ngs_server 0.1 → 0.2

data/ext/vcftools/cpp/vcf_file_index.cpp

@@ -0,0 +1,171 @@
+/*
+ * vcf_file.cpp
+ *
+ *  Created on: 3 Aug 2011
+ *      Author: auton
+ */
+
+#include "vcf_file.h"
+
+bool vcf_file::read_index_file(const string &index_filename)
+{
+	// Check index is newer than vcf file
+	struct stat stat_idx, stat_vcf;
+	stat(index_filename.c_str(), &stat_idx);
+	stat(filename.c_str(), &stat_vcf);
+	if (stat_vcf.st_mtime > stat_idx.st_mtime)
+	{
+		warning("VCF index is older than VCF file. Will regenerate.");
+		return false;
+	}
+
+	printLOG("Reading Index file.\n");
+	big_endian_machine = is_big_endian();
+	gzFile in = gzopen(index_filename.c_str(), "rb");
+	if (in == NULL)
+		return false;
+
+	char magic[7];
+	idx_read(in, magic, 7, sizeof(char));
+	if (strncmp(magic, "VCFIDX\1", 7) != 0)
+	{	// Doesn't appear to be an index file
+		gzclose(in);
+		warning("Index file doesn't appear to be valid. Will (try to) overwrite.\n");
+		return false;
+	}
+
+	uint32_t tmp;
+	uint64_t tmp64;
+	idx_read(in, &tmp, 1, sizeof(uint32_t));
+	N_entries = tmp;
+	idx_read(in, &tmp, 1, sizeof(uint32_t));
+	N_indv = tmp;
+	idx_read(in, &tmp, 1, sizeof(uint32_t));
+	unsigned int l_meta = tmp;
+	idx_read(in, &tmp, 1, sizeof(uint32_t));
+	unsigned int l_indv = tmp;
+
+	char *meta_buffer = new char [l_meta+1];
+	char *indv_buffer = new char [l_indv+1];
+
+	idx_read(in, meta_buffer, l_meta, 1);
+	idx_read(in, indv_buffer, l_indv, 1);
+
+	// Split the strings
+	meta.resize(0);
+	char * pch;
+	pch = strtok(meta_buffer,"\n");
+	while (pch != NULL)
+	{
+		meta.push_back(pch);
+		pch = strtok(NULL, "\n");
+	}
+
+	indv.resize(0);
+	pch = strtok (indv_buffer,"\n");
+	while (pch != NULL)
+	{
+		indv.push_back(pch);
+		pch = strtok (NULL, "\n");
+	}
+
+	delete [] indv_buffer;
+	delete [] meta_buffer;
+
+	entry_file_locations.resize(N_entries);
+	for (unsigned int ui=0; ui<N_entries; ui++)
+	{
+		idx_read(in, &tmp64, 1, sizeof(uint64_t));
+		entry_file_locations[ui] = tmp64;
+	}
+
+	gzclose(in);
+	return true;
+}
+
+
+void vcf_file::write_index_file(const string &index_filename)
+{
+	printLOG("Writing Index file.\n");
+	big_endian_machine = is_big_endian();
+
+	gzFile out = gzopen(index_filename.c_str(), "wb");
+	if (out == NULL)
+	{
+		warning("Could not write index file.\n");
+		return;
+	}
+
+	unsigned int l_meta = 0;
+	for (unsigned int ui=0; ui<meta.size(); ui++)
+		l_meta += meta[ui].size() + 1;
+
+	unsigned int l_indv = 0;
+	for (unsigned int ui=0; ui<indv.size(); ui++)
+		l_indv += indv[ui].size() + 1;
+
+	idx_write(out, (char*)"VCFIDX\1", 7, 1);
+
+	uint32_t tmp;
+	uint64_t tmp64;
+	tmp = N_entries; idx_write(out, &tmp, 1, sizeof(uint32_t));
+	tmp = N_indv; idx_write(out, &tmp, 1, sizeof(uint32_t));
+	tmp = l_meta; idx_write(out, &tmp, 1, sizeof(uint32_t));
+	tmp = l_indv; idx_write(out, &tmp, 1, sizeof(uint32_t));
+
+	for (unsigned int ui=0; ui<meta.size(); ui++)
+	{
+		string str = meta[ui] + "\n";
+		idx_write(out, (char*)(str.c_str()), str.size(), 1);
+	}
+
+	for (unsigned int ui=0; ui<indv.size(); ui++)
+	{
+		string str = indv[ui] + "\n";
+		idx_write(out, (char*)(str.c_str()), str.size(), 1);
+	}
+
+	for (unsigned int ui=0; ui<entry_file_locations.size(); ui++)
+	{
+		tmp64 = entry_file_locations[ui];
+		idx_write(out, &tmp64, 1, sizeof(uint64_t));
+	}
+
+	gzclose(out);
+}
+
+
+inline void vcf_file::ByteSwap(unsigned char *b, int n) const
+{
+   int i = 0;
+   int j = n-1;
+   while (i<j)
+   {
+      swap(b[i], b[j]);
+      i++, j--;
+   }
+}
+
+
+int vcf_file::idx_read(gzFile &in, void *buffer, unsigned int len, size_t size)
+{
+	int ret = gzread(in, buffer, size*len);
+	if ((big_endian_machine) && (size > 1))	// Note: don't bother swapping character arrays - index is defined as little endian.
+	{
+		unsigned int ui;
+		for (ui=0; ui<len; ui++)
+			ByteSwap((unsigned char *)buffer+(size*ui), size);
+	}
+	return ret;
+}
+
+void vcf_file::idx_write(gzFile &out, void *buffer, unsigned int len, size_t size)
+{
+	if ((big_endian_machine) && (size > 1))
+	{
+		unsigned int ui;
+		for (ui=0; ui<len; ui++)
+			ByteSwap((unsigned char *)buffer+(size*ui), size);
+	}
+	gzwrite(out, buffer, size*len);
+}