Commit f02450ec authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.1.15

parent 3f8323dd

.tarball-version

0 → 100644
+1 −0
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0.1.15

README.md

+1 −1
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@@ -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

+7 −7
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@@ -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

src/cpp/Makefile.am

+1 −1
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bin_PROGRAMS = vcftools



vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS)

vcftools_CPPFLAGS = $(ZLIB_CFLAGS)

vcftools_LDADD = $(ZLIB_LIBS)



vcftools_SOURCES = \

src/cpp/parameters.cpp

+8 −3
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@@ -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);