.tarball-version

+0.1.15

README.md

@@ -34,7 +34,7 @@ General help about the building process's configuration step can be acquired via
 make
 make install
 ```
-You many need `sudo` permissions to run `make install`.
+You may need `sudo` permissions to run `make install`.
 
 ### Build from GitHub
 

configure.ac

@@ -18,9 +18,9 @@ AC_PROG_CPP
 
 # Checks for perl.
 AC_PATH_PROGS([PERL], [perl] [perl5], [false])
-if test "x$PERL" = xfalse ; then
+AS_IF([test "x$PERL" = "xfalse"],[
   AC_MSG_ERROR([Perl not found; check your \$PATH.])
-fi
+])
 
 pmdir_relative_path=`\
 $PERL -MConfig \
@@ -34,12 +34,12 @@ AC_ARG_WITH(
       [--with-pmdir=DIR],
       [install Perl modules in DIR]),
     [PMDIR=${withval}],
-    [PMDIR='${prefix}'/"$pmdir_relative_path"])
+    [PMDIR="$pmdir_relative_path"])
 
 AC_SUBST([PMDIR])
 
 # Checks for libraries.
-PKG_CHECK_MODULES(ZLIB, zlib)
+PKG_CHECK_MODULES([ZLIB], [zlib])
 
 # Checks for header files.
 AC_CHECK_HEADERS([arpa/inet.h fcntl.h limits.h netdb.h stdint.h stdlib.h string.h sys/socket.h unistd.h])
@@ -73,9 +73,9 @@ AC_ARG_ENABLE([pca],
               [pca=${enableval}],
               [pca=no])
 
-if test "x${pca}" = "xyes" ; then
-  AC_CHECK_LIB(lapack, dgeev_)
-fi
+AS_IF([test "x$pca" = "xyes"],[
+  AC_SEARCH_LIBS([dgeev_], [lapack])
+])
 
 # Generate output.
 AC_CONFIG_FILES([Makefile

debian/changelog

-vcftools (0.1.14+dfsg-5) UNRELEASED; urgency=medium
+vcftools (0.1.15-1) unstable; urgency=medium
 
+  * New upstream version
+
+  [ Steffen Moeller ]
   * debian/upstream/metadata:
     - added references to registries
     - yamllint cleanliness
 
- -- Steffen Moeller <moeller@debian.org>  Sun, 10 Sep 2017 12:31:38 +0200
+  [ Andreas Tille ]
+  * Standards-Version: 4.1.3
+  * debhelper 11
+  * d/rules: do not parse d/changelog
+
+ -- Andreas Tille <tille@debian.org>  Sun, 18 Feb 2018 20:08:00 +0100
 
 vcftools (0.1.14+dfsg-4) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -4,11 +4,10 @@ Uploaders: Thorsten Alteholz <debian@alteholz.de>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
-               dh-autoreconf,
+Build-Depends: debhelper (>= 11),
                pkg-config,
                zlib1g-dev
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/vcftools.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/vcftools.git
 Homepage: https://vcftools.github.io/

debian/patches/manpage.patch

@@ -6,10 +6,10 @@ Description: Fix manpage syntax
 +++ b/src/cpp/vcftools.1
 @@ -1,7 +1,7 @@
  .\" Manpage for vcftools.
