaddinfo.cpp
@@ -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) {
diff --git a/src/vcfafpath.cpp b/src/vcfafpath.cpp
index e87ab80..b8f5270 100644
--- a/src/vcfafpath.cpp
+++ b/src/vcfafpath.cpp
@@ -4,7 +4,7 @@
#include <map>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfallelicprimitives.cpp b/src/vcfallelicprimitives.cpp
index 95b6333..d68b023 100644
--- a/src/vcfallelicprimitives.cpp
+++ b/src/vcfallelicprimitives.cpp
@@ -6,7 +6,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
#define ALLELE_NULL -1
diff --git a/src/vcfaltcount.cpp b/src/vcfaltcount.cpp
index 756b5fc..4cf88c0 100644
--- a/src/vcfaltcount.cpp
+++ b/src/vcfaltcount.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfannotate.cpp b/src/vcfannotate.cpp
index 3499083..335fbfd 100644
--- a/src/vcfannotate.cpp
+++ b/src/vcfannotate.cpp
@@ -3,7 +3,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfannotategenotypes.cpp b/src/vcfannotategenotypes.cpp
index 1bb65d3..4107d41 100644
--- a/src/vcfannotategenotypes.cpp
+++ b/src/vcfannotategenotypes.cpp
@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void annotateWithBlankGenotypes(Variant& var, string& annotationTag) {
diff --git a/src/vcfbreakmulti.cpp b/src/vcfbreakmulti.cpp
index f462111..48c26a9 100644
--- a/src/vcfbreakmulti.cpp
+++ b/src/vcfbreakmulti.cpp
@@ -4,7 +4,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
double convertStrDbl(const string& s) {
diff --git a/src/vcfcat.cpp b/src/vcfcat.cpp
index cf40921..fce5e9f 100644
--- a/src/vcfcat.cpp
+++ b/src/vcfcat.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfcheck.cpp b/src/vcfcheck.cpp
index d370ae1..5ed13c9 100644
--- a/src/vcfcheck.cpp
+++ b/src/vcfcheck.cpp
@@ -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
diff --git a/src/vcfclassify.cpp b/src/vcfclassify.cpp
index 42624ee..f4ad595 100644
--- a/src/vcfclassify.cpp
+++ b/src/vcfclassify.cpp
@@ -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")) ||
diff --git a/src/vcfcleancomplex.cpp b/src/vcfcleancomplex.cpp
index c0b3c71..7e8fd0f 100644
--- a/src/vcfcleancomplex.cpp
+++ b/src/vcfcleancomplex.cpp
@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfcombine.cpp b/src/vcfcombine.cpp
index 09201c4..89a3e55 100644
--- a/src/vcfcombine.cpp
+++ b/src/vcfcombine.cpp
@@ -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
diff --git a/src/vcfcommonsamples.cpp b/src/vcfcommonsamples.cpp
index ee594cb..b8964d4 100644
--- a/src/vcfcommonsamples.cpp
+++ b/src/vcfcommonsamples.cpp
@@ -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) {
diff --git a/src/vcfcountalleles.cpp b/src/vcfcountalleles.cpp
index 9ce6aae..55b1dac 100644
--- a/src/vcfcountalleles.cpp
+++ b/src/vcfcountalleles.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfcreatemulti.cpp b/src/vcfcreatemulti.cpp
index d4ac13c..c3f8443 100644
--- a/src/vcfcreatemulti.cpp
+++ b/src/vcfcreatemulti.cpp
@@ -5,7 +5,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
double convertStrDbl(const string& s) {
diff --git a/src/vcfdistance.cpp b/src/vcfdistance.cpp
index 61e798e..9512f0e 100644
--- a/src/vcfdistance.cpp
+++ b/src/vcfdistance.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfecho.cpp b/src/vcfecho.cpp
index b850440..a5f7b18 100644
--- a/src/vcfecho.cpp
+++ b/src/vcfecho.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfentropy.cpp b/src/vcfentropy.cpp
index 4f92691..1b55f27 100644
--- a/src/vcfentropy.cpp
+++ b/src/vcfentropy.cpp
@@ -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
diff --git a/src/vcfevenregions.cpp b/src/vcfevenregions.cpp
index 5888c98..2d3b55a 100644
--- a/src/vcfevenregions.cpp
+++ b/src/vcfevenregions.cpp
@@ -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
diff --git a/src/vcffilter.cpp b/src/vcffilter.cpp
index 9150ff1..ca7fd35 100644
--- a/src/vcffilter.cpp
+++ b/src/vcffilter.cpp
@@ -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
