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/* The MIT License
Copyright (c) 2013 Adrian Tan <atks@umich.edu>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
*/
#include "view.h"
namespace
{
class Igor : Program
{
public:
///////////
//options//
///////////
std::string input_vcf_file;
std::string output_vcf_file;
int32_t compression_level;
std::string streaming_selection_bed_file;
uint32_t left_window;
uint32_t right_window;
std::vector<GenomeInterval> intervals;
std::vector<std::string> samples;
std::string variant;
uint32_t sort_window_size;
bool stream_selection;
bool print_header;
bool print_header_only;
bool print_sites_only;
bool print;
bool debug;
int32_t no_subset_samples;
///////
//i/o//
///////
BCFOrderedReader *odr;
BCFOrderedWriter *odw;
//////////
//filter//
//////////
std::string fexp;
Filter filter;
bool filter_exists;
/////////
//stats//
/////////
uint32_t no_variants;
uint32_t no_samples;
/////////
//tools//
/////////
VariantManip *vm;
OrderedRegionOverlapMatcher *orom_regions;
Igor(int argc, char **argv)
{
version = "0.5";
//////////////////////////
//options initialization//
//////////////////////////
try
{
std::string desc = "Views a VCF or BCF or VCF.GZ file.";
TCLAP::CmdLine cmd(desc, ' ', version);
VTOutput my;
cmd.setOutput(&my);
TCLAP::ValueArg<std::string> arg_intervals("i", "i", "intervals []", false, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_interval_list("I", "I", "file containing list of intervals []", false, "", "file", cmd);
TCLAP::ValueArg<std::string> arg_streaming_selection_bed_file("t", "t", "bed file for variant selection via streaming []", false, "", "file", cmd);
TCLAP::ValueArg<int32_t> arg_compression_level("c", "c", "compression level 0-9, 0 and -1 denotes uncompressed with the former being wrapped in bgzf.[6]", false, 6, "int", cmd);
TCLAP::ValueArg<uint32_t> arg_left_window("l", "l", "left window size for overlap []", false, 0, "int", cmd);
TCLAP::ValueArg<uint32_t> arg_right_window("r", "r", "right window size for overlap []", false, 0, "int", cmd);
TCLAP::SwitchArg arg_print("p", "p", "print options and summary [false]", cmd, false);
TCLAP::SwitchArg arg_print_header("h", "h", "omit header, this option is honored only for STDOUT [false]", cmd, false);
TCLAP::SwitchArg arg_print_header_only("H", "H", "print header only, this option is honored only for STDOUT [false]", cmd, false);
TCLAP::SwitchArg arg_print_sites_only("s", "s", "print site information only without genotypes [false]", cmd, false);
TCLAP::ValueArg<uint32_t> arg_sort_window_size("w", "w", "local sorting window size [0]", false, 0, "int", cmd);
TCLAP::SwitchArg arg_debug("d", "d", "debug [false]", cmd, false);
//TCLAP::ValueArg<std::string> arg_sample_list("s", "s", "file containing list of sample []", false, "", "file", cmd);
TCLAP::ValueArg<std::string> arg_fexp("f", "f", "filter expression []", false, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_output_vcf_file("o", "o", "output VCF/VCF.GZ/BCF file [-]", false, "-", "str", cmd);
TCLAP::UnlabeledValueArg<std::string> arg_input_vcf_file("<in.vcf>", "input VCF file", true, "","file", cmd);
cmd.parse(argc, argv);
input_vcf_file = arg_input_vcf_file.getValue();
output_vcf_file = arg_output_vcf_file.getValue();
compression_level = arg_compression_level.getValue();
parse_intervals(intervals, arg_interval_list.getValue(), arg_intervals.getValue());
fexp = arg_fexp.getValue();
streaming_selection_bed_file = arg_streaming_selection_bed_file.getValue();
left_window = arg_left_window.getValue();
right_window = arg_right_window.getValue();
print_header = arg_print_header.getValue();
