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Removed index_t typedef as it conflicted with a system definition #13

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4 changes: 2 additions & 2 deletions src/common/alignment.h
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Expand Up @@ -267,9 +267,9 @@ inline int M5RecordOvlpSize(const M5Record& m)

//struct Overlap
//{
// index_t qid, qoff, qend, qsize, qext;
// idx_t qid, qoff, qend, qsize, qext;
// int qdir;
// index_t sid, soff, send, ssize, sext;
// idx_t sid, soff, send, ssize, sext;
// int sdir;
//};

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1 change: 0 additions & 1 deletion src/common/defs.h
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Expand Up @@ -19,7 +19,6 @@ typedef uint64_t u8_t;
typedef i8_t idx_t;

typedef u1_t uint1;
typedef idx_t index_t;

#define INVALID_IDX (-1)

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12 changes: 6 additions & 6 deletions src/common/packed_db.h
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Expand Up @@ -26,23 +26,23 @@ class PackedDB
safe_calloc(pac, u1_t, bytes);
}

void GetSequence(const index_t id, const bool fwd, char* seq, const index_t size_in_ovlp)
void GetSequence(const idx_t id, const bool fwd, char* seq, const idx_t size_in_ovlp)
{
const index_t offset = seq_idx[id].offset;
const index_t size = seq_idx[id].size;
const idx_t offset = seq_idx[id].offset;
const idx_t size = seq_idx[id].size;
r_assert(size == size_in_ovlp);
index_t idx = 0;
idx_t idx = 0;
if (fwd)
{
for (index_t i = 0; i < size; ++i)
for (idx_t i = 0; i < size; ++i)
{
uint1 c = get_char(offset + i);
seq[idx++] = c;
}
}
else
{
for (index_t i = size - 1; i >= 0; --i)
for (idx_t i = size - 1; i >= 0; --i)
{
uint1 c = get_char(offset + i);
c = 3 - c;
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22 changes: 10 additions & 12 deletions src/filter_reads/filter_reads.cpp
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Expand Up @@ -6,8 +6,6 @@

using namespace std;

typedef index_t idx;

void print_usage(const char* prog)
{
const char sep = ' ';
Expand All @@ -19,27 +17,27 @@ void print_usage(const char* prog)
<< "max-length" << endl;
}

idx parse_int(const char* arg)
idx_t parse_int(const char* arg)
{
istringstream in(arg);
idx n;
idx_t n;
in >> n;
if (!in) ERROR("failed to transfer '%s' to integer.", arg);
return n;
}

void
output_one_read(Sequence& read, int& id, const idx min_size, const idx max_size, ostream& out)
output_one_read(Sequence& read, int& id, const idx_t min_size, const idx_t max_size, ostream& out)
{
idx n = read.size();
idx l = 0, r, left = n;
idx_t n = read.size();
idx_t l = 0, r, left = n;
Sequence::str_t& seq = read.sequence();
while (left) {
r = min(n, l + max_size);
idx s = r - l;
idx_t s = r - l;
if (s < min_size) break;
out << ">" << id++ << "\n";
for (idx i = l; i < r; ++i) {
for (idx_t i = l; i < r; ++i) {
out << seq[i];
}
out << "\n";
Expand All @@ -56,16 +54,16 @@ int main(int argc, char* argv[])
}
const char* input = argv[1];
const char* output = argv[2];
const idx min_size = parse_int(argv[3]);
const idx max_size = parse_int(argv[4]);
const idx_t min_size = parse_int(argv[3]);
const idx_t max_size = parse_int(argv[4]);