diff --git a/src/vcffixup.cpp b/src/vcffixup.cpp
index be79d36..9af77b4 100644
--- a/src/vcffixup.cpp
+++ b/src/vcffixup.cpp
@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int countAlts(Variant& var, int alleleIndex) {
int alts = 0;
diff --git a/src/vcfflatten.cpp b/src/vcfflatten.cpp
index f528360..199a464 100644
--- a/src/vcfflatten.cpp
+++ b/src/vcfflatten.cpp
@@ -2,7 +2,7 @@
#include "convert.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
double convertStrDbl(const string& s) {
diff --git a/src/vcfgeno2alleles.cpp b/src/vcfgeno2alleles.cpp
index 9fd66f2..318b9ba 100644
--- a/src/vcfgeno2alleles.cpp
+++ b/src/vcfgeno2alleles.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfgeno2haplo.cpp b/src/vcfgeno2haplo.cpp
index f821c2d..505a4a7 100644
--- a/src/vcfgeno2haplo.cpp
+++ b/src/vcfgeno2haplo.cpp
@@ -6,7 +6,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfgenosamplenames.cpp b/src/vcfgenosamplenames.cpp
index 32e065a..7d7d2de 100644
--- a/src/vcfgenosamplenames.cpp
+++ b/src/vcfgenosamplenames.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfgenosummarize.cpp b/src/vcfgenosummarize.cpp
index 526bca1..1efb42a 100644
--- a/src/vcfgenosummarize.cpp
+++ b/src/vcfgenosummarize.cpp
@@ -6,7 +6,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfgenotypecompare.cpp b/src/vcfgenotypecompare.cpp
index c81043f..10da0fe 100644
--- a/src/vcfgenotypecompare.cpp
+++ b/src/vcfgenotypecompare.cpp
@@ -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) {
diff --git a/src/vcfgenotypes.cpp b/src/vcfgenotypes.cpp
index 4fe7965..7884e7c 100644
--- a/src/vcfgenotypes.cpp
+++ b/src/vcfgenotypes.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfglbound.cpp b/src/vcfglbound.cpp
index 0b42f22..5d57862 100644
--- a/src/vcfglbound.cpp
+++ b/src/vcfglbound.cpp
@@ -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
diff --git a/src/vcfglxgt.cpp b/src/vcfglxgt.cpp
index 5909bdc..59ca79f 100644
--- a/src/vcfglxgt.cpp
+++ b/src/vcfglxgt.cpp
@@ -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
diff --git a/src/vcfhetcount.cpp b/src/vcfhetcount.cpp
index 3dd4561..679fcb0 100644
--- a/src/vcfhetcount.cpp
+++ b/src/vcfhetcount.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfhethomratio.cpp b/src/vcfhethomratio.cpp
index 10e39f8..9d309ef 100644
--- a/src/vcfhethomratio.cpp
+++ b/src/vcfhethomratio.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfindex.cpp b/src/vcfindex.cpp
index 24a9401..0f5aaa1 100644
--- a/src/vcfindex.cpp
+++ b/src/vcfindex.cpp
@@ -3,7 +3,7 @@
#include <vector>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfinfo2qual.cpp b/src/vcfinfo2qual.cpp
index 2c4b961..176e706 100644
--- a/src/vcfinfo2qual.cpp
+++ b/src/vcfinfo2qual.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfinfosummarize.cpp b/src/vcfinfosummarize.cpp
index 3e0f0f9..d40d01e 100644
--- a/src/vcfinfosummarize.cpp
+++ b/src/vcfinfosummarize.cpp
@@ -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
diff --git a/src/vcfintersect.cpp b/src/vcfintersect.cpp
index 27f272e..c2aec9b 100644
--- a/src/vcfintersect.cpp
+++ b/src/vcfintersect.cpp
@@ -8,7 +8,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfkeepgeno.cpp b/src/vcfkeepgeno.cpp
index 5616b22..d0c1ecd 100644
--- a/src/vcfkeepgeno.cpp
+++ b/src/vcfkeepgeno.cpp
@@ -5,7 +5,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfkeepinfo.cpp b/src/vcfkeepinfo.cpp
index 916ca89..0b33fa2 100644
--- a/src/vcfkeepinfo.cpp
+++ b/src/vcfkeepinfo.cpp
@@ -5,7 +5,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfkeepsamples.cpp b/src/vcfkeepsamples.cpp
index 935c8a1..0b71534 100644
--- a/src/vcfkeepsamples.cpp
+++ b/src/vcfkeepsamples.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfleftalign.cpp b/src/vcfleftalign.cpp
index f4b992e..91a7e0a 100644
--- a/src/vcfleftalign.cpp
+++ b/src/vcfleftalign.cpp
@@ -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.
