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update for 0.2.0

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This commit is contained in:
chhylp123
2020-02-07 14:52:14 -05:00
parent 6edf54048c
commit 6246132702
7 changed files with 6126 additions and 686 deletions
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Overlaps.h
+77 -5
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@@ -17,7 +17,12 @@
///#define MAX_BUBBLE_DIST 10000000
#define SMALL_BUBBLE_SIZE (uint32_t)-1
//#define SMALL_BUBBLE_SIZE 1000
#define PRIMARY_LABLE 0
#define ALTER_LABLE 1
#define HAP_LABLE 2
// #define PRIMARY_LABLE 1
// #define ALTER_LABLE 2
// #define HAP_LABLE 4
#define Get_qn(RECORD) ((uint32_t)((RECORD).qns>>32))
#define Get_qs(RECORD) ((uint32_t)((RECORD).qns))
@@ -36,6 +41,8 @@
#define LOOP 7
///query is the read itself
typedef struct {
uint64_t qns;
@@ -46,7 +53,6 @@ typedef struct {
uint8_t no_l_indel;
} ma_hit_t;
typedef struct {
ma_hit_t* buffer;
uint32_t size;
@@ -241,7 +247,7 @@ static inline void asg_seq_del(asg_t *g, uint32_t s)
static inline void asg_seq_drop(asg_t *g, uint32_t s)
{
///s is not at primary
if(g->seq[s].c)
if(g->seq[s].c == ALTER_LABLE)
{
uint32_t k;
for (k = 0; k < 2; ++k)
@@ -254,8 +260,10 @@ static inline void asg_seq_drop(asg_t *g, uint32_t s)
{
if(av[i].del) continue;
///if output node is at primary
if(g->seq[(av[i].v>>1)].c == 0)
{
/****************************may have hap bugs********************************/
///if(g->seq[(av[i].v>>1)].c == PRIMARY_LABLE)
if(g->seq[(av[i].v>>1)].c == PRIMARY_LABLE || g->seq[(av[i].v>>1)].c == HAP_LABLE)
{/****************************may have hap bugs********************************/
av[i].del = 1;
asg_arc_del(g, av[i].v^1, v^1, 1);
}
@@ -313,6 +321,36 @@ typedef struct {
uint32_t pre_n_seq, seqID;
} C_graph;
typedef struct {
kvec_t(uint32_t) a;
uint32_t i;
} kvec_t_u32_warp;
typedef struct {
kvec_t(uint64_t) a;
uint64_t i;
} kvec_t_u64_warp;
typedef struct {
uint32_t q_pos;
uint32_t t_pos;
uint32_t t_id;
uint32_t is_color;
} Hap_Align;
typedef struct {
kvec_t(Hap_Align) x;
uint64_t i;
} Hap_Align_warp;
typedef struct {
buf_t* b_0;
uint32_t untigI;
uint32_t readI;
uint32_t offset;
} rIdContig;
// count the number of outgoing arcs, including reduced arcs
static inline int count_out_with_del(const asg_t *g, uint32_t v)
{
@@ -350,4 +388,38 @@ void remove_overlaps(ma_hit_t_alloc* source_paf, uint64_t* source_index, long lo
void add_overlaps_from_different_sources(ma_hit_t_alloc* source_paf_list, ma_hit_t_alloc* dest_paf,
uint64_t* source_index, long long listLen);
void print_revise_edges(ma_hit_t_alloc* source_paf, uint64_t* source_index, long long listLen);
#define EvaluateLen(U, id) ((U).a[(id)].start)
#define IsMerge(U, id) ((U).a[(id)].end)
#define kv_reuse(v, rn, rm, r) ((v).n = (rn), (v).m = (rm), (v).a = (r))
#define long_tip(U, id, threshold) ((EvaluateLen((U), (id))>=(threshold))&&(!((U).a[(id)].circ)))
///there are threee cases:
///1. if this untig is too long (>maxShortUntig), it must be not short untig/must be a long untig
///2. if this untig is long (>minLongUntig && EvaluateLen(ug->u, av[i].v>>1) > (EvaluateLen(ug->u, v>>1)*l_untig_rate)), it might be a long tip
#define check_long_tip(U, id, minLongUntig, maxShortUntig, ShortUntigRate, mainLen) \
((!((U).a[(id)].circ)) \
&& \
((EvaluateLen((U), (id)) > (maxShortUntig))\
||\
((long_tip((U), (id), (minLongUntig)))\
&&\
(EvaluateLen((U), (id)) > (ShortUntigRate)*(mainLen)))))
#define Get_vis(visit, v, d) (((visit)[(v)>>1])&(((((v)<<(d))&1)+1)))
#define Set_vis(visit, v, d) (((visit)[(v)>>1])|=(((((v)<<(d))&1)+1)))
typedef struct {
uint64_t len;
uint32_t* index;
} R_to_U;
void init_R_to_U(R_to_U* x, uint64_t len);
void destory_R_to_U(R_to_U* x);
void set_R_to_U(R_to_U* x, uint32_t rID, uint32_t uID, uint32_t is_Unitig);
void get_R_to_U(R_to_U* x, uint32_t rID, uint32_t* uID, uint32_t* is_Unitig);
void transfor_R_to_U(R_to_U* x);
#endif