--.TH vcftools man page 1 "27 August 2014" "0.1.13" "vcftools man page"
-+.TH VCFTOOLS "1" "27 August 2014" "0.1.13" "vcftools man page"
+-.TH vcftools man page 1 "05 January 2016" "0.1.14" "vcftools man page"
++.TH VCFTOOLS "1" "05 January 2017" "0.1.15" "vcftools man page"
  .SH NAME
--vcftools v0.1.13 \- Utilities for the variant call format (VCF) and binary variant call format (BCF)
+-vcftools v0.1.14 \- Utilities for the variant call format (VCF) and binary variant call format (BCF)
 +vcftools \- Utilities for the variant call format (VCF) and binary variant call format (BCF)
  .SH SYNOPSIS
  .B vcftools

debian/rules

@@ -6,14 +6,15 @@ export DH_VERBOSE=1
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
-DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-sampledir:=$(CURDIR)/debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME)/examples
+include /usr/share/dpkg/default.mk
+
+sampledir:=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples
 
 %:
-	dh $@ --with autoreconf
+	dh $@
 
 override_dh_auto_configure:
-	dh_auto_configure -- --with-pmdir=/usr/share/perl5
+	dh_auto_configure -- --with-pmdir=/share/perl5
 
 override_dh_installchangelogs:
 	dh_installchangelogs src/perl/ChangeLog

src/cpp/Makefile.am

 bin_PROGRAMS = vcftools
 
-vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS)
+vcftools_CPPFLAGS = $(ZLIB_CFLAGS)
 vcftools_LDADD = $(ZLIB_LIBS)
 
 vcftools_SOURCES = \

src/cpp/parameters.cpp

@@ -86,6 +86,7 @@ parameters::parameters(int argc, char *argv[])
 	output_as_IMPUTE = false;
 	output_as_ldhat_phased = false;
 	output_as_ldhat_unphased = false;
+	output_as_ldhelmet = false;
 	output_BEAGLE_genotype_likelihoods_GL = false;
 	output_BEAGLE_genotype_likelihoods_PL = false;
 	output_counts = false;
@@ -144,7 +145,9 @@ parameters::parameters(int argc, char *argv[])
 	stream_in = false;
 	stream_out = false;
 	suppress_allele_output = false;
-	temp_dir = "/tmp/";
+	const char* raw = getenv("TMPDIR");	// Get environment variable
+        temp_dir = raw?raw:"";	// Handle case where TMPDIR is NULL.
+	if(temp_dir.empty()) temp_dir = "/tmp/";
 	vcf_filename="";
 	vcf_format = false;
 	vcf_compressed = false;
@@ -269,6 +272,7 @@ void parameters::read_parameters()
 		else if (in_str == "--ld-window-min") { ld_snp_window_min = atoi(get_arg(i+1).c_str()); i++; }		// Max SNP distance for LD output
 		else if (in_str == "--ldhat-geno") { output_as_ldhat_unphased = true; num_outputs++;}
 		else if (in_str == "--ldhat") { output_as_ldhat_phased = true; phased_only = true; num_outputs++;} // Output as LDhat format
+		else if (in_str == "--ldhelmet") { output_as_ldhelmet = true; phased_only = true; remove_indels = true; num_outputs++; } // Output as LDhelmet format
 		else if (in_str == "--LROH") {output_LROH = true; num_outputs++;}
 		else if (in_str == "--mac") { min_mac = atoi(get_arg(i+1).c_str()); i++; }								// Minimum Site MAC
 		else if (in_str == "--maf") { min_maf = atof(get_arg(i+1).c_str()); i++; }								// Minimum Site MAF
@@ -411,7 +415,7 @@ void parameters::print_params()
 	if (indv_exclude_files.size() != 0)
 	{
 		for (unsigned int ui=0; ui<indv_exclude_files.size(); ui++)
-			LOG.printLOG("\t--exclude " + indv_exclude_files[ui] + "\n");
+			LOG.printLOG("\t--remove " + indv_exclude_files[ui] + "\n");
 	}
 	if (indv_keep_files.size() != 0)
 	{
@@ -520,6 +524,7 @@ void parameters::print_params()
 	if (temp_dir != defaults.temp_dir) LOG.printLOG("\t--temp " + temp_dir + "\n");
 	if (output_Tajima_D_bin_size != defaults.output_Tajima_D_bin_size) LOG.printLOG("\t--TajimaD " + output_log::int2str(output_Tajima_D_bin_size) + "\n");
 	if (output_as_ldhat_phased) LOG.printLOG("\t--ldhat\n");
+	if (output_as_ldhelmet) LOG.printLOG("\t--ldhelmet\n");
