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structural_variation.c
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#include "valorconfig.h"
#include "structural_variation.h"
#include <stdio.h>
#include "progress.h"
#include "sonic/sonic.h"
#include "cnv.h"
void sv_fprint(FILE *stream, int chr, sv_t *t){
fprintf(stream,"%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%s\n",
chr,
t->AB.start1,
t->AB.end1,
t->AB.start2,
t->AB.end2,
t->CD.start1,
t->CD.end1,
t->CD.start2,
t->CD.end2,
t->supports[0],
t->supports[1],
sv_type_name(t->type));
}
int _svcmp(const void *v1, const void *v2, size_t size){
const sv_t *s1 = v1;
const sv_t *s2 = v2;
if(s1->AB.start1 != s2->AB.start2){
return s1->AB.start1 - s2->AB.start1;
}
if(s1->AB.end1 != s2->AB.end1){
return s1->AB.end1 - s2->AB.end1;
}
if(s1->AB.start2 != s2->AB.start2){
return s1->AB.start2 - s2->AB.start2;
}
if(s1->AB.end2 != s2->AB.end2){
return s1->AB.end2 - s2->AB.end2;
}
if(s1->CD.start1 != s2->CD.start2){
return s1->CD.start1 - s2->CD.start1;
}
if(s1->CD.end1 != s2->CD.end1){
return s1->CD.end1 - s2->CD.end1;
}
if(s1->CD.start2 != s2->CD.start2){
return s1->CD.start2 - s2->CD.start2;
}
if(s1->CD.end2 != s2->CD.end2){
return s1->CD.end2 - s2->CD.end2;
}
return 0;
}
int sv_compd(const void *v1, const void *v2, size_t val){
return sv_comp(v1,v2);
}
int sv_comp(const void *v1, const void *v2){
sv_t *s1 = *(void **)v1;
sv_t *s2 = *(void **)v2;
if(s1->AB.start1 != s2->AB.start2){
return s1->AB.start1 - s2->AB.start1;
}
if(s1->AB.end1 != s2->AB.end1){
return s1->AB.end1 - s2->AB.end1;
}
if(s1->AB.start2 != s2->AB.start2){
return s1->AB.start2 - s2->AB.start2;
}
if(s1->AB.end2 != s2->AB.end2){
return s1->AB.end2 - s2->AB.end2;
}
if(s1->CD.start1 != s2->CD.start2){
return s1->CD.start1 - s2->CD.start1;
}
if(s1->CD.end1 != s2->CD.end1){
return s1->CD.end1 - s2->CD.end1;
}
if(s1->CD.start2 != s2->CD.start2){
return s1->CD.start2 - s2->CD.start2;
}
if(s1->CD.end2 != s2->CD.end2){
return s1->CD.end2 - s2->CD.end2;
}
return 0;
}
//TODO consider barcode
int sv_equals(const void *i1, const void *i2){
const sv_t *ii1 = i1;
const sv_t *ii2 = i2;
return !(ii1->AB.start1 == ii2->AB.start1 &&
ii1->AB.start2 == ii2->AB.start2 &&
ii1->AB.end1 == ii2->AB.end1 &&
ii1->AB.end2 == ii2->AB.end2 &&
ii1->CD.start1 == ii2->CD.start1 &&
ii1->CD.start2 == ii2->CD.start2 &&
ii1->CD.end1 == ii2->CD.end1 &&
ii1->CD.end2 == ii2->CD.end2 &&
ii1->AB.barcode == ii2->AB.barcode &&
ii1->CD.barcode == ii2->CD.barcode &&
ii1->type == ii2->type);
// return memcmp(&(ii1->AB),&(ii2->AB),sizeof(splitmolecule_t)) &&
// memcmp(&(ii1->CD),&(ii2->CD),sizeof(splitmolecule_t));
}
void sv_g_dfs_step(graph_t *g, vector_t *comp, sv_t *sv){
sv->covered = 1;
vector_put(comp,sv);
vector_t *edges = graph_get_edges(g,sv);
int i;
for(i=0;i<edges->size;i++){
sv_t **val = vector_get(edges,i);
