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bcf_genotyping_buffered_reader.cpp
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bcf_genotyping_buffered_reader.cpp
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/* The MIT License
Copyright (c) 2015 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 "bcf_genotyping_buffered_reader.h"
/**
* Constructor.
*/
BCFGenotypingBufferedReader::BCFGenotypingBufferedReader(std::string filename, std::vector<GenomeInterval>& intervals, std::string ref_fasta_file)
{
/////////////////////
//io initialization//
/////////////////////
odr = new BCFOrderedReader(filename, intervals);
//////////////////////////
//options initialization//
//////////////////////////
output_annotations = false;
////////////////////////
//stats initialization//
////////////////////////
no_snps_genotyped = 0;
no_indels_genotyped = 0;
no_vntrs_genotyped = 0;
////////////////////////
//tools initialization//
////////////////////////
vm = new VariantManip();
fai = fai_load(ref_fasta_file.c_str());
if (fai==NULL)
{
fprintf(stderr, "[%s:%d %s] Cannot load genome index: %s\n", __FILE__, __LINE__, __FUNCTION__, ref_fasta_file.c_str());
exit(1);
}
}
/**
* Collects sufficient statistics from read for variants to be genotyped.
*
* The VCF records in the buffer must never occur before
*/
void BCFGenotypingBufferedReader::process_read(bam_hdr_t *h, bam1_t *s)
{
//wrap bam1_t in AugmentBAMRecord
as.initialize(h, s);
uint32_t tid = bam_get_tid(s);
uint32_t beg1 = as.beg1;
uint32_t end1 = as.end1;
//collect statistics for variant records that are in the buffer and overlap with the read
GenotypingRecord* g;
for (std::list<GenotypingRecord*>::iterator i=buffer.begin(); i!=buffer.end(); ++i)
{
g = *i;
// std::cerr << g->pos1 << " " << g->beg1 << " " << g->end1 << " ";
//same chromosome
if (tid==g->rid)
{
if (end1 < g->beg1)
{
//can terminate
return;
}
else if (beg1 > g->end1)
{
//this should not occur if the buffer was flushed before invoking process read
continue;
}
//else if (beg1 <= g->beg1 && g->end1 <= end1)
else if (beg1 <= g->pos1 && g->pos1 <= end1)
{
collect_sufficient_statistics(*i, as);
}
else
{
//other types of overlap, just ignore
}
// std::cerr << "\n";
}
//prior chromosome
else if (tid<g->rid)
{
//this should not occur if the buffer was flushed before invoking process read
return;
}
//latter chromosome
else if (tid>g->rid)
{
//in case if the buffer has a VCF record later in the list which matches it
continue;
}
}
//you will only reach here if a read occurs after or overlaps the last record in the buffer
//adding new VCF records and collecting statistics if necessary
bcf1_t *v = bcf_init();
while (odr->read(v))
{
int32_t vtype = vm->classify_variant(odr->hdr, v, variant);
g = new GenotypingRecord(odr->hdr, v, vtype);
buffer.push_back(g);
if (tid==g->rid)
{
//if (end1>=g->beg1 && pos1<=g->end1)
if (beg1 <= g->pos1 && g->pos1 <= end1)
{
collect_sufficient_statistics(g, as);
}
}
//VCF record occurs after the read
if (tid < g->rid || end1 < g->beg1)
{
return;
}
else
{
v = bcf_init();
}
}
//this means end of file
bcf_destroy(v);
}
//*************************************************
//BACKUP version of sufficient statistics collector
//*************************************************
///**
// * Collects sufficient statistics from read for variants to be genotyped.