FastaReader reader(input);
Sequence read;
ofstream out;
open_fstream(out, output, ios::out);
int id = 0;
while (1) {
idx s = reader.read_one_seq(read);
idx_t s = reader.read_one_seq(read);
if (s == -1) break;
output_one_read(read, id, min_size, max_size, out);
}
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6 changes: 3 additions & 3 deletions src/mecat2cns/argument.h
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Expand Up @@ -20,13 +20,13 @@ class Argument
class IntegerArgument : public Argument
{
public:
IntegerArgument(const std::string* an, const std::string* ad, const index_t v) : Argument(an, ad), val(v) {}
IntegerArgument(const std::string* an, const std::string* ad, const idx_t v) : Argument(an, ad), val(v) {}
virtual ~IntegerArgument() {}
virtual int ProcessArgument(int argc, char** argv);
index_t value() { return val; }
idx_t value() { return val; }

private:
index_t val;
idx_t val;
};

class DoubleArgument : public Argument
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58 changes: 29 additions & 29 deletions src/mecat2cns/mecat_correction.cpp
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Expand Up @@ -27,18 +27,18 @@ struct CompareOverlapByOverlapSize
{
bool operator()(const Overlap& a ,const Overlap& b)
{
const index_t ovlp_a = std::max(a.qend - a.qoff, a.send - a.soff);
const index_t ovlp_b = std::max(b.qend - b.qoff, b.send - b.soff);
const idx_t ovlp_a = std::max(a.qend - a.qoff, a.send - a.soff);
const idx_t ovlp_b = std::max(b.qend - b.qoff, b.send - b.soff);
return ovlp_a > ovlp_b;
}
};

void
meap_add_one_aln(const std::string& qaln, const std::string& saln, index_t start_soff, CnsTableItem* cns_table, const char* org_seq)
meap_add_one_aln(const std::string& qaln, const std::string& saln, idx_t start_soff, CnsTableItem* cns_table, const char* org_seq)
{
r_assert(qaln.size() == saln.size());
const index_t aln_size = qaln.size();
index_t i = 0;
const idx_t aln_size = qaln.size();
idx_t i = 0;
const char kGap = '-';
while (i < aln_size)
{
Expand All @@ -51,7 +51,7 @@ meap_add_one_aln(const std::string& qaln, const std::string& saln, index_t start
else
{
r_assert(s == kGap);
index_t j = i + 1;
idx_t j = i + 1;
while (j < aln_size && saln[j] == kGap) ++j;
++cns_table[start_soff - 1].del_cnt;
i = j;
Expand Down Expand Up @@ -155,8 +155,8 @@ get_effective_ranges(std::vector<MappingRange>& mranges, std::vector<MappingRang
void
output_cns_result(std::vector<CnsResult>& cns_results,
CnsResult& cr,
const index_t beg,
const index_t end,
const idx_t beg,
const idx_t end,
std::string& cns_seq)
{
const size_t MaxSeqSize = 60000;
Expand Down Expand Up @@ -214,7 +214,7 @@ consensus_worker(CnsTableItem* cns_table,
const int read_id,
std::vector<CnsResult>& cns_results)
{
index_t beg = 0, end;
idx_t beg = 0, end;
CnsResult cns_result;
std::string cns_seq;
cns_result.id = read_id;
Expand Down Expand Up @@ -242,7 +242,7 @@ consensus_worker(CnsTableItem* cns_table,
}

void
consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid)
consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid)
{
PackedDB& reads = *ctd->reads;
ExtensionCandidate* overlaps = ctd->candidates;
Expand All @@ -251,7 +251,7 @@ consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const index_t read_id, co
M5Record* m5 = ctd->m5;
CnsAlns& cns_vec = ctd->cns_alns;
std::vector<CnsResult>& cns_results = ctd->cns_results;
const index_t read_size = overlaps[sid].ssize;
const idx_t read_size = overlaps[sid].ssize;
std::vector<char>& qstr = ctd->query;
std::vector<char>& tstr = ctd->target;
tstr.resize(read_size);
Expand All @@ -261,7 +261,7 @@ consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const index_t read_id, co
const int min_align_size = ctd->rco.min_align_size;
const int max_added = 60;

