ngs_server 0.1 → 0.2

data/ext/vcftools/cpp/vcftools.cpp

@@ -0,0 +1,107 @@
+/*
+ * vcftools.cpp
+ *
+ *  Created on: Aug 19, 2009
+ *      Author: Adam Auton
+ *      ($Revision: 249 $)
+ */
+#include "vcftools.h"
+
+ofstream LOG;
+
+int main(int argc, char *argv[])
+{
+	time_t start,end;
+	time(&start);
+
+	// The following turns off sync between C and C++ streams.
+	// Apparently it's faster to turn sync off, and as I don't use C streams, it's okay to turn off.
+	ios_base::sync_with_stdio(false);
+
+	parameters params(argc, argv);
+	params.print_help();
+	params.read_parameters();
+
+	LOG.open((params.output_prefix + ".log").c_str());
+
+	printLOG("\nVCFtools - " + VCFTOOLS_VERSION + "\n");
+	printLOG("(C) Adam Auton 2009\n\n");
+
+	params.print_params();
+
+	vcf_file vcf(params.vcf_filename, params.vcf_compressed, params.chr_to_keep, params.chr_to_exclude, params.force_write_index);
+
+	// Apply various filters as required.
+	vcf.apply_filters(params);
+
+	unsigned int N_indv = vcf.N_kept_individuals();
+	unsigned int N_sites = vcf.N_kept_sites();
+	printLOG("After filtering, kept " + int2str(N_indv) + " out of " + int2str(vcf.N_indv) + " Individuals\n");
+	printLOG("After filtering, kept " + int2str(N_sites) + " out of a possible " + int2str(vcf.N_entries) + " Sites\n");
+	if (N_sites == 0)
+		error("No data left for analysis!");
+
+	if (params.diff_file != "")
+	{	// Merge files - cannot be run with other output options.
+		vcf_file vcf_diff(params.diff_file, params.diff_file_compressed, params.chr_to_keep, params.chr_to_exclude, params.force_write_index);
+		vcf_diff.apply_filters(params);	// Apply various filters as required.
+		vcf.output_indv_in_files(params.output_prefix, vcf_diff);
+		vcf.output_sites_in_files(params.output_prefix, vcf_diff);
+
+		if (params.diff_site_discordance == true) vcf.output_discordance_by_site(params.output_prefix, vcf_diff);
+		if (params.diff_discordance_matrix == true) vcf.output_discordance_matrix(params.output_prefix, vcf_diff);
+		if (params.diff_indv_discordance == true) vcf.output_discordance_by_indv(params.output_prefix, vcf_diff);
+		if (params.diff_switch_error == true) vcf.output_switch_error(params.output_prefix, vcf_diff);
+	}
+
+	vcf.output_INFO_for_each_site(params.output_prefix, params.INFO_to_extract);
+	vcf.output_FORMAT_information(params.output_prefix, params.FORMAT_id_to_extract);
+	if (params.output_indv_depth == true) vcf.output_individuals_by_mean_depth(params.output_prefix);
+	if (params.output_geno_depth == true) vcf.output_genotype_depth(params.output_prefix);
+	if (params.output_site_depth == true) vcf.output_site_depth(params.output_prefix, false);
+	if (params.output_site_mean_depth == true) vcf.output_site_depth(params.output_prefix, true);
+	if (params.output_freq == true) vcf.output_frequency(params.output_prefix, false, params.suppress_allele_output);
+	if (params.output_counts == true) vcf.output_frequency(params.output_prefix, true, params.suppress_allele_output);
+	if (params.plink_output == true) vcf.output_as_plink(params.output_prefix);
+	if (params.plink_tped_output == true) vcf.output_as_plink_tped(params.output_prefix);
+	if (params.output_HWE == true) vcf.output_hwe(params.output_prefix);