if(!(*val)->covered){
sv_g_dfs_step(g,comp,*val);
}
}
}
vector_t *sv_g_dfs_components(graph_t *g){
adjlist_t *al = graph_to_al(g);
vector_t *comps = vector_init(sizeof(vector_t),16);
comps->rmv = &vector_free;
int i;
for(i=0;i<al->size;i++){
sv_t *sv = al_get_value(al,i);
if( !sv->covered){
vector_t *comp = vector_init(sizeof(sv_t),40);
comp->rmv = &sv_destroy;
sv_g_dfs_step(g,comp,sv);
vector_soft_put(comps,comp);
}
}
vector_free(al);
return comps;
}
#define BIG_PRIME 1300501
size_t sv_hf(hashtable_t *table, const void *vsv){
const sv_t *sv = vsv;
size_t hash = 0;
hash+=sv->AB.barcode;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->CD.barcode;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->AB.start1;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->AB.start2;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->AB.end1;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->AB.end2;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->CD.start1;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->CD.start2;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->CD.end1;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->CD.end2;
hash*=BIG_PRIME;
hash= hash % table->size;
hash+=sv->type;
hash*=BIG_PRIME;
hash= hash % table->size;
return hash;
//return SuperFastHash((vsv),2*sizeof(splitmolecule_t)) % table->size;
}
int splitmolecule_indicates_inverted_duplication(splitmolecule_t s1, splitmolecule_t s2){
if( !(s1.start1 < s2.start1 &&
s1.end1 < s2.end1 &&
s1.start2 > s2.start2 &&
s1.end2 > s2.end2)){
return 0;
}
interval_10X A = (interval_10X){s1.start1,s1.end1,s1.barcode};
interval_10X B = (interval_10X){s1.start2,s1.end2,s1.barcode};
interval_10X C = (interval_10X){s2.start1,s2.end1,s2.barcode};
interval_10X D = (interval_10X){s2.start2,s2.end2,s2.barcode};
if(interval_inner_distance(A,C) < DUP_GAP &&
interval_inner_distance(A,C) > DUP_OVERLAP &&
interval_outer_distance(B,D) < DUP_MAX_SIZE &&
interval_outer_distance(B,D) > DUP_MIN_SIZE){
return DUP_BACK_COPY;
}
else if(interval_inner_distance(B,D) < DUP_GAP &&
interval_inner_distance(B,D) > DUP_OVERLAP &&
interval_outer_distance(A,C) < DUP_MAX_SIZE &&
interval_outer_distance(A,C) > DUP_MIN_SIZE){
return DUP_FORW_COPY;
}
return 0;
}
//TODO Sanity Check
int splitmolecule_indicates_duplication(splitmolecule_t s1, splitmolecule_t s2){
if( !(s1.start1 < s2.start1 &&
s1.end1 < s2.end1 &&
s1.start2 < s2.start2 &&
s1.end2 < s2.end2)){
return 0;
}
interval_10X A = (interval_10X){s1.start1,s1.end1,s1.barcode};
interval_10X B = (interval_10X){s1.start2,s1.end2,s1.barcode};
interval_10X C = (interval_10X){s2.start1,s2.end1,s2.barcode};
interval_10X D = (interval_10X){s2.start2,s2.end2,s2.barcode};
if(interval_inner_distance(A,C) < DUP_GAP &&
interval_inner_distance(A,C) > DUP_OVERLAP &&
interval_outer_distance(B,D) < DUP_MAX_SIZE &&