 	if (output_as_ldhat_unphased) LOG.printLOG("\t--ldhat-geno\n");
 
 	if (site_filter_flags_to_exclude.size() > 0)
@@ -709,7 +714,7 @@ void parameters::check_parameters()
 	if (max_alleles < min_alleles) error("Max Number of Alleles must be greater than Min Number of Alleles.", 6);
 	if (max_mean_depth < min_mean_depth) error("Max Mean Depth must be greater the Min Mean Depth.", 7);
 	if (max_genotype_depth < min_genotype_depth) error("Max Genotype Depth must be greater than Min Genotype Depth.", 9);
-	if (((output_as_ldhat_phased == true) || (output_as_ldhat_unphased)) && (chrs_to_keep.size() != 1)) error("Require a chromosome (--chr) when outputting LDhat format.", 11);
+	if (((output_as_ldhat_phased == true) || (output_as_ldhat_unphased) || (output_as_ldhelmet)) && (chrs_to_keep.size() != 1)) error("Require a chromosome (--chr) when outputting LDhat format.", 11);
 	if ((output_BEAGLE_genotype_likelihoods_GL == true) && (chrs_to_keep.size() != 1)) error("Require a chromosome (--chr) when outputting Beagle likelihoods.", 11);
 	if ((output_BEAGLE_genotype_likelihoods_PL == true) && (chrs_to_keep.size() != 1)) error("Require a chromosome (--chr) when outputting Beagle likelihoods.", 11);
 	if (min_kept_mask_value > 9) error("Min Mask value must be between 0 and 9.", 14);

src/cpp/parameters.h

@@ -113,6 +113,7 @@ public:
 	bool output_as_IMPUTE;
 	bool output_as_ldhat_phased;
 	bool output_as_ldhat_unphased;
+	bool output_as_ldhelmet;
 	bool output_BEAGLE_genotype_likelihoods_GL;
 	bool output_BEAGLE_genotype_likelihoods_PL;
 	bool output_counts;

src/cpp/variant_file.h

@@ -130,6 +130,7 @@ public:
 	void output_as_IMPUTE(const parameters &params);
 	void output_as_LDhat_phased(const parameters &params);
 	void output_as_LDhat_unphased(const parameters &params);
+	void output_as_LDhelmet(const parameters &params);
 	void output_FORMAT_information(const parameters &params);
 
 	void output_weir_and_cockerham_fst(const parameters &params);

src/cpp/variant_file_format_convert.cpp

@@ -979,6 +979,183 @@ void variant_file::output_as_LDhat_unphased(const parameters &params)
 	sites.close();
 }
 
+// Output LDhelmet format
+void variant_file::output_as_LDhelmet(const parameters &params)
+{
+	if (meta_data.has_genotypes == false)
+		LOG.error("Require Genotypes in VCF file in order to output LDhelmet format.");
+
+	LOG.printLOG("Outputting in LDhelmet format\n");
+
+	unsigned int n_snps = 0;
+	int max_pos = -1;
+	int ret = -1;
+
+	string new_tmp = params.temp_dir+"/vcftools.XXXXXX";
+	char tmpname[new_tmp.size()];
+	strcpy(tmpname, new_tmp.c_str());
+
+	ret = mkstemp(tmpname);
+	string pos_tmp_filename(tmpname);
+	if (ret == -1)
+		LOG.error(" Could not open temporary file.\n", 12);
+	::close(ret);
+	ofstream pos_tmp_file(tmpname, std::ios::out | std::ios::binary);
+
+	string snps_file = params.output_prefix + ".ldhelmet.snps";
+	string pos_file = params.output_prefix + ".ldhelmet.pos";
+
+	ofstream snps(snps_file.c_str());
+	if (!snps.is_open())
+		LOG.error("Could not open LDhelmet snps Output File: " + snps_file, 2);
+	ofstream pos(pos_file.c_str());
+	if (!pos.is_open())
+		LOG.error("Could not open LDhelmet pos Output File: " + pos_file, 2);
+
+	unsigned int n_indv = N_kept_individuals();
+	pair<int, int> genotypes;
+	vector<string> alleles;
+
+	vector<ofstream *> tmp_files(2*meta_data.N_indv);
+	vector<string> tmp_filenames(2*meta_data.N_indv);
+	for (unsigned int ui=0; ui<meta_data.N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+
+		char tmpname[new_tmp.size()];
+		strcpy(tmpname, new_tmp.c_str());
+		ret = mkstemp(tmpname);
+		ofstream *tmp_file = new ofstream(tmpname);
+		if (ret == -1)
+		{	// Clean up temp files.