// */
//void BCFGenotypingBufferedReader::collect_sufficient_statistics(GenotypingRecord *g, AugmentedBAMRecord& as)
//{
// if (g->vtype==VT_SNP)
// {
// if (bcf_get_n_allele(g->v)==2)
// {
// bam1_t *s = as.s;
//
// char strand = bam_is_rev(s) ? 'R' : 'F';
// int32_t allele = 0;
// uint32_t pos1 = bam_get_pos1(s);
// uint8_t* seq = bam_get_seq(s);
// uint8_t* qual = bam_get_qual(s);
// int32_t rlen = bam_get_l_qseq(s);
// uint8_t mapq = bam_get_mapq(s);
// uint32_t q = 30;
// int32_t cycle = 0;
//
// std::vector<uint32_t>& aug_cigar = as.aug_cigar;
// std::vector<std::string>& aug_ref = as.aug_ref;
// std::vector<std::string>& aug_alt = as.aug_alt;
//
// int32_t vpos1 = g->pos1;
// int32_t cpos1 = bam_get_pos1(s);
// int32_t rpos0 = 0;
//
// for (uint32_t i=0; i<aug_cigar.size(); ++i)
// {
// uint32_t oplen = bam_cigar_oplen(aug_cigar[i]);
// char opchr = bam_cigar_opchr(aug_cigar[i]);
//
// if (opchr=='S')
// {
// rpos0 += oplen;
// }
// else if (opchr=='=')
// {
// if (vpos1>=cpos1 && vpos1<=(cpos1+oplen-1))
// {
// rpos0 += vpos1-cpos1;
// allele = 0;
// q = qual[rpos0];
// cycle = rpos0<(rlen>>1) ? (rpos0+1) : -(rlen - rpos0 + 1);
//
// break;
// }
// else
// {
// cpos1 += oplen;
// rpos0 += oplen;
// }
// }
// else if (opchr=='X')
// {
// if (vpos1==cpos1)
// {
//// std::cerr << i << ") " << vpos1 << "," << cpos1 << "," << rpos0 << " : " << aug_ref[i] << "/" << aug_alt[i] << " vs " <<bcf_get_allele(g->v)[1][0] << "\n";
//
// allele = aug_alt[i].at(0) == bcf_get_allele(g->v)[1][0] ? 1 : -1;
// q = qual[rpos0];
// cycle = rpos0<(rlen>>1) ? (rpos0+1) : -(rlen - rpos0 + 1);
//
// break;
// }
//
// ++cpos1;
// ++rpos0;
// }
// else if (opchr=='I')
// {
// rpos0 += oplen;
// }
// else if (opchr=='D')
// {
// cpos1 += oplen;
// }
// else
// {
// std::cerr << "unrecognized cigar state " << opchr << "\n";
// // exit(1);
// }
// }
//
// if (allele==0)
// {
// if (strand=='F')
// {
// ++g->depth_fwd;
// ++g->allele_depth_fwd[0];
// }
// else
// {
// ++g->depth_rev;
// ++g->allele_depth_rev[0];
// }
// }
// else //non ref
// {
// ++g->no_nonref;
//
// if (strand=='F')
// {
// ++g->depth_fwd;
// ++g->allele_depth_fwd[1];
// }
// else
// {
// ++g->depth_rev;
// ++g->allele_depth_rev[1];
// }
// }
//
// //update no. of mismatches
// uint32_t no_mismatches = as.no_mismatches;
// if (allele!=0 && q<20)
// {
// ++no_mismatches;
// }
//
// if (allele!=0 && no_mismatches==0)
// {
// std::cerr << "something wrong\n";
// }
//
// g->base_qualities_sum += q;
//
// ++g->depth;
// g->quals.push_back(q);
// g->map_quals.push_back(mapq);
// g->cycles.push_back(cycle);
// g->alleles.push_back(allele);
// g->strands.append(1, strand);
// g->no_mismatches.push_back(no_mismatches);
// }
// else //multiallelic
// {
// }
// }
// else if (g->vtype==VT_INDEL)
// {
// if (bcf_get_n_allele(g->v)==2)
// {
// if (as.beg1 <= g->beg1 && g->end1 <= as.end1)
// {
// bam1_t *s = as.s;
//
// char strand = bam_is_rev(s) ? 'R' : 'F';
// int32_t allele = 0;
// uint32_t pos1 = bam_get_pos1(s);
// uint8_t* seq = bam_get_seq(s);
// uint8_t* qual = bam_get_qual(s);
// uint32_t rlen = bam_get_l_qseq(s);
// uint8_t mapq = bam_get_mapq(s);
//
//
// int32_t dlen = g->dlen;
// uint32_t len = g->len;
// std::string& indel = g->indel;
//
// uint32_t q = len*30;
// uint32_t cycle = 10;
//
// std::vector<uint32_t>& aug_cigar = as.aug_cigar;
// std::vector<std::string>& aug_ref = as.aug_ref;
// std::vector<std::string>& aug_alt = as.aug_alt;
//
// int32_t vpos1 = g->pos1;
//
// int32_t cpos1 = bam_get_pos1(s);
// int32_t rpos0 = 0;
//
// for (uint32_t i=0; i<aug_cigar.size(); ++i)
// {
// uint32_t oplen = bam_cigar_oplen(aug_cigar[i]);