diff --git a/src/vcflength.cpp b/src/vcflength.cpp
index ebcc1a2..8e2e920 100644
--- a/src/vcflength.cpp
+++ b/src/vcflength.cpp
@@ -3,7 +3,7 @@
#include <vector>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfnumalt.cpp b/src/vcfnumalt.cpp
index a7c66cb..763161b 100644
--- a/src/vcfnumalt.cpp
+++ b/src/vcfnumalt.cpp
@@ -5,7 +5,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfoverlay.cpp b/src/vcfoverlay.cpp
index 1bb415c..67a178c 100644
--- a/src/vcfoverlay.cpp
+++ b/src/vcfoverlay.cpp
@@ -2,7 +2,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfparsealts.cpp b/src/vcfparsealts.cpp
index 5b4e508..95c5153 100644
--- a/src/vcfparsealts.cpp
+++ b/src/vcfparsealts.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfprimers.cpp b/src/vcfprimers.cpp
index 2a5c46a..b2cef79 100644
--- a/src/vcfprimers.cpp
+++ b/src/vcfprimers.cpp
@@ -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
diff --git a/src/vcfqual2info.cpp b/src/vcfqual2info.cpp
index 71c3335..196a613 100644
--- a/src/vcfqual2info.cpp
+++ b/src/vcfqual2info.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfrandom.cpp b/src/vcfrandom.cpp
index debab84..3af2528 100644
--- a/src/vcfrandom.cpp
+++ b/src/vcfrandom.cpp
@@ -5,7 +5,7 @@
#include <cmath>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfrandomsample.cpp b/src/vcfrandomsample.cpp
index 3cc565b..b6c66c3 100644
--- a/src/vcfrandomsample.cpp
+++ b/src/vcfrandomsample.cpp
@@ -7,7 +7,7 @@
#include "convert.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfremap.cpp b/src/vcfremap.cpp
index 82c9997..60c403b 100644
--- a/src/vcfremap.cpp
+++ b/src/vcfremap.cpp
@@ -8,7 +8,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfremoveaberrantgenotypes.cpp b/src/vcfremoveaberrantgenotypes.cpp
index 75ebc32..362e8e7 100644
--- a/src/vcfremoveaberrantgenotypes.cpp
+++ b/src/vcfremoveaberrantgenotypes.cpp
@@ -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();
diff --git a/src/vcfremovesamples.cpp b/src/vcfremovesamples.cpp
index b4b31df..33bab0c 100644
--- a/src/vcfremovesamples.cpp
+++ b/src/vcfremovesamples.cpp
@@ -4,7 +4,7 @@
#include <iostream>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
// remove elements in a from b
template<class T>
diff --git a/src/vcfroc.cpp b/src/vcfroc.cpp
index e77562e..5207f45 100644
--- a/src/vcfroc.cpp
+++ b/src/vcfroc.cpp
@@ -8,7 +8,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfsample2info.cpp b/src/vcfsample2info.cpp
index 2beab59..cd8b8d4 100644
--- a/src/vcfsample2info.cpp
+++ b/src/vcfsample2info.cpp
@@ -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
diff --git a/src/vcfsamplediff.cpp b/src/vcfsamplediff.cpp
index 09ca242..ccb6204 100644
--- a/src/vcfsamplediff.cpp
+++ b/src/vcfsamplediff.cpp
@@ -6,7 +6,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
bool samplesDiffer(vector<string>& samples, Variant& var) {
diff --git a/src/vcfsamplenames.cpp b/src/vcfsamplenames.cpp
index 23f68f7..1104577 100644
--- a/src/vcfsamplenames.cpp
+++ b/src/vcfsamplenames.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfsamplestats.cpp b/src/vcfsamplestats.cpp
index ceceb98..6710176 100644
--- a/src/vcfsamplestats.cpp
+++ b/src/vcfsamplestats.cpp
@@ -4,7 +4,7 @@
#include <iostream>
#include <getopt.h>
-using namespace vcf;
+using namespace vcflib;
void printSummary(char** argv) {
diff --git a/src/vcfsitesummarize.cpp b/src/vcfsitesummarize.cpp
index 067d0d4..afeee49 100644
--- a/src/vcfsitesummarize.cpp
+++ b/src/vcfsitesummarize.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfsom.cpp b/src/vcfsom.cpp
index 1e53ec1..59eb47d 100644
--- a/src/vcfsom.cpp
+++ b/src/vcfsom.cpp
@@ -10,7 +10,7 @@
#include <cmath>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
double mean(const vector<double>& data) {
double total = 0;
diff --git a/src/vcfstats.cpp b/src/vcfstats.cpp
index da8137b..33652de 100644
--- a/src/vcfstats.cpp
+++ b/src/vcfstats.cpp
@@ -4,7 +4,7 @@
#include <getopt.h>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
bool isTransition(const string& ref, const string& alt) {
if (((ref == "A" && alt == "G") || (ref == "G" && alt == "A")) ||
diff --git a/src/vcfstreamsort.cpp b/src/vcfstreamsort.cpp
index 834de64..769b301 100644
--- a/src/vcfstreamsort.cpp
+++ b/src/vcfstreamsort.cpp
@@ -4,7 +4,7 @@
#include "convert.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
bool listContains(list<string>& l, string& v) {
for (list<string>::iterator i = l.begin(); i != l.end(); ++i) {
diff --git a/src/vcfuniq.cpp b/src/vcfuniq.cpp
index 30ad21b..736631c 100644
--- a/src/vcfuniq.cpp
+++ b/src/vcfuniq.cpp
@@ -1,7 +1,7 @@
#include "Variant.h"
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
diff --git a/src/vcfuniqalleles.cpp b/src/vcfuniqalleles.cpp
index 3c1c7e2..1c3ea9f 100644
--- a/src/vcfuniqalleles.cpp
+++ b/src/vcfuniqalleles.cpp
@@ -2,7 +2,7 @@
#include <set>
using namespace std;
-using namespace vcf;
+using namespace vcflib;
int main(int argc, char** argv) {
--
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