[med-svn] [Git][med-team/vcftools][master] 6 commits: New upstream version 0.1.16
Andreas Tille
gitlab at salsa.debian.org
Fri Aug 3 14:59:01 BST 2018
Andreas Tille pushed to branch master at Debian Med / vcftools
Commits:
99c96e52 by Andreas Tille at 2018-08-03T13:56:17Z
New upstream version 0.1.16
- - - - -
b77ea7db by Andreas Tille at 2018-08-03T13:56:18Z
Update upstream source from tag 'upstream/0.1.16'
Update to upstream version '0.1.16'
with Debian dir 225694d657e0a90b430ccc9674e69d04325d76aa
- - - - -
de74df76 by Andreas Tille at 2018-08-03T13:56:18Z
New upstream version
- - - - -
02993abb by Andreas Tille at 2018-08-03T13:56:22Z
Point Vcs fields to salsa.debian.org
- - - - -
0650fc22 by Andreas Tille at 2018-08-03T13:56:22Z
Standards-Version: 4.1.5
- - - - -
689edd9e by Andreas Tille at 2018-08-03T13:58:36Z
Close bug in changelog
- - - - -
10 changed files:
- .tarball-version
- configure.ac
- debian/changelog
- debian/control
- src/cpp/header.cpp
- src/cpp/variant_file_output.cpp
- src/cpp/vcftools.1
- src/perl/FaSlice.pm
- src/perl/Vcf.pm
- src/perl/vcf-haplotypes
Changes:
=====================================
.tarball-version
=====================================
--- a/.tarball-version
+++ b/.tarball-version
@@ -1 +1 @@
-0.1.15
+0.1.16
=====================================
configure.ac
=====================================
--- a/configure.ac
+++ b/configure.ac
@@ -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
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+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 at debian.org> Fri, 03 Aug 2018 15:56:18 +0200
+
vcftools (0.1.15-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -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
=====================================
--- a/src/cpp/header.cpp
+++ b/src/cpp/header.cpp
@@ -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
=====================================
--- a/src/cpp/variant_file_output.cpp
+++ b/src/cpp/variant_file_output.cpp
@@ -4287,8 +4287,10 @@ void variant_file::output_removed_sites(const parameters ¶ms)
N_entries += e->apply_filters(params);
if(e->passed_filters)
+ {
+ N_kept_entries++;
continue;
- N_kept_entries++;
+ }
e->parse_basic_entry();
POS = e->get_POS();
@@ -4798,7 +4800,7 @@ void variant_file::output_indv_relatedness_Yang(const parameters ¶ms)
void variant_file::output_PCA(const parameters ¶ms)
{
-#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 ¶ms)
{
// 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
=====================================
--- a/src/cpp/vcftools.1
+++ b/src/cpp/vcftools.1
@@ -1,7 +1,7 @@
.\" 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 at einstein.yu.edu)
+Adam Auton
.br
-Anthony Marcketta (anthony.marcketta at einstein.yu.edu)
+Anthony Marcketta
=====================================
src/perl/FaSlice.pm
=====================================
--- a/src/perl/FaSlice.pm
+++ b/src/perl/FaSlice.pm
@@ -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 $$self{file}.fai");
=====================================
src/perl/Vcf.pm
=====================================
--- a/src/perl/Vcf.pm
+++ b/src/perl/Vcf.pm
@@ -2351,7 +2351,7 @@ sub validate_info_field
my $nr = -1;
if ( $$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
=====================================
--- a/src/perl/vcf-haplotypes
+++ b/src/perl/vcf-haplotypes
@@ -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",
View it on GitLab: https://salsa.debian.org/med-team/vcftools/compare/44e1975c9812b7ffdd628750dc73d8cdcebd8eda...689edd9ebcf278e67d44f8c469a20a9aed156dcc
--
View it on GitLab: https://salsa.debian.org/med-team/vcftools/compare/44e1975c9812b7ffdd628750dc73d8cdcebd8eda...689edd9ebcf278e67d44f8c469a20a9aed156dcc
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