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|
/* The MIT License
Copyright (c) 2014 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 "annotate_indels.h"
namespace
{
class Igor : Program
{
public:
std::string version;
///////////
//options//
///////////
std::string input_vcf_file;
std::string ref_fasta_file;
std::string output_vcf_file;
std::vector<GenomeInterval> intervals;
std::string interval_list;
bool debug;
bool override_tag;
bool add_flank_annotation; //add flank annotation
//exact alignment related statistics
std::string EX_MOTIF;
std::string EX_MLEN;
std::string EX_RU;
std::string EX_BASIS;
std::string EX_BLEN;
std::string EX_REPEAT_TRACT;
std::string EX_COMP;
std::string EX_ENTROPY;
std::string EX_ENTROPY2;
std::string EX_KL_DIVERGENCE;
std::string EX_KL_DIVERGENCE2;
std::string EX_REF;
std::string EX_RL;
std::string EX_LL;
std::string EX_RU_COUNTS;
std::string EX_SCORE;
std::string EX_TRF_SCORE;
//fuzzy alignment related statistics
std::string FZ_MOTIF;
std::string FZ_MLEN;
std::string FZ_RU;
std::string FZ_BASIS;
std::string FZ_BLEN;
std::string FZ_REPEAT_TRACT;
std::string FZ_COMP;
std::string FZ_ENTROPY;
std::string FZ_ENTROPY2;
std::string FZ_KL_DIVERGENCE;
std::string FZ_KL_DIVERGENCE2;
std::string FZ_REF;
std::string FZ_RL;
std::string FZ_LL;
std::string FZ_RU_COUNTS;
std::string FZ_SCORE;
std::string FZ_TRF_SCORE;
std::string FLANKSEQ;
std::string EXACT_RU_AMBIGUOUS;
//////////
//filter//
//////////
std::string fexp;
Filter filter;
bool filter_exists;
///////
//i/o//
///////
BCFOrderedReader *odr;
BCFOrderedWriter *odw;
/////////
//stats//
/////////
int32_t no_indels_annotated;
////////////////
//common tools//
////////////////
VariantManip* vm;
VNTRAnnotator* va;
ReferenceSequence* rs;
Igor(int argc, char **argv)
{
version = "0.5";
//////////////////////////
//options initialization//
//////////////////////////
try
{
std::string desc = "annotates indels with VNTR information and adds a VNTR record.";
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, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_output_vcf_file("o", "o", "output VCF file [-]", false, "-", "str", cmd);
TCLAP::ValueArg<std::string> arg_ref_fasta_file("r", "r", "reference sequence fasta file []", true, "", "str", cmd);
TCLAP::SwitchArg arg_debug("d", "d", "debug [false]", cmd, false);
TCLAP::UnlabeledValueArg<std::string> arg_input_vcf_file("<in.vcf>", "input VCF file", true, "","file", cmd);
TCLAP::ValueArg<std::string> arg_fexp("f", "f", "filter expression []", false, "", "str", cmd);
TCLAP::SwitchArg arg_override_tag("x", "x", "override tags [false]", cmd, false);
cmd.parse(argc, argv);
input_vcf_file = arg_input_vcf_file.getValue();
output_vcf_file = arg_output_vcf_file.getValue();
parse_intervals(intervals, arg_interval_list.getValue(), arg_intervals.getValue());
fexp = arg_fexp.getValue();
debug = arg_debug.getValue();
ref_fasta_file = arg_ref_fasta_file.getValue();
}
catch (TCLAP::ArgException &e)
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << std::endl;
abort();
}
};
~Igor()
{
};
void initialize()
{
///////////
//options//
///////////
/////////////////////////
//filter initialization//
/////////////////////////
filter.parse(fexp.c_str(), false);
filter_exists = fexp=="" ? false : true;
//////////////////////
//i/o initialization//
//////////////////////
odr = new BCFOrderedReader(input_vcf_file, intervals);
odw = new BCFOrderedWriter(output_vcf_file, 10000);
odw->link_hdr(odr->hdr);
//////////////////////////////
//INFO header adding for VCF//
//////////////////////////////
bool rename = false;
//motif related
// END = bcf_hdr_append_info_with_backup_naming(odw->hdr, "END", "1", "Integer", "End position of the variant.", rename);
// MOTIF = bcf_hdr_append_info_with_backup_naming(odw->hdr, "MOTIF", "1", "String", "Canonical motif in a VNTR.", rename);
// RU = bcf_hdr_append_info_with_backup_naming(odw->hdr, "RU", "1", "String", "Repeat unit in the reference sequence.", rename);
