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/*
* 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)
{
LOG.warning("VCF index is older than VCF file. Will regenerate.");
return false;
}
LOG.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);
LOG.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)
{
LOG.printLOG("Writing Index file.\n");
big_endian_machine = is_big_endian();
gzFile out = gzopen(index_filename.c_str(), "wb");
if (out == NULL)
{
LOG.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);
}
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