+	if (params.output_SNP_density_bin_size > 0) vcf.output_SNP_density(params.output_prefix, params.output_SNP_density_bin_size);
+	if (params.output_missingness == true) vcf.output_missingness(params.output_prefix);
+	if (params.output_geno_rsq == true) vcf.output_genotype_r2(params.output_prefix, params.ld_snp_window_size, params.ld_bp_window_size, params.min_r2);
+	if (params.output_interchromosomal_rsq == true) vcf.output_interchromosomal_genotype_r2(params.output_prefix, params.min_r2);
+	if (params.output_hap_rsq == true) vcf.output_haplotype_r2(params.output_prefix, params.ld_snp_window_size, params.ld_bp_window_size, params.min_r2);
+	if (params.output_het == true) vcf.output_het(params.output_prefix);
+	if (params.output_site_quality == true) vcf.output_site_quality(params.output_prefix);
+	if (params.output_012_matrix == true) vcf.output_as_012_matrix(params.output_prefix);
+	if (params.output_as_IMPUTE == true) vcf.output_as_IMPUTE(params.output_prefix);
+	if (params.output_BEAGLE_genotype_likelihoods == true) vcf.output_BEAGLE_genotype_likelihoods(params.output_prefix);
+	if (params.output_as_ldhat_unphased == true) vcf.output_as_LDhat_unphased(params.output_prefix, params.chr_to_keep);
+	if (params.output_as_ldhat_phased == true) vcf.output_as_LDhat_phased(params.output_prefix, params.chr_to_keep);
+	if (params.output_singletons == true) vcf.output_singletons(params.output_prefix);
+	if (params.output_site_pi == true) vcf.output_per_site_nucleotide_diversity(params.output_prefix);
+	if (params.pi_window_size > 0) vcf.output_windowed_nucleotide_diversity(params.output_prefix, params.pi_window_size);
+	if (params.output_Tajima_D_bin_size > 0) vcf.output_Tajima_D(params.output_prefix, params.output_Tajima_D_bin_size);
+	if (params.output_TsTv_bin_size > 0) vcf.output_TsTv(params.output_prefix, params.output_TsTv_bin_size);
+	if (params.output_TsTv_by_count) vcf.output_TsTv_by_count(params.output_prefix);
+	if (params.output_TsTv_by_qual) vcf.output_TsTv_by_quality(params.output_prefix);
+	if (params.recode == true) vcf.print(params.output_prefix, params.recode_INFO_to_keep, params.recode_all_INFO);
+	if (params.output_filter_summary == true) vcf.output_FILTER_summary(params.output_prefix);
+	if (params.output_filtered_sites == true) vcf.output_kept_and_removed_sites(params.output_prefix);
+	if (params.output_LROH == true) vcf.output_LROH(params.output_prefix);
+	if (params.output_relatedness == true) vcf.output_indv_relatedness(params.output_prefix);
+	if (params.output_PCA == true) vcf.output_PCA(params.output_prefix, !params.PCA_no_normalisation, params.output_N_PCA_SNP_loadings);
+	if (params.fst_populations.size() > 0) vcf.output_fst_version_2(params.output_prefix, params.fst_populations);
+
+	if (params.fst_file != "")
+	{
+		vcf_file vcf_fst(params.fst_file, params.fst_file_compressed, params.chr_to_keep);
+		vcf_fst.apply_filters(params);	// Apply various filters as required.
+		vcf.output_fst(params.output_prefix, vcf_fst);
+	}
+
+	time(&end);
+	double running_time = difftime(end,start);
+	printLOG("Run Time = " + dbl2str_fixed(running_time, 2) + " seconds\n");
+	LOG.close();
+	return 0;
+}