// BASIS = bcf_hdr_append_info_with_backup_naming(odw->hdr, "BASIS", "1", "String", "Basis nucleotides in the motif.", rename);
// MLEN = bcf_hdr_append_info_with_backup_naming(odw->hdr, "MLEN", "1", "Integer", "Motif length.", rename);
// BLEN = bcf_hdr_append_info_with_backup_naming(odw->hdr, "BLEN", "1", "Integer", "Basis length.", rename);
//exact alignment related statisitcs
EX_MOTIF = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_MOTIF", "1", "String", "Canonical motif in a VNTR.", rename);
EX_RU = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_RU", "1", "String", "Repeat unit in the reference sequence.", rename);
EX_BASIS = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_BASIS", "1", "String", "Basis nucleotides in the motif.", rename);
EX_MLEN = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_MLEN", "1", "Integer", "Motif length.", rename);
EX_BLEN = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_BLEN", "1", "Integer", "Basis length.", rename);
EX_REPEAT_TRACT = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_REPEAT_TRACT", "2", "Integer", "Boundary of the repeat tract detected by exact alignment.", rename);
EX_COMP = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_COMP", "4", "Integer", "Composition(%) of bases in an exact repeat tract.", rename);
EX_ENTROPY = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_ENTROPY", "1", "Float", "Entropy measure of an exact repeat tract [0,2].", rename);
EX_ENTROPY2 = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_ENTROPY2", "1", "Float", "Dinucleotide entropy measure of an exact repeat tract [0,4].", rename);
EX_KL_DIVERGENCE = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_KL_DIVERGENCE", "1", "Float", "Kullback-Leibler Divergence of an exact repeat tract.", rename);
EX_KL_DIVERGENCE2 = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_KL_DIVERGENCE2", "1", "Float", "Dinucleotide Kullback-Leibler Divergence of an exact repeat tract.", rename);
EX_REF = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_REF", ".", "Float", "Allele lengths in repeat units from exact alignment.", rename);
EX_RL = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_RL", "1", "Integer", "Reference exact repeat tract length in bases.", rename);
EX_LL = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_LL", "1", "Integer", "Longest exact repeat tract length in bases.", rename);
EX_RU_COUNTS = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_RU_COUNTS", "2", "Integer", "Number of exact repeat units and total number of repeat units in exact repeat tract.", rename);
EX_SCORE = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_SCORE", "1", "Float", "Score of repeat unit in exact repeat tract.", rename);
EX_TRF_SCORE = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EX_TRF_SCORE", "1", "Integer", "TRF Score for M/I/D as 2/-7/-7 in exact repeat tract.", rename);
//fuzzy alignment related statisitcs
FZ_MOTIF = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_MOTIF", "1", "String", "Canonical motif in a VNTR.", rename);
FZ_RU = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_RU", "1", "String", "Repeat unit in the reference sequence.", rename);
FZ_BASIS = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_BASIS", "1", "String", "Basis nucleotides in the motif.", rename);
FZ_MLEN = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_MLEN", "1", "Integer", "Motif length.", rename);
FZ_BLEN = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_BLEN", "1", "Integer", "Basis length.", rename);
FZ_REPEAT_TRACT = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_REPEAT_TRACT", "2", "Integer", "Boundary of the repeat tract detected by fuzzy alignment.", rename);
FZ_COMP = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_COMP", "4", "Integer", "Composition(%) of bases in a fuzzy repeat tract.", rename);
FZ_ENTROPY = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_ENTROPY", "1", "Float", "Entropy measure of a fuzzy repeat tract (0-2).", rename);