index_t L, R;
idx_t L, R;
if (eid - sid <= max_added)
{
L = sid;
Expand All @@ -277,13 +277,13 @@ consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const index_t read_id, co
CnsTableItem* cns_table = ctd->cns_table;
std::for_each(cns_table, cns_table + read_size, CnsTableItemCleaner());
cns_vec.clear();
for (index_t i = L; i < R; ++i)
for (idx_t i = L; i < R; ++i)
{
Overlap& ovlp = overlaps[i];
qstr.resize(ovlp.qsize);
reads.GetSequence(ovlp.qid, ovlp.qdir == FWD, qstr.data(), ovlp.qsize);
index_t qext = ovlp.qext;
index_t sext = ovlp.sext;
idx_t qext = ovlp.qext;
idx_t sext = ovlp.sext;
if (ovlp.qdir == REV) qext = ovlp.qsize - 1 - qext;
drd = drd_s;
bool r = GetAlignment(qstr.data(), qext, qstr.size(), tstr.data(), sext, tstr.size(), drd, *m5, 0.15, min_align_size);
Expand All @@ -303,7 +303,7 @@ consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const index_t read_id, co
}

void
consensus_one_read_m4_nanopore(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid)
consensus_one_read_m4_nanopore(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid)
{
PackedDB& reads = *ctd->reads;
ExtensionCandidate* overlaps = ctd->candidates;
Expand All @@ -312,7 +312,7 @@ consensus_one_read_m4_nanopore(ConsensusThreadData* ctd, const index_t read_id,
M5Record* m5 = ctd->m5;
CnsAlns& cns_vec = ctd->cns_alns;
std::vector<CnsResult>& cns_results = ctd->cns_results;
const index_t read_size = overlaps[sid].ssize;
const idx_t read_size = overlaps[sid].ssize;
std::vector<char>& qstr = ctd->query;
std::vector<char>& tstr = ctd->target;
tstr.resize(read_size);
Expand All @@ -322,7 +322,7 @@ consensus_one_read_m4_nanopore(ConsensusThreadData* ctd, const index_t read_id,
const int min_align_size = ctd->rco.min_align_size;
const double min_mapping_ratio = ctd->rco.min_mapping_ratio - 0.02;

index_t L, R;
idx_t L, R;
if (eid - sid <= MAX_CNS_OVLPS)
{
L = sid;
Expand All @@ -338,13 +338,13 @@ consensus_one_read_m4_nanopore(ConsensusThreadData* ctd, const index_t read_id,
CnsTableItem* cns_table = ctd->cns_table;
std::for_each(cns_table, cns_table + read_size, CnsTableItemCleaner());
cns_vec.clear();
for (index_t i = L; i < R; ++i)
for (idx_t i = L; i < R; ++i)
{
Overlap& ovlp = overlaps[i];
qstr.resize(ovlp.qsize);
reads.GetSequence(ovlp.qid, ovlp.qdir == FWD, qstr.data(), ovlp.qsize);
index_t qext = ovlp.qext;
index_t sext = ovlp.sext;
idx_t qext = ovlp.qext;
idx_t sext = ovlp.sext;
if (ovlp.qdir == REV) qext = ovlp.qsize - 1 - qext;
drd = drd_s;
bool r = GetAlignment(qstr.data(), qext, qstr.size(), tstr.data(), sext, tstr.size(), drd, *m5, 0.20, min_align_size);
Expand Down Expand Up @@ -389,7 +389,7 @@ check_cov_stats(u1_t* cov_stats, int soff, int send)
}

void
consensus_one_read_can_pacbio(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid)
consensus_one_read_can_pacbio(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid)
{
PackedDB& reads = *ctd->reads;
ExtensionCandidate* candidates = ctd->candidates;
Expand All @@ -398,7 +398,7 @@ consensus_one_read_can_pacbio(ConsensusThreadData* ctd, const index_t read_id, c
M5Record* m5 = ctd->m5;
CnsAlns& cns_vec = ctd->cns_alns;
std::vector<CnsResult>& cns_results = ctd->cns_results;
const index_t read_size = candidates[sid].ssize;
const idx_t read_size = candidates[sid].ssize;
std::vector<char>& qstr = ctd->query;
std::vector<char>& tstr = ctd->target;
tstr.resize(read_size);
Expand Down Expand Up @@ -427,8 +427,8 @@ consensus_one_read_can_pacbio(ConsensusThreadData* ctd, const index_t read_id, c
if (used_ids.find(ec.qid) != used_ids.end()) continue;
qstr.resize(ec.qsize);
reads.GetSequence(ec.qid, ec.qdir == FWD, qstr.data(), ec.qsize);
index_t qext = ec.qext;
index_t sext = ec.sext;
idx_t qext = ec.qext;
idx_t sext = ec.sext;
if (ec.qdir == REV) qext = ec.qsize - 1 - qext;
drd = drd_s;
bool r = GetAlignment(qstr.data(), qext, qstr.size(), tstr.data(), sext, tstr.size(), drd, *m5, 0.15, min_align_size);
Expand All @@ -453,7 +453,7 @@ consensus_one_read_can_pacbio(ConsensusThreadData* ctd, const index_t read_id, c
}