interval_outer_distance(B,D) > DUP_MIN_SIZE){
return DUP_BACK_COPY;
}
else if(interval_inner_distance(B,D) < DUP_GAP &&
interval_inner_distance(B,D) > DUP_OVERLAP &&
interval_outer_distance(A,C) < DUP_MAX_SIZE &&
interval_outer_distance(A,C) > DUP_MIN_SIZE){
return DUP_FORW_COPY;
}
return 0;
}
//TODO make sure different barcode
int splitmolecule_indicates_inversion(splitmolecule_t s1, splitmolecule_t s2){
if( abs(s2.end2-s1.start1)> INV_MAX_SIZE){ return 0;}
return s1.start1 < s2.start1 &&
s1.end1 < s2.end1 &&
s1.start2 < s2.start2 &&
s1.end2 < s2.end2 &&
i_distance(s2.start1,s1.start1,s2.end1,s1.end1) > INV_OVERLAP &&
i_distance(s2.start2,s1.start2,s2.end2,s1.end2) > INV_OVERLAP &&
i_distance(s2.start1,s1.start1,s2.end1,s1.end1) < INV_GAP &&
i_distance(s2.start2,s1.start2,s2.end2,s1.end2) < INV_GAP;
}
int splitmolecule_indicates_sv(splitmolecule_t *s1, splitmolecule_t *s2, sv_type type){
switch(type){
case SV_INVERSION:
return splitmolecule_indicates_inversion(*s1,*s2);
case SV_DIRECT_DUPLICATION:
return splitmolecule_indicates_duplication(*s1,*s2);
case SV_INVERTED_DUPLICATION:
return splitmolecule_indicates_inverted_duplication(*s1,*s2);
case SV_TRANSLOCATION:
return splitmolecule_indicates_duplication(*s1,*s2);
case SV_INVERTED_TRANSLOCATION:
return splitmolecule_indicates_inverted_duplication(*s1,*s2);
default:
fprintf(stderr,"Unknown SV type ordinal %d\n",type);
VALOR_LOG("Unknown SV type ordinal %d\n",type);
exit(-1);
}
return 0;
}
void sv_reset(sv_t *sv){
sv->covered = 0;
sv->tabu = 0;
sv->dv = 0;
sv->inactive = 0;
}
sv_t *sv_init(splitmolecule_t *sc1,splitmolecule_t *sc2,sv_type type){
sv_t *new_i = getMem(sizeof(sv_t));
memset(new_i,0,sizeof(sv_t));
new_i->supports[0] = 1;//TODO fix this
new_i->supports[1] = 1;//TODO fix this
new_i->covered = 0;
new_i->tabu = 0;
new_i->dv = 0;
new_i->inactive = 0;
new_i->AB=*sc1;
if(sc2!=NULL){//for sv's with 1 split molecule
new_i->CD=*sc2;
}
else{
new_i->CD=(splitmolecule_t){0,0,0,0,0L};
}
new_i->type=type;
return new_i;
}
void sv_destroy(void *sv){
freeMem(sv,sizeof(sv_t));
}
int inversion_overlaps(sv_t *i1, sv_t *i2){
return interval_pair_overlaps(
&(splitmolecule_t){
MIN(i1->AB.end1,i1->CD.start1),MAX(i1->AB.end1,i1->CD.start1),
MIN(i1->AB.end2,i1->CD.start2),MAX(i1->AB.end2,i1->CD.start2)
},
&(splitmolecule_t){
MIN(i2->AB.end1,i2->CD.start1),MAX(i2->AB.end1,i2->CD.start1),
MIN(i2->AB.end2,i2->CD.start2),MAX(i2->AB.end2,i2->CD.start2)
},CLONE_MEAN);
}
//TODO change this if it needs change
int duplication_overlaps(sv_t *i1, sv_t *i2){
return interval_pair_overlaps(
&(splitmolecule_t){
MIN(i1->AB.end1,i1->CD.start1),MAX(i1->AB.end1,i1->CD.start1),
MIN(i1->AB.end2,i1->CD.start2),MAX(i1->AB.end2,i1->CD.start2)
},
&(splitmolecule_t){
MIN(i2->AB.end1,i2->CD.start1),MAX(i2->AB.end1,i2->CD.start1),
MIN(i2->AB.end2,i2->CD.start2),MAX(i2->AB.end2,i2->CD.start2)