FZ_ENTROPY2 = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_ENTROPY2", "1", "Float", "Dinucleotide entropy measure of a fuzzy repeat tract (0-2).", rename);
FZ_KL_DIVERGENCE = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_KL_DIVERGENCE", "1", "Float", "Kullback-Leibler Divergence of a fuzzyt repeat tract.", rename);
FZ_KL_DIVERGENCE2 = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_KL_DIVERGENCE2", "1", "Float", "Dinucleotide Kullback-Leibler Divergence of a fuzzy repeat tract.", rename);
FZ_REF = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_REF", ".", "Float", "Allele lengths in repeat units from fuzzy alignment.", rename);
FZ_RL = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_RL", "1", "Integer", "Reference fuzzy repeat tract length in bases.", rename);
FZ_LL = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_LL", "1", "Integer", "Longest fuzzy repeat tract length in bases.", rename);
FZ_RU_COUNTS = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_RU_COUNTS", "2", "Integer", "Number of exact repeat units and total number of repeat units in fuzzy repeat tract.", rename);
FZ_SCORE = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_SCORE", "1", "Float", "Score of repeat unit in fuzzy repeat tract.", rename);
FZ_TRF_SCORE = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FZ_TRF_SCORE", "1", "Integer", "TRF Score for M/I/D as 2/-7/-7 in fuzzy repeat tract.", rename);
FLANKSEQ = bcf_hdr_append_info_with_backup_naming(odw->hdr, "FLANKSEQ", "1", "String", "Flanking sequence 10bp on either side of REF.", rename);
EXACT_RU_AMBIGUOUS = bcf_hdr_append_info_with_backup_naming(odw->hdr, "EXACT_RU_AMBIGUOUS", "0", "Flag", "Exact motif is ambiguous.", rename);
////////////////////////
//stats initialization//
////////////////////////
no_indels_annotated = 0;
////////////////////////
//tools initialization//
////////////////////////
vm = new VariantManip(ref_fasta_file);
va = new VNTRAnnotator(ref_fasta_file, debug);
rs = new ReferenceSequence(ref_fasta_file);
}
void print_options()
{
std::clog << "annotate_indels v" << version << "\n";
std::clog << "\n";
std::clog << "options: input VCF file(s) " << input_vcf_file << "\n";
std::clog << " [o] output VCF file " << output_vcf_file << "\n";
std::clog << " [k] add_flank_annotation " << (add_flank_annotation ? "true" : "false") << "\n";
print_boo_op(" [d] debug ", debug);
print_ref_op(" [r] ref FASTA file ", ref_fasta_file);
print_int_op(" [i] intervals ", intervals);
std::clog << "\n";
}
void print_stats()
{
std::clog << "\n";
std::cerr << "stats: no. of indels annotated " << no_indels_annotated << "\n";
std::clog << "\n";
}
/**
* Updates the FLANKSEQ INFO field.
*/
void update_flankseq(bcf_hdr_t* h, bcf1_t *v, const char* chrom, int32_t lflank_beg1, int32_t lflank_end1, int32_t rflank_beg1, int32_t rflank_end1)
{
std::string flanks;
char* seq = rs->fetch_seq(chrom, lflank_beg1, lflank_end1);
flanks.assign(seq);
if (seq) free(seq);
flanks.append(1, '[');
seq = rs->fetch_seq(chrom, lflank_end1+1, rflank_beg1-1);
flanks.append(seq);
if (seq) free(seq);
flanks.append(1, ']');
seq = rs->fetch_seq(chrom, rflank_beg1, rflank_end1);
flanks.append(seq);
if (seq) free(seq);
bcf_update_info_string(h, v, "FLANKSEQ", flanks.c_str());
}
void annotate_indels()
{
odw->write_hdr();
bcf1_t *v = odw->get_bcf1_from_pool();
bcf_hdr_t *h = odw->hdr;
Variant variant;
kstring_t old_alleles = {0,0,0};
int32_t no_exact = 0;
int32_t no_inexact = 0;
while (odr->read(v))
{
int32_t vtype = vm->classify_variant(odr->hdr, v, variant);
if (filter_exists)
{
if (!filter.apply(h, v, &variant, false))
{
continue;
}
}
//require normalization
if (!vm->is_normalized(v))
{
// std::string var = variant.get_variant_string();
// fprintf(stderr, "[%s:%d %s] Variant is not normalized, annotate_indels requires that variants are normalized: %s\n", __FILE__, __LINE__, __FUNCTION__, var.c_str());
// odw->write(v);
// v = odw->get_bcf1_from_pool();
continue;
}
//variants with N crashes the alignment models!!!!!! :(
if (vm->contains_N(v))
{
// std::string var = variant.get_variant_string();