void
consensus_one_read_can_nanopore(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid)
consensus_one_read_can_nanopore(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid)
{
PackedDB& reads = *ctd->reads;
ExtensionCandidate* candidates = ctd->candidates;
Expand All @@ -462,7 +462,7 @@ consensus_one_read_can_nanopore(ConsensusThreadData* ctd, const index_t read_id,
M5Record* m5 = ctd->m5;
CnsAlns& cns_vec = ctd->cns_alns;
std::vector<CnsResult>& cns_results = ctd->cns_results;
const index_t read_size = candidates[sid].ssize;
const idx_t read_size = candidates[sid].ssize;
std::vector<char>& qstr = ctd->query;
std::vector<char>& tstr = ctd->target;
tstr.resize(read_size);
Expand Down Expand Up @@ -490,8 +490,8 @@ consensus_one_read_can_nanopore(ConsensusThreadData* ctd, const index_t read_id,
if (used_ids.find(ec.qid) != used_ids.end()) continue;
qstr.resize(ec.qsize);
reads.GetSequence(ec.qid, ec.qdir == FWD, qstr.data(), ec.qsize);
index_t qext = ec.qext;
index_t sext = ec.sext;
idx_t qext = ec.qext;
idx_t sext = ec.sext;
if (ec.qdir == REV) qext = ec.qsize - 1 - qext;
drd = drd_s;
bool r = GetAlignment(qstr.data(), qext, qstr.size(), tstr.data(), sext, tstr.size(), drd, *m5, 0.20, min_align_size);
Expand Down
8 changes: 4 additions & 4 deletions src/mecat2cns/mecat_correction.h
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Expand Up @@ -6,16 +6,16 @@
namespace ns_meap_cns {

void
consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid);
consensus_one_read_m4_pacbio(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid);

void
consensus_one_read_m4_nanopore(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid);
consensus_one_read_m4_nanopore(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid);

void
consensus_one_read_can_pacbio(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid);
consensus_one_read_can_pacbio(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid);

void
consensus_one_read_can_nanopore(ConsensusThreadData* ctd, const index_t read_id, const index_t sid, const index_t eid);
consensus_one_read_can_nanopore(ConsensusThreadData* ctd, const idx_t read_id, const idx_t sid, const idx_t eid);

} // namespace ns_meap_cns

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4 changes: 2 additions & 2 deletions src/mecat2cns/options.cpp
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Expand Up @@ -9,7 +9,7 @@ using namespace std;

static int input_type_pacbio = 1;
static int num_threads_pacbio = 1;
static index_t batch_size_pacbio = 100000;
static idx_t batch_size_pacbio = 100000;
static double mapping_ratio_pacbio = 0.9;
static int align_size_pacbio = 2000;
static int cov_pacbio = 6;
Expand All @@ -19,7 +19,7 @@ static int tech_pacbio = TECH_PACBIO;

static int input_type_nanopore = 1;
static int num_threads_nanopore = 1;
static index_t batch_size_nanopore = 100000;
static idx_t batch_size_nanopore = 100000;
static double mapping_ratio_nanopore = 0.4;
static int align_size_nanopore = 400;
static int cov_nanopore = 6;
Expand Down
4 changes: 2 additions & 2 deletions src/mecat2cns/options.h
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Expand Up @@ -13,11 +13,11 @@ struct ConsensusOptions
const char* reads;
const char* corrected_reads;
int num_threads;
index_t batch_size;
idx_t batch_size;
double min_mapping_ratio;
int min_align_size;
int min_cov;
index_t min_size;
idx_t min_size;
bool print_usage_info;
int tech;
};
Expand Down
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