+			tmp_file->close(); remove(tmpname);
+			pos_tmp_file.close(); remove(pos_tmp_filename.c_str());
+			for (unsigned int uj=0; uj<ui; uj++)
+			{
+				(tmp_files[2*uj])->close(); remove(tmp_filenames[2*uj].c_str());
+				(tmp_files[2*uj+1])->close(); remove(tmp_filenames[2*uj+1].c_str());
+			}
+			LOG.error("\n\nCould not open temporary file.\n\n"
+					"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+					"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+		}
+		::close(ret);
+
+		tmp_files[2*ui] = tmp_file;
+		tmp_filenames[2*ui] = tmpname;
+
+		char tmpname2[new_tmp.size()];
+		strcpy(tmpname2, new_tmp.c_str());
+		ret = mkstemp(tmpname2);
+		ofstream *tmp_file2 = new ofstream(tmpname2);
+		if (ret == -1)
+		{	// Clean up temp files.
+			tmp_file2->close(); remove(tmpname2);
+			pos_tmp_file.close(); remove(pos_tmp_filename.c_str());
+			for (unsigned int uj=0; uj<ui; uj++)
+			{
+				(tmp_files[2*uj])->close(); remove(tmp_filenames[2*uj].c_str());
+				(tmp_files[2*uj+1])->close(); remove(tmp_filenames[2*uj+1].c_str());
+			}
+			(tmp_files[2*ui])->close(); remove(tmp_filenames[2*ui].c_str());
+			LOG.error("\n\nCould not open temporary file.\n\n"
+				"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+				"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+		}
+		::close(ret);
+
+		tmp_files[2*ui+1] = tmp_file2;
+		tmp_filenames[2*ui+1] = tmpname2;
+	}
+
+	vector<char> variant_line;
+	entry *e = get_entry_object();
+	ofstream *tmp_file;
+	int POS;
+
+	while(!eof())
+	{
+		get_entry(variant_line);
+		e->reset(variant_line);
+		N_entries += e->apply_filters(params);
+
+		if(!e->passed_filters)
+			continue;
+		N_kept_entries++;
+		e->parse_basic_entry(true);
+
+		POS = e->get_POS();
+		max_pos = max(POS, max_pos);
+		pos_tmp_file << POS << endl;
+		for (unsigned int ui=0; ui<meta_data.N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			e->parse_genotype_entry(ui, true);
+			e->get_indv_GENOTYPE_ids(ui, genotypes);
+			e->get_alleles_vector(alleles);
+
+			for (unsigned int k=0; k<2; k++)
+			{
+				tmp_file = tmp_files[(2*ui)+k];
+
+				int geno;
+				if (k == 0)
+					geno = genotypes.first;
+				else
+					geno = genotypes.second;
+
+				if ((geno >= 0) && (e->include_genotype[ui]==true))
+					(*tmp_file) << alleles[geno];
+				else
+					(*tmp_file) << "N";
+			}
+		}
+		n_snps++;
+	}
+
+	pos.setf(ios::fixed,ios::floatfield);
+	pos.precision(4);
+	ifstream pos_read_file(pos_tmp_filename.c_str());
+	string tmp_line;
+	for (unsigned int ui=0; ui<n_snps; ui++)
+	{
+		getline(pos_read_file,tmp_line);
+		POS = header::str2int(tmp_line);
+		pos << POS << endl;
+	}
+	pos.close();
+	for (unsigned int ui=0; ui<meta_data.N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+
+		for (unsigned int k=0; k<2; k++)
+		{
+			ofstream *tmp_file = tmp_files[2*ui+k];
+			(*tmp_file) << endl;
+			tmp_file->close();
+			delete tmp_file;
+
+			ifstream read_file(tmp_filenames[2*ui+k].c_str());
+			if (!read_file.good())
+				LOG.error("\n\nCould not open temporary file.\n\n"
+				"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+				"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+			getline(read_file, tmp_line);
+			snps << ">" << meta_data.indv[ui] << "-" << k << endl;
+			snps << tmp_line << endl;
+			read_file.close();
+			remove(tmp_filenames[2*ui+k].c_str());
+		}
+	}
+	delete e;
+	remove(pos_tmp_filename.c_str());
+	snps.close();
+}
+
 // Output INFO fields in tab-delimited format
 void variant_file::output_INFO_for_each_site(const parameters &params)
 {

src/cpp/variant_file_output.cpp

@@ -1567,7 +1567,7 @@ void variant_file::output_haplotype_r2(const parameters &params)
 				if ((r2 < min_r2) | (r2 != r2))
 					continue;
 
-			out << CHROM << "\t" << POS << "\t" << POS2 << "\t" << chr_count << "\t" << r2 << "\t" << D << "\t" << Dprime << "\t" << endl;
+			out << CHROM << "\t" << POS << "\t" << POS2 << "\t" << chr_count << "\t" << r2 << "\t" << D << "\t" << Dprime << endl;
 		}
 	}
 	tmp_file.close();

src/cpp/vcftools.1

 .\" Manpage for vcftools.