// char opchr = bam_cigar_opchr(aug_cigar[i]);
//
// if (opchr=='S')
// {
// rpos0 += oplen;
// }
// else if (opchr=='=')
// {
// if (vpos1>=cpos1 && vpos1<=(cpos1+oplen-1))
// {
// cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
// }
//
// cpos1 += oplen;
// rpos0 += oplen;
// }
// else if (opchr=='X')
// {
// if (cpos1-1==vpos1)
// {
// cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
// }
//
// ++cpos1;
// ++rpos0;
// }
// else if (opchr=='I')
// {
// // std::cerr << "dlen " << dlen << "\n";
// // std::cerr << "cpos1 " << cpos1 << "\n";
// // std::cerr << "vpos1 " << vpos1 << "\n";
// // std::cerr << "indel " << aug_alt[i] << "\n";
//
// if (dlen>0 && cpos1-1==vpos1)
// {
// if (indel==aug_alt[i])
// {
// q = len*30;
// allele = 1;
// }
// else
// {
// q = abs(len-aug_ref[i].size())*30;
// allele = -1;
// }
//
// cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
// break;
// }
// else if (dlen<0 && cpos1-1==vpos1)
// {
// q = 30;
// allele = -3;
//
// cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
// break;
// }
//
// rpos0 += oplen;
// }
// else if (opchr=='D')
// {
// // std::cerr << "dlen " << dlen << "\n";
// // std::cerr << "cpos1 " << cpos1 << "\n";
// // std::cerr << "vpos1 " << vpos1 << "\n";
// // std::cerr << "indel " << aug_ref[i] << "\n";
//
// if (dlen<0 && cpos1-1==vpos1)
// {
// if (indel==aug_ref[i])
// {
// q = len*30;
// allele = 1;
// }
// else
// {
// q = abs(len-aug_ref[i].size())*30;
// allele = -1;
// }
//
// cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
// break;
// }
// else if (dlen>0 && cpos1-1==vpos1)
// {
// q = 30;
// allele = -2;
//
// cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
// break;
// }
//
// cpos1 += oplen;
// }
// else
// {
// std::cerr << "unrecognized cigar state " << opchr << "\n";
// }
// }
//
// if (allele==0)
// {
// if (strand=='F')
// {
// ++g->depth_fwd;
// ++g->allele_depth_fwd[0];
// }
// else
// {
// ++g->depth_rev;
// ++g->allele_depth_rev[0];
// }
// }
// else //non ref
// {
// ++g->no_nonref;
//
// if (strand=='F')
// {
// ++g->depth_fwd;
// ++g->allele_depth_fwd[1];
// }
// else
// {
// ++g->depth_rev;
// ++g->allele_depth_rev[1];
// }
// }
//
// if (allele!=0)
// {
// ++g->no_nonref;
// }
//
// if (strand=='F')
// {
// ++g->depth_fwd;
// }
// else
// {
// ++g->depth_rev;
// }
//
// g->base_qualities_sum += q;
//
// ++g->depth;
// g->quals.push_back(q);
// g->cycles.push_back(cycle);
// g->alleles.push_back(allele);
// g->strands.append(1, strand);
// g->no_mismatches.push_back(as.no_mismatches);
// }
// else
// {
// ++g->depth;
// g->quals.push_back(0);
// g->quals.push_back(0);
// g->cycles.push_back(-1);
// g->alleles.push_back(-1);
// g->strands.append(1, (bam_is_rev(as.s) ? 'R' : 'F'));
// g->no_mismatches.push_back(as.no_mismatches);
// }
// }
// else //multiallelic
// {
// }
// }
// else if (g->vtype==VT_VNTR)
// {
// bam1_t *s = as.s;
//
// char strand = bam_is_rev(s) ? 'R' : 'F';
// int32_t allele = 0;
// uint32_t pos1 = bam_get_pos1(s);
// uint8_t* seq = bam_get_seq(s);
// uint8_t* qual = bam_get_qual(s);
// uint32_t rlen = bam_get_l_qseq(s);
// uint8_t mapq = bam_get_mapq(s);
//
// std::vector<uint32_t>& aug_cigar = as.aug_cigar;
// std::vector<std::string>& aug_ref = as.aug_ref;
// std::vector<std::string>& aug_alt = as.aug_alt;
//
// //genomic bookend positions of VNTR
// int32_t vpos1 = g->beg1-1;
// int32_t vend1 = g->end1+1;
//
// //position with respect to read
// int32_t cpos1 = bam_get_pos1(s);
// int32_t rpos0 = 0;
//
// //genomic bookend positions of VNTR translated to read position
// int32_t pos0 = -1;
// int32_t end0 = -1;
//
//
// //locate repeat region on read.
