Commit 99c96e52 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.1.16

parent f02450ec

.tarball-version

+1 −1
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0.1.15
 
0.1.16

configure.ac

+1 −1
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@@ -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.

src/cpp/header.cpp

+20 −3
Original line number Diff line number Diff line
@@ -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

+5 −3
Original line number Diff line number Diff line
@@ -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

+4 −4
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.\" 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