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improved N50

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chhylp123
2020-01-14 10:46:35 -05:00
parent 387c64c5fc
commit c63ce670f7
4 changed files with 733 additions and 86 deletions
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1
CommandLines.cpp
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@@ -46,6 +46,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
void init_opt(hifiasm_opt_t* asm_opt)
{
asm_opt->coverage = -1;
asm_opt->num_reads = 0;
asm_opt->read_file_names = NULL;
asm_opt->output_file_name = (char*)(DEFAULT_OUTPUT);

1
CommandLines.h
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@@ -36,6 +36,7 @@ typedef struct {
long long num_bases;
long long num_corrected_bases;
long long num_recorrected_bases;
long long coverage;
} hifiasm_opt_t;
extern hifiasm_opt_t asm_opt;

808
Overlaps.cpp
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File diff suppressed because it is too large Load Diff

9
Overlaps.h
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@@ -102,6 +102,8 @@ typedef struct {
uint32_t m_arc, n_arc:31, is_srt:1;
asg_arc_t *arc;
uint32_t m_seq, n_seq:31, is_symm:1;
uint32_t r_seq;
asg_seq_t *seq;
uint64_t *idx;
@@ -304,6 +306,13 @@ typedef struct {
kvec_t(uint32_t) e; // visited edges/arcs
} buf_t;
typedef struct {
kvec_t(uint64_t) Nodes;
kvec_t(uint64_t) Edges;
uint32_t pre_n_seq, seqID;
} C_graph;
// count the number of outgoing arcs, including reduced arcs
static inline int count_out_with_del(const asg_t *g, uint32_t v)
{