int GenomeMaps::report_mapped_region(Chromosome const &chr, int chr_start, int chr_end, int num_matches)
{
reported_mapped_regions++ ;
//fprintf(stdout, "mapped_region:\tchr=%s\tstart=%i\tend=%i\tmatches=%i\n", CHR_DESC[chr], chr_start, chr_end, num_matches) ;
//assert(chr_start>=0 && chr_start<CHR_LENGTH[chr]) ;
//assert(chr_end>=0 && chr_end<CHR_LENGTH[chr]) ;
if (!(chr_start>=0 && (size_t)chr_start<=chr.length()))
{
if (_config.VERBOSE>0)
fprintf(stdout, "report_mapped_region: start out of bounds\n") ;
if (chr_start<0)
chr_start = 0 ;
else
chr_start = chr.length() ;
}
if (!(chr_end>=0 && (size_t)chr_end<=chr.length()))
{
if (_config.VERBOSE>0)
fprintf(stdout, "report_mapped_region: end out of bounds\n") ;
if (chr_end<0)
chr_end = 0 ;
else
chr_end = chr.length() ;
}
for (int i=chr_start; i<chr_end; i++)
if ((CHR_MAP(chr,i) & MASK_MAPPED_REGION) ==0 )
{
covered_mapped_region_positions++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i) + MASK_MAPPED_REGION) ;
}
return 0 ;
}
int GenomeMaps::report_repetitive_seed(Chromosome const &chr, int chr_start, int count)
{
//fprintf(stdout, "repetitive_seed:\tchr=%s\tpos=%i\tcount=%i\n", CHR_DESC[chr], chr_start, count) ;
if (count<Config::REPORT_REPETITIVE_SEED_COUNT)
return 0 ;
if (!(chr_start>=0 && (size_t)chr_start<=chr.length()))
{
if (_config.VERBOSE>0)
fprintf(stdout, "report_mapped_region: start out of bounds\n") ;
if (chr_start<0)
chr_start = 0 ;
else
chr_start = chr.length() ;
}
assert(chr_start>=0 && (size_t)chr_start<chr.length()) ;
//fprintf(stdout, "repetitive_seed:\tchr=%s\tpos=%i\tcount=%i\n", CHR_DESC[chr], chr_start, count) ;
reported_repetitive_seeds++ ;
for (unsigned int i=chr_start; i<chr_start+_config.INDEX_DEPTH+REPORT_REPETITIVE_SEED_DEPTH_EXTRA && i<chr.length(); i++)
if ((CHR_MAP(chr,i) & MASK_REPETITIVE_SEED) == 0)
{
covered_repetitive_seed_positions++ ;
CHR_MAP_set(chr,i, CHR_MAP(chr,i) + MASK_REPETITIVE_SEED) ;
}
do_reporting() ;
if (count<Config::REPORT_REPETITIVE_SEED_COUNT_MANY1)
return 0 ;
for (unsigned int i=chr_start; i<chr_start+_config.INDEX_DEPTH+REPORT_REPETITIVE_SEED_DEPTH_EXTRA && i<chr.length(); i++)
if ((CHR_MAP(chr,i) & MASK_REPETITIVE_SEED_MANY1) == 0)
{
covered_repetitive_seed_positions_many1++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i) + MASK_REPETITIVE_SEED_MANY1) ;
}
if (count<Config::REPORT_REPETITIVE_SEED_COUNT_MANY2)
return 0 ;
for (unsigned int i=chr_start; i<chr_start+_config.INDEX_DEPTH+REPORT_REPETITIVE_SEED_DEPTH_EXTRA && i<chr.length(); i++)
if ((CHR_MAP(chr,i) & MASK_REPETITIVE_SEED_MANY2) == 0)
{
covered_repetitive_seed_positions_many2++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i) + MASK_REPETITIVE_SEED_MANY2) ;
}
return 1 ;
}
int GenomeMaps::report_spliced_read(Chromosome const &chr, std::vector<int> & exons, int num_matches, int nbest_hit)
{
reported_spliced_reads++ ;
//fprintf(stdout, "mapped_read: \tchr=%s\tstart=%i\tend=%i\tmatches=%i\tnbest=%i\n", CHR_DESC[chr], start, end, num_matches, nbest_hit) ;
if (exons.size()==2)
{
return report_mapped_read(chr, exons[0], exons[1], num_matches, nbest_hit) ;
}
for (size_t e=0; e<exons.size(); e+=2)
{
int start = exons[e] ;
int end = exons[e+1] ;
if (!(start>=0 && (size_t)start<=chr.length()))
{