// fprintf(stderr, "[%s:%d %s] Variant contains N bases, skipping annotation: %s\n", __FILE__, __LINE__, __FUNCTION__, var.c_str());
// odw->write(v);
// v = odw->get_bcf1_from_pool();
continue;
}
// bcf_print_liten(h,v);
if (debug)
{
bcf_print_liten(h,v);
}
if (vtype&VT_INDEL)
{
va->annotate(variant, EXACT|FUZZY);
VNTR& vntr = variant.vntr;
//shared fields
bcf_set_rid(v, variant.rid);
//exact characteristics
bcf_update_info_string(h, v, EX_MOTIF.c_str(), vntr.exact_motif.c_str());
bcf_update_info_int32(h, v, EX_MLEN.c_str(), &vntr.exact_mlen, 1);
bcf_update_info_string(h, v, EX_RU.c_str(), vntr.exact_ru.c_str());
bcf_update_info_string(h, v, EX_BASIS.c_str(), vntr.exact_basis.c_str());
bcf_update_info_int32(h, v, EX_BLEN.c_str(), &vntr.exact_blen, 1);
int32_t exact_flank_pos1[2] = {vntr.exact_beg1, vntr.exact_end1};
bcf_update_info_int32(h, v, EX_REPEAT_TRACT.c_str(), &exact_flank_pos1, 2);
bcf_update_info_int32(h, v, EX_COMP.c_str(), &vntr.exact_comp[0], 4);
bcf_update_info_float(h, v, EX_ENTROPY.c_str(), &vntr.exact_entropy, 1);
bcf_update_info_float(h, v, EX_ENTROPY2.c_str(), &vntr.exact_entropy2, 1);
bcf_update_info_float(h, v, EX_KL_DIVERGENCE.c_str(), &vntr.exact_kl_divergence, 1);
bcf_update_info_float(h, v, EX_KL_DIVERGENCE2.c_str(), &vntr.exact_kl_divergence2, 1);
bcf_update_info_float(h, v, EX_REF.c_str(), &vntr.exact_ref, 1);
bcf_update_info_int32(h, v, EX_RL.c_str(), &vntr.exact_rl, 1);
bcf_update_info_int32(h, v, EX_LL.c_str(), &vntr.exact_ll, 1);
int32_t exact_ru_count[2] = {vntr.exact_no_perfect_ru, vntr.exact_no_ru};
bcf_update_info_int32(h, v, EX_RU_COUNTS.c_str(), &exact_ru_count, 2);
bcf_update_info_float(h, v, EX_SCORE.c_str(), &vntr.exact_score, 1);
bcf_update_info_int32(h, v, EX_TRF_SCORE.c_str(), &vntr.exact_trf_score, 1);
if (vntr.exact_ru_ambiguous) bcf_update_info_flag(h, v, "EXACT_RU_AMBIGUOUS", NULL, 1);
//fuzzy characteristics
bcf_update_info_string(h, v, FZ_MOTIF.c_str(), vntr.fuzzy_motif.c_str());
bcf_update_info_int32(h, v, FZ_MLEN.c_str(), &vntr.fuzzy_mlen, 1);
bcf_update_info_string(h, v, FZ_RU.c_str(), vntr.fuzzy_ru.c_str());
bcf_update_info_string(h, v, FZ_BASIS.c_str(), vntr.fuzzy_basis.c_str());
bcf_update_info_int32(h, v, FZ_BLEN.c_str(), &vntr.fuzzy_blen, 1);
int32_t fuzzy_flank_pos1[2] = {vntr.fuzzy_beg1, vntr.fuzzy_end1};
bcf_update_info_int32(h, v, FZ_REPEAT_TRACT.c_str(), &fuzzy_flank_pos1, 2);
bcf_update_info_int32(h, v, FZ_COMP.c_str(), &vntr.fuzzy_comp[0], 4);
bcf_update_info_float(h, v, FZ_ENTROPY.c_str(), &vntr.fuzzy_entropy, 1);
bcf_update_info_float(h, v, FZ_ENTROPY2.c_str(), &vntr.fuzzy_entropy2, 1);
bcf_update_info_float(h, v, FZ_KL_DIVERGENCE.c_str(), &vntr.fuzzy_kl_divergence, 1);
bcf_update_info_float(h, v, FZ_KL_DIVERGENCE2.c_str(), &vntr.fuzzy_kl_divergence2, 1);
bcf_update_info_float(h, v, FZ_REF.c_str(), &vntr.fuzzy_ref, 1);
bcf_update_info_int32(h, v, FZ_RL.c_str(), &vntr.fuzzy_rl, 1);
bcf_update_info_int32(h, v, FZ_LL.c_str(), &vntr.fuzzy_ll, 1);
int32_t fuzzy_ru_count[2] = {vntr.fuzzy_no_perfect_ru, vntr.fuzzy_no_ru};
bcf_update_info_int32(h, v, FZ_RU_COUNTS.c_str(), &fuzzy_ru_count, 2);
bcf_update_info_float(h, v, FZ_SCORE.c_str(), &vntr.fuzzy_score, 1);
bcf_update_info_int32(h, v, FZ_TRF_SCORE.c_str(), &vntr.fuzzy_trf_score, 1);
update_flankseq(h, v, variant.chrom.c_str(),
variant.beg1-10, variant.beg1-1,
variant.end1+1, variant.end1+10);
++no_indels_annotated;
}
else if (vtype==VT_VNTR)
{
update_flankseq(h, v, variant.chrom.c_str(),
variant.beg1-10, variant.beg1-1,
variant.end1+1, variant.end1+10);
}
else if (vtype==VT_SNP || vtype==VT_MNP)
{
update_flankseq(h, v, variant.chrom.c_str(),
variant.beg1-10, variant.beg1-1,
variant.end1+1, variant.end1+10);
}
else //SVs?
{
//do nothing
}
odw->write(v);
v = odw->get_bcf1_from_pool();
}
odw->close();
odr->close();
};
private:
};
}
void annotate_indels(int argc, char ** argv)
{
Igor igor(argc, argv);
igor.print_options();
igor.initialize();
igor.annotate_indels();
igor.print_stats();
};
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