print_header_only = arg_print_header_only.getValue();
no_subset_samples = arg_print_sites_only.getValue() ? 0 : -1;
print = arg_print.getValue();
sort_window_size = arg_sort_window_size.getValue();
debug = arg_debug.getValue();
}
catch (TCLAP::ArgException &e)
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << "\n";
abort();
}
};
void initialize()
{
//////////////////////
//i/o initialization//
//////////////////////
stream_selection = false;
if (streaming_selection_bed_file != "")
{
orom_regions = new OrderedRegionOverlapMatcher(streaming_selection_bed_file);
stream_selection = true;
}
odr = new BCFOrderedReader(input_vcf_file, intervals);
odw = new BCFOrderedWriter(output_vcf_file, sort_window_size, compression_level);
if (no_subset_samples==-1)
{
odw->link_hdr(odr->hdr);
}
else if (no_subset_samples==0)
{
odw->link_hdr(bcf_hdr_subset(odr->hdr, 0, 0, 0));
}
/////////////////////////
//filter initialization//
/////////////////////////
filter.parse(fexp.c_str(), debug);
filter_exists = fexp=="" ? false : true;
////////////////////////
//stats initialization//
////////////////////////
no_variants = 0;
no_samples = 0;
///////////////////////
//tool initialization//
///////////////////////
vm = new VariantManip("");
}
void view()
{
if (print_header_only && output_vcf_file == "-")
{
odw->write_hdr();
odr->close();
odw->close();
return;
}
if (print_header || output_vcf_file != "-") odw->write_hdr();
bcf1_t *v = odw->get_bcf1_from_pool();
bcf_hdr_t *h = odr->hdr;
Variant variant;
while (odr->read(v))
{
// bcf_print(h,v);
if (stream_selection)
{
bcf_unpack(v, BCF_UN_STR);
std::string chrom = bcf_get_chrom(odr->hdr,v);
int32_t start1 = bcf_get_pos1(v);
int32_t end1 = bcf_get_end1(v);
if (!orom_regions->overlaps_with(chrom, start1-left_window, end1+right_window))
{
continue;
}
}
if (filter_exists)
{
vm->classify_variant(h, v, variant);
if (!filter.apply(h, v, &variant, debug))
{
continue;
}
}
if (no_subset_samples==0)
{
bcf_subset(odw->hdr, v, 0, 0);
//maybe add some additional adhoc fixing for BCF files that do not have a complete header.
}
odw->write(v);
if (sort_window_size)
{
v = odw->get_bcf1_from_pool();
}
++no_variants;
}
odw->close();
odr->close();
delete(odw);
delete(odr);
};
void print_options()
{
if (!print) return;
std::clog << "view v" << version << "\n\n";
std::clog << "options: input VCF file " << input_vcf_file << "\n";
std::clog << " [o] output VCF file " << output_vcf_file << "\n";
std::clog << " [w] sort window size " << sort_window_size << "\n";
print_str_op(" [t] streaming selection bed file ", streaming_selection_bed_file);
print_num_op(" [l] left window ", left_window);
print_num_op(" [r] right window ", right_window);
std::clog << " [h] print header " << (print_header ? "yes" : "no") << "\n";
std::clog << " [H] print header only " << (print_header_only ? "yes" : "no") << "\n";
std::clog << " [s] print site information only " << (print_sites_only ? "yes" : "no") << "\n";
std::clog << " [p] print options and stats " << (print ? "yes" : "no") << "\n";
std::clog << " [c] compression level " << compression_level << "\n";
print_str_op(" [f] filter ", fexp);
print_int_op(" [i] intervals ", intervals);
std::clog << "\n";
}
void print_stats()
{
if (!print) return;
std::clog << "\n";
std::clog << "stats: no. variants : " << no_variants << "\n";
std::clog << " no. samples : " << no_samples << "\n";
std::clog << "\n";
};
~Igor() {};
private:
};
}
bool view(int argc, char ** argv)
{
Igor igor(argc, argv);
igor.print_options();
igor.initialize();
igor.view();
igor.print_stats();
return igor.print;
};
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