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configure.ac
View file @ 689edd9e
......@@ -74,7 +74,7 @@ AC_ARG_ENABLE([pca],
[pca=no])
AS_IF([test "x$pca" = "xyes"],[
AC_SEARCH_LIBS([dgeev_], [lapack])
AC_CHECK_LIB([lapack], [dgeev_])
])
# Generate output.
......
debian/changelog
View file @ 689edd9e
vcftools (0.1.16-1) UNRELEASED; urgency=medium
* New upstream version dealing with CVE-2018-11099, CVE-2018-11129 and
CVE-2018-11130
Closes: #902190
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
-- Andreas Tille <tille@debian.org> Fri, 03 Aug 2018 15:56:18 +0200
vcftools (0.1.15-1) unstable; urgency=medium
* New upstream version
......
debian/control
View file @ 689edd9e
......@@ -7,9 +7,9 @@ Priority: optional
Build-Depends: debhelper (>= 11),
pkg-config,
zlib1g-dev
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
Standards-Version: 4.1.5
Vcs-Browser: https://salsa.debian.org/med-team/vcftools
Vcs-Git: https://salsa.debian.org/med-team/vcftools.git
Homepage: https://vcftools.github.io/
Package: vcftools
......
src/cpp/header.cpp
View file @ 689edd9e
......@@ -110,7 +110,6 @@ int header::add_INFO_descriptor(const string &in, int index)
I.Field = "INFO";
vector<string> tokens;
tokenize(details, ',', tokens);
if (tokens.size() < 4)
LOG.error("Expected at least 4 parts in INFO definition: " + in);
......@@ -118,7 +117,11 @@ int header::add_INFO_descriptor(const string &in, int index)
for (unsigned int ui=0; ui<tokens.size(); ui++)
{
tokenize(tokens[ui], '=', entry);
if (entry.size() < 2)
{
LOG.warning("Warning: Expected at least 2 parts in INFO entry: " + in);
continue;
}
if (entry[0] == "ID") I.ID = entry[1];
else if (entry[0] == "Number")
{
......@@ -205,7 +208,6 @@ int header::add_FORMAT_descriptor(const string &in, int index)
tokenize(details, ',', tokens);
Field_description I;
I.Field = "FORMAT";
if (tokens.size() < 4)
LOG.error("Expected at least 4 parts in FORMAT definition: " + in);
......@@ -213,6 +215,11 @@ int header::add_FORMAT_descriptor(const string &in, int index)
for (unsigned int ui=0; ui<tokens.size(); ui++)
{
tokenize(tokens[ui], '=', entry);
if (entry.size() < 2)
{
LOG.warning("Warning: Expected at least 2 parts in FORMAT entry: " + in);
continue;
}
if (entry[0] == "ID") I.ID = entry[1];
else if (entry[0] == "Number")
{
......@@ -303,6 +310,11 @@ void header::add_CONTIG_descriptor(const string &in, int index)
for (unsigned int ui=0; ui<tokens.size(); ui++)
{
tokenize(tokens[ui], '=', entry);
if (entry.size() < 2)
{
LOG.warning("Warning: Expected at least 2 parts in CONTIG entry: " + in);
continue;
}
if (entry[0] == "ID")
{
I.ID = entry[1];
......@@ -342,6 +354,11 @@ int header::add_FILTER_descriptor(const string &in, int index)
for (unsigned int ui=0; ui<tokens.size(); ui++)
{
tokenize(tokens[ui], '=', entry);
if (entry.size() < 2)
{
LOG.warning("Warning: Expected at least 2 parts in FORMAT entry: " + in);
continue;
}
if (entry[0] == "ID") I.ID = entry[1];
else if (entry[0] == "Description")
{
......
src/cpp/variant_file_output.cpp
View file @ 689edd9e
......@@ -4287,8 +4287,10 @@ void variant_file::output_removed_sites(const parameters &params)
N_entries += e->apply_filters(params);
if(e->passed_filters)
continue;
{
N_kept_entries++;
continue;
}
e->parse_basic_entry();
POS = e->get_POS();
......@@ -4798,7 +4800,7 @@ void variant_file::output_indv_relatedness_Yang(const parameters &params)
void variant_file::output_PCA(const parameters &params)
{
#ifndef VCFTOOLS_PCA
#if !(HAVE_LIBLAPACK)
string out = "Cannot run PCA analysis. Vcftools has been compiled without PCA enabled (requires LAPACK).";
LOG.error(out);
#else
......@@ -4973,7 +4975,7 @@ void variant_file::output_PCA_SNP_loadings(const parameters &params)
{
// TODO: This function duplicates a lot of what is in the output PCA function. Would be better to combine in a more
// sensible fashion.
#ifndef VCFTOOLS_PCA
#if !(HAVE_LIBLAPACK)
string out = "Cannot run PCA analysis. Vcftools has been compiled without PCA enabled (requires LAPACK).";
LOG.error(out);
#else
......
src/cpp/vcftools.1
View file @ 689edd9e
.\" Manpage for vcftools.
.TH vcftools man page 1 "05 January 2016" "0.1.14" "vcftools man page"
.TH vcftools man page 1 "2 August 2018" "0.1.16" "vcftools man page"
.SH NAME
vcftools v0.1.14 \- Utilities for the variant call format (VCF) and binary variant call format (BCF)
vcftools v0.1.16 \- Utilities for the variant call format (VCF) and binary variant call format (BCF)
.SH SYNOPSIS
.B vcftools
[
......@@ -772,6 +772,6 @@ This option calculates a discordance matrix. This option only works with bi-alle
This option calculates phasing errors (specifically "switch errors"). This option creates an output file describing switch errors found between sites, with suffix ".diff.switch".
.RE
.SH AUTHORS
Adam Auton (adam.auton@einstein.yu.edu)
Adam Auton
.br
Anthony Marcketta (anthony.marcketta@einstein.yu.edu)
Anthony Marcketta
src/perl/FaSlice.pm
View file @ 689edd9e
......@@ -102,7 +102,7 @@ sub cache_chr_lengths
while (my $line=<$fh>)
{
my @items = split(/\t/,$line);
my $chr = $$self{chr_naming}.$items[0];
my $chr = $items[0];
$$self{chr_lengths}{$chr} = $items[1];
}
close($fh) or $self->throw("close $$self{file}.fai");
......
src/perl/Vcf.pm
View file @ 689edd9e
......@@ -2351,7 +2351,7 @@ sub validate_info_field
my $nr = -1;
if ( $$self{version}>4.0 )
{
if ( $$alts[0] eq '.' ) { $ng=1; $na=1; }
if ( $$alts[0] eq '.' ) { $ng=1; $na=1; $nr = 1; }
else
{
$na = @$alts;
......
src/perl/vcf-haplotypes 100644 → 100755
View file @ 689edd9e
......@@ -24,7 +24,7 @@ sub error
croak @msg;
}
die
"Usage: cat ref.fa | vcf-consensus [OPTIONS] in.vcf.gz \n",
"Usage: cat ref.fa | vcf-haplotypes [OPTIONS] in.vcf.gz \n",
"Options:\n",
" -h, -?, --help This help message.\n",
" -H, --haplotypes [<int>] Apply variants for the given haplotypes (1,2). If not given, both haplotypes are applied.\n",
......