// //translating genomic coordinates to read positions
// for (uint32_t i=0; i<aug_cigar.size(); ++i)
// {
// uint32_t oplen = bam_cigar_oplen(aug_cigar[i]);
// char opchr = bam_cigar_opchr(aug_cigar[i]);
//
// if (opchr=='S')
// {
// rpos0 += oplen;
// }
// else if (opchr=='=')
// {
// if (pos0==-1 && (cpos1<=vpos1 && vpos1<=(cpos1+oplen-1)))
// {
// pos0 = rpos0 + (vpos1-cpos1+1);
// }
//
// if (end0==-1 && (cpos1<=vend1 && vend1<=(cpos1+oplen-1)))
// {
// end0 = rpos0 + (vend1-cpos1+1);
// break;
// }
//
// cpos1 += oplen;
// rpos0 += oplen;
// }
// else if (opchr=='X')
// {
// if (pos0==-1 && (cpos1==vpos1))
// {
// pos0 = rpos0;
// }
//
// if (end0==-1 && (cpos1==vend1))
// {
// end0 = rpos0;
// break;
// }
//
// ++cpos1;
// ++rpos0;
// }
// else if (opchr=='I')
// {
// rpos0 += oplen;
// }
// else if (opchr=='D')
// {
// cpos1 += oplen;
// }
// else
// {
// std::cerr << "unrecognized cigar state " << opchr << "\n";
// }
// }
//
// //compute repeat tract units
// float counts = 0;
//
//// std::cerr << "pos0,end0 = " << pos0 << "," <<end0 << " (" << g->motif.size() <<")\n";
//
// if (pos0!=-1 && end0!=-1)
// {
// counts = ((float)(end0-pos0+1))/g->motif.size();
// }
//
// if (counts)
// {
// //update genotyping record
// ++g->depth;
// g->counts.push_back(counts);
// g->strands.append(1, strand);
// g->no_mismatches.push_back(as.no_mismatches);
// }
// }
//}
/**
* Collects sufficient statistics from read for variants to be genotyped.
*/
void BCFGenotypingBufferedReader::collect_sufficient_statistics(GenotypingRecord *g, AugmentedBAMRecord& as)
{
if (g->vtype==VT_SNP)
{
if (bcf_get_n_allele(g->v)==2)
{
bam1_t *s = as.s;
char strand = bam_is_rev(s) ? 'R' : 'F';
int32_t allele = 0;
uint32_t pos1 = bam_get_pos1(s);
uint8_t* seq = bam_get_seq(s);
uint8_t* qual = bam_get_qual(s);
int32_t rlen = bam_get_l_qseq(s);
uint8_t mapq = bam_get_mapq(s);
uint32_t q = 30;
int32_t cycle = 0;
std::vector<uint32_t>& aug_cigar = as.aug_cigar;
std::vector<std::string>& aug_ref = as.aug_ref;
std::vector<std::string>& aug_alt = as.aug_alt;
int32_t vpos1 = g->pos1;
int32_t cpos1 = bam_get_pos1(s);
int32_t rpos0 = 0;
for (uint32_t i=0; i<aug_cigar.size(); ++i)
{
uint32_t oplen = bam_cigar_oplen(aug_cigar[i]);
char opchr = bam_cigar_opchr(aug_cigar[i]);
if (opchr=='S')
{
rpos0 += oplen;
}
else if (opchr=='=')
{
if (vpos1>=cpos1 && vpos1<=(cpos1+oplen-1))
{
rpos0 += vpos1-cpos1;
allele = 0;
q = qual[rpos0];
cycle = rpos0<(rlen>>1) ? (rpos0+1) : -(rlen - rpos0 + 1);
break;
}
else
{
cpos1 += oplen;
rpos0 += oplen;
}
}
else if (opchr=='X')
{
if (vpos1==cpos1)
{
// std::cerr << i << ") " << vpos1 << "," << cpos1 << "," << rpos0 << " : " << aug_ref[i] << "/" << aug_alt[i] << " vs " <<bcf_get_allele(g->v)[1][0] << "\n";
allele = aug_alt[i].at(0) == bcf_get_allele(g->v)[1][0] ? 1 : -1;
q = qual[rpos0];