-.TH vcftools man page 1 "27 August 2014" "0.1.13" "vcftools man page"
+.TH vcftools man page 1 "05 January 2016" "0.1.14" "vcftools man page"
 .SH NAME
-vcftools v0.1.13 \- Utilities for the variant call format (VCF) and binary variant call format (BCF)
+vcftools v0.1.14 \- Utilities for the variant call format (VCF) and binary variant call format (BCF)
 .SH SYNOPSIS
 .B vcftools
 [
@@ -693,9 +693,11 @@ This option outputs phased haplotypes in IMPUTE reference-panel format. As IMPUT
 .PP
 .B --ldhat
 .br
+.B --ldhelmet
+.br
 .B --ldhat-geno
 .RS 2
-These options output data in LDhat format. This option requires the "--chr" filter option to also be used. The first option outputs phased data only, and therefore also implies "--phased" be used, leading to unphased individuals and genotypes being excluded. The second option treats all of the data as unphased, and therefore outputs LDhat files in genotype/unphased format. Two output files are generated with the suffixes ".ldhat.sites" and ".ldhat.locs", which correspond to the LDhat "sites" and "locs" input files respectively.
+These options output data in LDhat/LDhelmet format. This option requires the "--chr" filter option to also be used. The two first options output phased data only, and therefore also implies "--phased" be used, leading to unphased individuals and genotypes being excluded. For LDhelmet, only snps will be considered, and therefore it implies "--remove-indels". The second option treats all of the data as unphased, and therefore outputs LDhat files in genotype/unphased format. Two output files are generated with the suffixes ".ldhat.sites" and ".ldhat.locs", which correspond to the LDhat "sites" and "locs" input files respectively; for LDhelmet, the two files generated have the suffixes ".ldhelmet.snps" and ".ldhelmet.pos", which corresponds to the "SNPs" and "positions" files. 
 .RE
 .PP
 .B --BEAGLE-GL

src/cpp/vcftools.cpp

@@ -89,6 +89,7 @@ int main(int argc, char *argv[])
 	if (params.output_BEAGLE_genotype_likelihoods_PL == true) vf->output_BEAGLE_genotype_likelihoods(params, 1);
 	if (params.output_as_ldhat_unphased == true) vf->output_as_LDhat_unphased(params);
 	if (params.output_as_ldhat_phased == true) vf->output_as_LDhat_phased(params);
+	if (params.output_as_ldhelmet == true) vf->output_as_LDhelmet(params);
 	if (params.output_singletons == true) vf->output_singletons(params);
 	if (params.output_site_pi == true) vf->output_per_site_nucleotide_diversity(params);
 	if (params.pi_window_size > 0) vf->output_windowed_nucleotide_diversity(params);

src/perl/FaSlice.pm

@@ -121,10 +121,10 @@ sub read_chunk
         return;
     }
     my $to = $pos + $$self{size};
-    my $cmd = "samtools faidx $$self{file} $chr:$pos-$to";
+    my $cmd = "samtools faidx \Q$$self{file}\E \Q$chr:$pos-$to\E";
     my @out = $self->cmd($cmd) or $self->throw("$cmd: $!");
     my $line = shift(@out);
-    if ( !($line=~/^>$chr:(\d+)-(\d+)/) ) { $self->throw("Could not parse: $line"); }
+    if ( !($line=~/^>\Q$chr\E:(\d+)-(\d+)/) ) { $self->throw("Could not parse: $line"); }
     $$self{from} = $1;
     my $chunk = '';
     while ($line=shift(@out))

src/perl/Makefile.am

@@ -24,7 +24,7 @@ dist_bin_SCRIPTS = \
 	vcf-tstv \
 	vcf-validator
 
-pmdir = $(PMDIR)
+pmdir = $(exec_prefix)/$(PMDIR)
 
 dist_pm_DATA = \
