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renaming local alignment namespace and adding bsflags to sam flags
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@guilhermesena1
guilhermesena1 committed Jul 26, 2020
1 parent e3c6b9d commit 8cc4c41
Showing 1 changed file with 27 additions and 28 deletions.
55 changes: 27 additions & 28 deletions src/abismal.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -70,13 +70,6 @@ flip_strand_code(const flags_t sc) {
return (sc ^ samflags::read_rc) ^ bsflags::a_rich;
}

namespace align_scores {
static const score_t match = 1,
mismatch = -1,
indel = -1;
static const vector<score_t> score_lookup = {match, mismatch};
};

struct ReadLoader {
ReadLoader(const string &fn,
const size_t bs = numeric_limits<size_t>::max()) :
Expand Down Expand Up @@ -171,6 +164,7 @@ struct se_element {
template<const sam_record_type type>
uint16_t sam_flags() const {
return
(elem_is_a_rich()) * bsflags::a_rich |
(type != single) * (samflags::read_paired |
samflags::read_pair_mapped) |
(rc()) * samflags::read_rc |
Expand Down Expand Up @@ -786,10 +780,18 @@ prep_for_seeds(const Read &pread_seed, Read &pread_even, Read &pread_odd) {
for (i = 1; i < sz; i += 2) pread_odd[j++] = pread_seed[i];
}

static inline score_t
mismatch_score(const char q_base, const uint8_t t_base) {
return align_scores::score_lookup[the_comp(q_base, t_base)];
}
namespace local_aln {
static const score_t match = 1,
mismatch = -1,
indel = -1;

// this lookup improves speed when running alignment
static const vector<score_t> score_lookup = {match, mismatch};
static inline score_t mismatch_score(const char q_base,
const uint8_t t_base) {
return score_lookup[the_comp(q_base, t_base)];
}
};

template <score_t (*scr_fun)(const char, const uint8_t),
score_t indel_pen>
Expand All @@ -799,8 +801,8 @@ align_read(se_element &res, string &cigar, const string &read,
// ends early if alignment is nearly diagonal
if (res.diffs <= 3) {
cigar = std::to_string(read.length())+"M";
res.aln_score = align_scores::match * (read.length() - res.diffs) +
align_scores::mismatch * res.diffs;
res.aln_score = local_aln::match * (read.length() - res.diffs) +
local_aln::mismatch * res.diffs;
} else {
uint32_t len; // the region of the read the alignment spans
if (res.rc()) {
Expand Down Expand Up @@ -896,7 +898,7 @@ map_single_ended(const bool VERBOSE,
{
Read pread;
string tmp_cigar;
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand Down Expand Up @@ -1009,7 +1011,7 @@ map_single_ended_rand(const bool VERBOSE,
{
Read pread;
string tmp_cigar;
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand Down Expand Up @@ -1090,7 +1092,7 @@ static void
best_pair(const pe_candidates &res1, const pe_candidates &res2,
const string &read1, const string &read2,
string &cig1, string &cig2,
AbismalAlign<mismatch_score, align_scores::indel> &aln,
AbismalAlign<local_aln::mismatch_score, local_aln::indel> &aln,
pe_result &best) {

auto j1 = begin(res1.v);
Expand Down Expand Up @@ -1139,7 +1141,7 @@ select_maps(const string &read1, const string &read2,
string &cig1, string &cig2,
pe_candidates &res1, pe_candidates &res2,
se_result &res_se1, se_result &res_se2,
AbismalAlign<mismatch_score, align_scores::indel> &aln,
AbismalAlign<local_aln::mismatch_score, local_aln::indel> &aln,
pe_result &best) {
res1.prepare_for_mating();
res2.prepare_for_mating();
Expand Down Expand Up @@ -1215,7 +1217,7 @@ map_paired_ended(const bool VERBOSE,

#pragma omp parallel
{
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand All @@ -1235,7 +1237,7 @@ map_paired_ended(const bool VERBOSE,

#pragma omp parallel
{
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand All @@ -1251,7 +1253,7 @@ map_paired_ended(const bool VERBOSE,
{
Read pread;
string tmp_cigar;
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand Down Expand Up @@ -1358,7 +1360,7 @@ map_paired_ended_rand(const bool VERBOSE,
res1, res2);
#pragma omp parallel
{
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand All @@ -1377,7 +1379,7 @@ map_paired_ended_rand(const bool VERBOSE,
res2, res1);
#pragma omp parallel
{
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand All @@ -1396,7 +1398,7 @@ map_paired_ended_rand(const bool VERBOSE,
res1, res2);
#pragma omp parallel
{
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand All @@ -1415,7 +1417,7 @@ map_paired_ended_rand(const bool VERBOSE,
res2, res1);
#pragma omp parallel
{
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand All @@ -1432,7 +1434,7 @@ map_paired_ended_rand(const bool VERBOSE,
{
Read pread;
string tmp_cigar;
AbismalAlign<mismatch_score, align_scores::indel>
AbismalAlign<local_aln::mismatch_score, local_aln::indel>
aln(gi, genome_size, max_batch_read_length);

#pragma omp for
Expand Down Expand Up @@ -1547,9 +1549,6 @@ int main(int argc, const char **argv) {
false, random_pbat);
opt_parse.add_opt("a-rich", 'A', "indicates reads are a-rich (se mode)",
false, GA_conversion);
//opt_parse.add_opt("match", 'x', "match score", false, align_scores::match);
//opt_parse.add_opt("mismatch", 'm', "mismatch score", false,
// align_scores::mismatch);
opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
vector<string> leftover_args;
opt_parse.parse(argc, argv, leftover_args);
Expand Down

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