cycle = rpos0<(rlen>>1) ? (rpos0+1) : -(rlen - rpos0 + 1);
break;
}
++cpos1;
++rpos0;
}
else if (opchr=='I')
{
rpos0 += oplen;
}
else if (opchr=='D')
{
cpos1 += oplen;
}
else
{
std::cerr << "unrecognized cigar state " << opchr << "\n";
// exit(1);
}
}
if (allele==0)
{
if (strand=='F')
{
++g->depth_fwd;
++g->allele_depth_fwd[0];
}
else
{
++g->depth_rev;
++g->allele_depth_rev[0];
}
}
else //non ref
{
++g->no_nonref;
if (strand=='F')
{
++g->depth_fwd;
++g->allele_depth_fwd[1];
}
else
{
++g->depth_rev;
++g->allele_depth_rev[1];
}
}
//update no. of mismatches
uint32_t no_mismatches = as.no_mismatches;
if (allele!=0 && q<20)
{
++no_mismatches;
}
if (allele!=0 && no_mismatches==0)
{
std::cerr << "something wrong\n";
}
g->base_qualities_sum += q;
++g->depth;
g->bqs.push_back(q);
g->mqs.push_back(mapq);
g->cys.push_back(cycle);
g->als.push_back(allele);
g->sts.append(1, strand);
g->nms.push_back(no_mismatches);
}
else //multiallelic
{
}
}
else if (g->vtype==VT_INDEL)
{
if (bcf_get_n_allele(g->v)==2)
{
if (as.beg1 <= g->beg1 && g->end1 <= as.end1)
{
bam1_t *s = as.s;
char strand = bam_is_rev(s) ? 'R' : 'F';
int32_t allele = 0;
uint32_t pos1 = bam_get_pos1(s);
uint8_t* seq = bam_get_seq(s);
uint8_t* qual = bam_get_qual(s);
uint32_t rlen = bam_get_l_qseq(s);
uint8_t mapq = bam_get_mapq(s);
int32_t dlen = g->dlen;
uint32_t len = g->len;
std::string& indel = g->indel;
uint32_t cycle = 10;
std::vector<uint32_t>& aug_cigar = as.aug_cigar;
std::vector<std::string>& aug_ref = as.aug_ref;
std::vector<std::string>& aug_alt = as.aug_alt;
int32_t vpos1 = g->pos1;
char lflank_state[3] = {'N', 'N', 'N'};
char rflank_state[3] = {'N', 'N', 'N'};
uint32_t lflank_qual[3] = {0, 0, 0};
uint32_t rflank_qual[3] = {0, 0, 0};
char fuzzy_lflank_state[3] = {'N', 'N', 'N'};
char fuzzy_rflank_state[3] = {'N', 'N', 'N'};
uint32_t fuzzy_lflank_qual[3] = {0, 0, 0};
uint32_t fuzzy_rflank_qual[3] = {0, 0, 0};
int32_t cpos1 = bam_get_pos1(s);
int32_t cend1 = 0;
int32_t rpos0 = 0;
int32_t lend1 = g->lend1;
int32_t lmid1 = g->lend1 - 1;
int32_t lbeg1 = g->lend1 - 2;
int32_t rbeg1 = g->rbeg1;
int32_t rmid1 = g->rbeg1 + 1;
int32_t rend1 = g->rbeg1 + 2;
int32_t abeg1 = lend1 + 1;
int32_t aend1 = rbeg1 - 1;
std::string observed_allele;
for (uint32_t i=0; i<aug_cigar.size(); ++i)
{
uint32_t oplen = bam_cigar_oplen(aug_cigar[i]);
char opchr = bam_cigar_opchr(aug_cigar[i]);
if (opchr=='S')
{
rpos0 += oplen;
}
else if (opchr=='=')
{
cend1 = cpos1+oplen-1;
//collect lflank information
if (cpos1<=lend1 && lbeg1<=cend1)
{
if (cpos1<=lbeg1)
{
lflank_state[0] = '=';
lflank_qual[0] = qual[rpos0+lbeg1-cpos1];
}
if (cpos1<=lmid1 && lmid1<=cend1)
{
lflank_state[1] = '=';
lflank_qual[1] = qual[rpos0+lmid1-cpos1];
}
if (lend1<=cend1)
{
lflank_state[2] = '=';
lflank_qual[2] = qual[rpos0+lend1-cpos1];
}
}
//collect allele information