 	FaSlice.pm \

src/perl/Vcf.pm

 package Vcf;
 
-our $VERSION = 'r953';
+our $VERSION = 'v0.1.14-12-gcdb80b8';
 
 # http://vcftools.sourceforge.net/specs.html
 # http://samtools.github.io/hts-specs/
@@ -410,6 +410,7 @@ sub _set_version
     elsif ( $$self{version} eq '4.0' ) { $reader=Vcf4_0->new(%$self); }
     elsif ( $$self{version} eq '4.1' ) { $reader=Vcf4_1->new(%$self); }
     elsif ( $$self{version} eq '4.2' ) { $reader=Vcf4_2->new(%$self); }
+    elsif ( $$self{version} eq '4.3' ) { $reader=Vcf4_3->new(%$self); }
     else 
     { 
         $self->warn(qq[The version "$$self{version}" not supported, assuming VCFv$$self{default_version}\n]);
@@ -1612,6 +1613,7 @@ sub event_type
     elsif ( $allele=~/^[ACGT]$/ ) { $len=1; $type='s'; $ht=$allele; }
     elsif ( $allele=~/^I/ ) { $len=length($allele)-1; $type='i'; $ht=$'; }
     elsif ( $allele=~/^D(\d+)/ ) { $len=-$1; $type='i'; $ht=''; }
+    elsif ( length($allele)==length($ref) && $allele=~/^[ACGTN]+$/ && $ref=~/^[ACGTN]+$/ ) { $len = length($allele); $type='s'; $ht=$allele; }
     else 
     { 
         my $chr = ref($rec) eq 'HASH' ? $$rec{CHROM} : 'undef';
@@ -2933,6 +2935,33 @@ sub Vcf4_0::format_header_line
         }
         $value = '<' .join(',',@items). '>';
     }
+    elsif ( $tmp_rec{key} =~ /vcfProcessLog(_.+)*/)
+    {
+       my %has = ( key=>1, handler=>1, default=>1 );
+       my @items;
+       my @knownKeys = qw(InputVCF InputVCFSource InputVCFVer InputVCFParam);
+        for my $key (qw(InputVCF InputVCFSource InputVCFVer InputVCFParam), sort keys %tmp_rec)
+        {
+
+            if ( !exists($tmp_rec{$key}) || $has{$key} || !grep(/^$key$/,@knownKeys)) { next; }
+            my $value;
+            if($key eq "InputVCFParam"){
+               $value=undef;
+               foreach my $ky(keys %{$tmp_rec{$key}}){
+                       if(defined($value)){
+                               $value .= ",";
+                       }
+                       $value .= $ky."=".$tmp_rec{$key}->{$ky};
+               }
+               #$value="<".$tmp_rec{$key}.">";
+            }else{
+               $value = $tmp_rec{$key};
+            }
+            push @items, "$key=<$value>";
+            $has{$key}=1;
+        }
+        $value = '<' .join(',',@items). '>';
+    }
     else { $value = $tmp_rec{value}; }
 
     my $line = "##$tmp_rec{key}=".$value."\n";
@@ -2981,7 +3010,15 @@ sub Vcf4_0::parse_header_line
             else { $self->throw(qq[Could not parse header line: $line\nStopped at [$tmp].\n]); }
         }
 
-        if ( $tmp=~/^[^,\\"]+/ ) { $attr_value .= $&; $tmp = $'; }
+
+        if( $tmp!~/>,/ && $tmp=~/^(<)(.+,{1}.+)(>)$/) {$tmp=$'; %$attr_value = split(/[,=]/,$2);}
+        if( $tmp=~ m/^<"([^,">]+)">/) {$tmp=$'; $attr_value = $1;}
+        if ( $tmp=~/^[^,\\"]+/) { $attr_value .= $&; $tmp = $';
+          if($attr_value =~ m/^<.+>$/){
+            $attr_value =~ s/^<//; $attr_value =~ s/>$//;
+          }
+        }
+
         if ( $tmp=~/^\\\\/ ) { $attr_value .= '\\\\'; $tmp = $'; next; }
         if ( $tmp=~/^\\"/ ) { $attr_value .= '\\"'; $tmp = $'; next; }
         if ( $tmp eq '' or ($tmp=~/^,/ && !$quoted) or $tmp=~/^"/ )
@@ -2994,6 +3031,10 @@ sub Vcf4_0::parse_header_line
                 $attr_value =~ s/^\s+//;
                 $attr_value =~ s/\s+$//;