data/ext/vcftools/cpp/vcftools.h

@@ -0,0 +1,25 @@
+/*
+ * vcftools.h
+ *
+ *  Created on: Aug 19, 2009
+ *      Author: Adam Auton
+ *      ($Revision: 122 $)
+ */
+
+#ifndef VCFTOOLS_H_
+#define VCFTOOLS_H_
+
+#include <cstring>
+#include <ctime>
+#include <iostream>
+#include <limits>
+#include <string>
+#include <vector>
+
+#include "output_log.h"
+#include "parameters.h"
+#include "vcf_file.h"
+
+using namespace std;
+
+#endif/* VCFTOOLS_H_ */

data/ext/vcftools/examples/.svn/all-wcprops

@@ -0,0 +1,185 @@
+K 25
+svn:wc:ra_dav:version-url
+V 39
+/svnroot/vcftools/!svn/ver/601/examples
+END
+annotate.out
+K 25
+svn:wc:ra_dav:version-url
+V 52
+/svnroot/vcftools/!svn/ver/565/examples/annotate.out
+END
+perl-api-1.pl
+K 25
+svn:wc:ra_dav:version-url
+V 53
+/svnroot/vcftools/!svn/ver/415/examples/perl-api-1.pl
+END
+subset.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 50
+/svnroot/vcftools/!svn/ver/348/examples/subset.vcf
+END
+shuffle-test.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 56
+/svnroot/vcftools/!svn/ver/403/examples/shuffle-test.vcf
+END
+cmp-test-a.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 54
+/svnroot/vcftools/!svn/ver/397/examples/cmp-test-a.vcf
+END
+annotate.txt
+K 25
+svn:wc:ra_dav:version-url
+V 52
+/svnroot/vcftools/!svn/ver/565/examples/annotate.txt
+END
+cmp-test-b.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 54
+/svnroot/vcftools/!svn/ver/397/examples/cmp-test-b.vcf
+END
+cmp-test-a-3.3.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 58
+/svnroot/vcftools/!svn/ver/397/examples/cmp-test-a-3.3.vcf
+END
+query-test.out
+K 25
+svn:wc:ra_dav:version-url
+V 54
+/svnroot/vcftools/!svn/ver/325/examples/query-test.out
+END
+subset.indels.out
+K 25
+svn:wc:ra_dav:version-url
+V 57
+/svnroot/vcftools/!svn/ver/348/examples/subset.indels.out
+END
+cmp-test-b-3.3.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 58
+/svnroot/vcftools/!svn/ver/397/examples/cmp-test-b-3.3.vcf
+END
+subset.SNPs.out
+K 25
+svn:wc:ra_dav:version-url
+V 55
+/svnroot/vcftools/!svn/ver/348/examples/subset.SNPs.out
+END
+merge-test.vcf.out
+K 25
+svn:wc:ra_dav:version-url
+V 58
+/svnroot/vcftools/!svn/ver/560/examples/merge-test.vcf.out
+END
+isec-n2-test.vcf.out
+K 25
+svn:wc:ra_dav:version-url
+V 60
+/svnroot/vcftools/!svn/ver/486/examples/isec-n2-test.vcf.out
+END
+annotate2.out
+K 25
+svn:wc:ra_dav:version-url
+V 53
+/svnroot/vcftools/!svn/ver/601/examples/annotate2.out
+END
+invalid-4.0.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 55
+/svnroot/vcftools/!svn/ver/270/examples/invalid-4.0.vcf
+END
+concat-a.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 52
+/svnroot/vcftools/!svn/ver/565/examples/concat-a.vcf
+END
+cmp-test.out
+K 25
+svn:wc:ra_dav:version-url
+V 52
+/svnroot/vcftools/!svn/ver/596/examples/cmp-test.out
+END
+annotate3.out
+K 25
+svn:wc:ra_dav:version-url
+V 53
+/svnroot/vcftools/!svn/ver/565/examples/annotate3.out
+END
+concat-b.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 52
+/svnroot/vcftools/!svn/ver/342/examples/concat-b.vcf
+END
+annotate-test.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 57
+/svnroot/vcftools/!svn/ver/466/examples/annotate-test.vcf
+END
+concat-c.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 52
+/svnroot/vcftools/!svn/ver/342/examples/concat-c.vcf
+END
+merge-test-a.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 56
+/svnroot/vcftools/!svn/ver/486/examples/merge-test-a.vcf
+END
+merge-test-b.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 56
+/svnroot/vcftools/!svn/ver/486/examples/merge-test-b.vcf
+END
+valid-4.0.vcf.stats
+K 25
+svn:wc:ra_dav:version-url
+V 59
+/svnroot/vcftools/!svn/ver/601/examples/valid-4.0.vcf.stats
+END
+merge-test-c.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 56
+/svnroot/vcftools/!svn/ver/325/examples/merge-test-c.vcf
+END
+valid-4.0.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 53
+/svnroot/vcftools/!svn/ver/549/examples/valid-4.0.vcf
+END
+valid-4.1.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 53
+/svnroot/vcftools/!svn/ver/596/examples/valid-4.1.vcf
+END
+concat.out
+K 25
+svn:wc:ra_dav:version-url
+V 50
+/svnroot/vcftools/!svn/ver/565/examples/concat.out
+END
+valid-3.3.vcf
+K 25
+svn:wc:ra_dav:version-url
+V 53
+/svnroot/vcftools/!svn/ver/234/examples/valid-3.3.vcf
+END

data/ext/vcftools/examples/.svn/dir-prop-base

@@ -0,0 +1,6 @@
+K 10
+svn:ignore
+V 5
+v3.3
+
+END