if (cpos1<=aend1 && abeg1<=cend1)
{
int32_t copy_beg0 = rpos0 + std::max(cpos1, abeg1)-cpos1;
int32_t copy_end0 = rpos0 + std::min(cend1, aend1)-cpos1;
for (uint32_t i = copy_beg0; i<=copy_end0; ++i)
{
observed_allele.append(1, bam_base2char(bam_seqi(seq, i)));
}
}
//collect rflank information
if (cpos1<=rend1 && rbeg1<=cend1)
{
if (cpos1<=rbeg1)
{
rflank_state[0] = '=';
rflank_qual[0] = qual[rpos0+rbeg1-cpos1];
}
if (cpos1<=rmid1 && rmid1<=cend1)
{
rflank_state[1] = '=';
rflank_qual[1] = qual[rpos0+rmid1-cpos1];
}
if (rend1<=cend1)
{
rflank_state[2] = '=';
rflank_qual[2] = qual[rpos0+rend1-cpos1];
}
}
if (vpos1>=cpos1 && vpos1<=cend1)
{
cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
}
cpos1 += oplen;
rpos0 += oplen;
}
else if (opchr=='X')
{
cend1 = cpos1+oplen-1;
//collect lleft and right flank information
if (cpos1==lbeg1)
{
lflank_state[0] = '=';
lflank_qual[0] = qual[rpos0];
}
else if (cpos1==lmid1)
{
lflank_state[1] = '=';
lflank_qual[1] = qual[rpos0];
}
else if (cpos1==lend1)
{
lflank_state[2] = '=';
lflank_qual[2] = qual[rpos0];
}
else if (cpos1==rbeg1)
{
rflank_state[0] = '=';
rflank_qual[0] = qual[rpos0];
}
else if (cpos1==rmid1)
{
rflank_state[1] = '=';
rflank_qual[1] = qual[rpos0];
}
else if (cpos1==rend1)
{
rflank_state[2] = '=';
rflank_qual[2] = qual[rpos0];
}
//collect allele information
if (abeg1<=cend1 && cpos1<=aend1)
{
int32_t copy_beg0 = rpos0 + std::max(cpos1, abeg1)-cpos1;
int32_t copy_end0 = rpos0 + std::min(cend1, aend1)-cpos1;
for (uint32_t i = copy_beg0; i<=copy_end0; ++i)
{
observed_allele.append(1, bam_base2char(bam_seqi(seq, i)));
}
}
if (cpos1-1==vpos1)
{
cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
}
++cpos1;
++rpos0;
}
else if (opchr=='I')
{
// std::cerr << "dlen " << dlen << "\n";
// std::cerr << "cpos1 " << cpos1 << "\n";
// std::cerr << "vpos1 " << vpos1 << "\n";
// std::cerr << "indel " << aug_alt[i] << "\n";
if (cpos1-1==lend1)
{
observed_allele.append(aug_alt[i]);
cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
}
rpos0 += oplen;
}
else if (opchr=='D')
{
// std::cerr << "dlen " << dlen << "\n";
// std::cerr << "cpos1 " << cpos1 << "\n";
// std::cerr << "vpos1 " << vpos1 << "\n";
// std::cerr << "indel " << aug_ref[i] << "\n";
if (dlen<0 && cpos1-1==vpos1)
{
//don't do anything to allele
cycle = strand == 'F' ? (rpos0+1) : (rlen - rpos0);
break;
}
cpos1 += oplen;
}
else
{
std::cerr << "unrecognized cigar state " << opchr << "\n";
}
}
compute_indel_al(lflank_state, lflank_qual,
rflank_state, rflank_qual,
g->indel_alleles,
observed_allele,
g->aqs, g->als, g->dls);
//should return just the values?
if (allele==0)
{
if (strand=='F')
{
++g->depth_fwd;
++g->allele_depth_fwd[0];
}
else
{
++g->depth_rev;
++g->allele_depth_rev[0];
}
}
else //non ref
{
++g->no_nonref;
if (strand=='F')
{
++g->depth_fwd;
++g->allele_depth_fwd[1];
}
else