if (_config.VERBOSE>0)
fprintf(stdout, "report_spliced_read: start out of bounds\n") ;
if (start<0)
start = 0 ;
else
start = chr.length();
}
if (!(end>=0 && (size_t)end<=chr.length()))
{
if (_config.VERBOSE>0)
fprintf(stdout, "report_spliced_read: end out of bounds\n") ;
if (end<0)
end = 0 ;
else
end = chr.length();
}
//assert(start>=0 && (size_t)start<=CHR_LENGTH[chr]) ;
//assert(end>=0 && (size_t)end<=CHR_LENGTH[chr]) ;
int start_map = start - Config::QPALMA_USE_MAP_WINDOW ;
if (start_map<0)
start_map=0 ;
int end_map = end + Config::QPALMA_USE_MAP_WINDOW ;
if (end_map>(int)chr.length())
end_map=chr.length() ;
for (int i=start_map; i<end_map; i++)
{
if (nbest_hit==0 && (CHR_MAP(chr,i) & MASK_SPLICED_READ_BEST) == 0 )
{
covered_spliced_read_positions_best++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i)+MASK_SPLICED_READ_BEST) ;
}
#ifndef CHR_MAP_DNAARRAY
if ((CHR_MAP(chr,i) & MASK_SPLICED_READ) == 0 )
{
covered_spliced_read_positions++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i)+MASK_SPLICED_READ) ;
}
#else
#ifndef CHR_MAP_DNAARRAY_2BIT
if ((CHR_MAP(chr,i) & MASK_SPLICED_READ) == 0 )
{
covered_spliced_read_positions++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i)+MASK_SPLICED_READ) ;
}
#else
assert(MASK_SPLICED_READ_BEST<4) ;
#endif
#endif
}
if (_config.REPORT_GENOME_COVERAGE>0)
for (int i=start; i<end; i++)
{
if (CHR_MAP_cov(chr,i)<std::numeric_limits<unsigned int>::max())
{
CHR_MAP_set_cov(chr, i, CHR_MAP_cov(chr,i)+1) ;
}
}
}
return 0 ;
}
int GenomeMaps::report_mapped_read(Chromosome const &chr, int start, int end, int num_matches, int nbest_hit)
{
reported_mapped_reads++ ;
if (!(start>=0 && (size_t)start<=chr.length()))
{
if (_config.VERBOSE>0)
fprintf(stdout, "report_mapped_read: start out of bounds (start=%i no in [0,%i))\n", start, chr.length()) ;
if (start<0)
start = 0 ;
else
start = chr.length() ;
}
if (!(end>=0 && (size_t)end<=chr.length()))
{
if (_config.VERBOSE>0)
fprintf(stdout, "report_mapped_read: end out of bounds (end=%i not in [0,%i))\n", end, chr.length()) ;
if (end<0)
end = 0 ;
else
end = chr.length() ;
}
//fprintf(stdout, "mapped_read: \tchr=%s\tstart=%i\tend=%i\tmatches=%i\tnbest=%i\n", chr.desc(), start, end, num_matches, nbest_hit) ;
int start_map=start-Config::QPALMA_USE_MAP_WINDOW ;
if (start_map<0)
start_map=0 ;
int end_map=end+Config::QPALMA_USE_MAP_WINDOW ;
if (end_map>(int)chr.length())
end_map=chr.length() ;
for (int i=start_map; i<end_map; i++)
{
if (nbest_hit==0 && (CHR_MAP(chr,i) & MASK_MAPPED_READ_BEST) == 0 )
{
covered_mapped_read_positions_best++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i)+MASK_MAPPED_READ_BEST) ;
}
#ifndef CHR_MAP_DNAARRAY
if ((CHR_MAP(chr,i) & MASK_MAPPED_READ) == 0 )
{
covered_mapped_read_positions++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i)+ MASK_MAPPED_READ) ;
}
#else
#ifndef CHR_MAP_DNAARRAY_2BIT
if ((CHR_MAP(chr,i) & MASK_MAPPED_READ) == 0 )
{
covered_mapped_read_positions++ ;
CHR_MAP_set(chr, i, CHR_MAP(chr,i)+ MASK_MAPPED_READ) ;
}
#endif
#endif
}
if (_config.REPORT_GENOME_COVERAGE>0)
for (int i=start; i<end; i++)
{
if (CHR_MAP_cov(chr,i)<std::numeric_limits<unsigned int>::max())
{
CHR_MAP_set_cov(chr, i, CHR_MAP_cov(chr,i)+1) ;
}
}
do_reporting() ;
return 0 ;
}