             }
+            if($tmp =~ m/^(,([^=<].)+>),/){
+              $quoted = 1;
+              $attr_value.= $1;
+            }
             $$rec{$attr_key} = $attr_value;
             $tmp = $';
             if ( $quoted && $tmp=~/^,/ ) { $tmp = $'; }
@@ -3004,6 +3045,7 @@ sub Vcf4_0::parse_header_line
         $self->throw(qq[Could not parse header line: $line\nStopped at [$tmp].\n]);
     }
 
+    if( $key =~ m/vcfProcessLog/) {return $rec;}
     if ( $key eq 'INFO' or $key eq 'FILTER' or $key eq 'FORMAT' )
     {
         if ( $key ne 'PEDIGREE' && !exists($$rec{ID}) ) { $self->throw("Missing the ID tag in $line\n"); }
@@ -3324,6 +3366,7 @@ sub new
         reserved => 
         {
             FILTER  => { 0=>1 },
+            cols => {CHROM=>1,POS=>1,ID=>1,REF=>1,ALT=>1,QUAL=>1,FILTER=>1,INFO=>1,FORMAT=>1},
         },
 
         handlers =>
@@ -3518,5 +3561,79 @@ sub new
     return $self;
 }
 
+sub Vcf4_2::validate_alt_field
+{
+    my ($self,$values,$ref) = @_;
+
+    if ( @$values == 1 && $$values[0] eq '.' ) { return undef; }
+
+    my $ret = $self->_validate_alt_field($values,$ref);
+    if ( $ret ) { return $ret; }
+
+    my $ref_len = length($ref);
+    my $ref1 = substr($ref,0,1);
+
+    my @err;
+    my $msg = '';
+    for my $item (@$values)
+    {
+        if ( $item=~/^(.*)\[(.+)\[(.*)$/ or $item=~/^(.*)\](.+)\](.*)$/ )
+        {
+            if ( $1 ne '' && $3 ne '' ) { $msg=', two replacement strings given (expected one)'; push @err,$item; next; }
+            my $rpl;
+            if ( $1 ne '' )
+            {
+                $rpl  = $1;
+                if ( $rpl ne '.' )
+                {
+                    my $rref = substr($rpl,0,1);
+                    if ( $rref ne $ref1 ) { $msg=', the first base of the replacement string does not match the reference'; push @err,$item; next; }
+                }
+            }
+            else
+            {
+                $rpl  = $3;
+                if ( $rpl ne '.' )
+                {
+                    my $rref = substr($rpl,-1,1);
+                    if ( $rref ne $ref1 ) { $msg=', the last base of the replacement string does not match the reference'; push @err,$item; next; }
+                }
+            }
+            my $pos = $2;
+            if ( !($rpl=~/^[ACTGNacgtn]+$/) && $rpl ne '.' ) { $msg=', replacement string not valid (expected [ACTGNacgtn]+)'; push @err,$item; next; }
+            if ( !($pos=~/^\S+:\d+$/) ) { $msg=', cannot parse sequence:position'; push @err,$item; next; }
+            next;
+        }
+        if ( $item=~/^\.[ACTGNactgn]*([ACTGNactgn])$/ ) { next; }
+        elsif ( $item=~/^([ACTGNactgn])[ACTGNactgn]*\.$/ ) { next; }
+        elsif ( $item eq '*' ) { next; }
+        if ( !($item=~/^[ACTGNactgn]+$|^<[^<>\s]+>$/) ) { push @err,$item; next; }
+    }
+    if ( !@err ) { return undef; }
+    return 'Could not parse the allele(s) [' .join(',',@err). ']' . $msg;
+}
+
+#------------------------------------------------
+# Version 4.3 specific functions
+
+=head1 VCFv4.3
+
+VCFv4.2 specific functions
+
+=cut
+
+package Vcf4_3;
+use base qw(Vcf4_2);
+
+sub new
+{
+    my ($class,@args) = @_;
+    my $self = $class->SUPER::new(@args);
+    bless $self, ref($class) || $class;
+
+    $$self{version} = '4.3';
+    return $self;
+}
+
 1;