},CLONE_MEAN);
}
int tandem_duplication_overlaps(sv_t *i1, sv_t *i2){
return interval_pair_overlaps(
&(i1->AB),&(i2->AB)
,CLONE_MEAN);
}
int deletion_overlaps(sv_t *i1, sv_t *i2){
return interval_pair_overlaps(
&(i1->AB),&(i2->AB)
,CLONE_MEAN);
}
int sv_overlaps(sv_t *i1, sv_t *i2){
if(i1->type!=i2->type){ return 0;}
switch(i1->type){
case SV_INVERSION:
return inversion_overlaps(i1,i2);
case SV_DIRECT_DUPLICATION:
return duplication_overlaps(i1,i2);
case SV_INVERTED_DUPLICATION:
return duplication_overlaps(i1,i2);
case SV_TANDEM_DUPLICATION:
return tandem_duplication_overlaps(i1,i2);
case SV_TRANSLOCATION:
return duplication_overlaps(i1,i2);
case SV_INVERTED_TRANSLOCATION:
return duplication_overlaps(i1,i2);
case SV_DELETION:
return deletion_overlaps(i1,i2);
default:
fprintf(stderr,"Unknown SV type ordinal %d\n",i1->type);
VALOR_LOG("Unknown SV type ordinal %d\n",i1->type);
exit(-1);
}
return 0;
}
#define MAGIC_NODE_MARKER -126
/*
*
* This removes every element in the `items` from `g`
* Nodes in the `items` shouldn't have any edges outside of the `component`
*
* Achtung:
* sv->dv shouldn't be -126. Make sure it is not -126 outside of this function
* Make sure `g`->hf does not use sv->dv
* Make sure `g`->key_cmp does not use sv->dv
* (default is memcmp(a,b,sizeof(sv_t)), so Make sure it is changed)
*/
int g_remove_all(graph_t *g, vector_t *component,vector_t *items){
int i,j;
for(i=0;i<items->size;i++){
void *item = vector_get(items,i);
// graph_remove_node(g,item,G_REMOVE_SOFT);
sv_t *sv = ht_get(g,item)->key;
sv->dv = MAGIC_NODE_MARKER; //Hax
}
for(i=0;i<component->size;i++){
vector_t *edges = graph_get_edges(g,vector_get(component,i));
if(edges==NULL){continue;}
edges->REMOVE_POLICY = REMP_LAZY;
for(j=0;j<edges->size;j++){
sv_t **ptr = vector_get(edges,j);
if((*ptr)->dv==MAGIC_NODE_MARKER){
vector_remove(edges,j);
}
}
vector_defragment(edges);
edges->REMOVE_POLICY = REMP_FAST;
}
for(i=0;i<items->size;i++){
void *item = vector_get(items,i);
graph_remove_node(g,item,G_REMOVE_SOFT);
}
component->REMOVE_POLICY = REMP_LAZY;
for(i=0;i<component->size;i++){
void *ptr = vector_get(component,i);
if(!graph_have_node(g,ptr)){
vector_remove(component,i);
}
}
vector_defragment(component);
component->REMOVE_POLICY = REMP_SORTED;
return 0;
}
void sv_graph_reset(graph_t *g){
int i,j;
for(i=0;i<g->size;i++){
for(j=0;j<g->buckets[i]->size;j++){
pair_t *pair = vector_get(g->buckets[i],j);
sv_reset(pair->key);
}
}
}
graph_t *make_sv_graph(vector_t *svs){
graph_t *g = graph_init(svs->size * 2, sizeof(sv_t));
g->hf = &sv_hf;
g->key_cmp = &_svcmp;
int i,j;
for(i=0;i<svs->size;i++){
graph_put_node(g,vector_get(svs,i));
}
for(i=0;i<svs->size;i++){
sv_t *a = vector_get(svs,i);
for(j=i+1;j<svs->size;j++){
sv_t *b = vector_get(svs,j);
if(sv_overlaps(a,b)){
graph_put_edge(g,a,b);
graph_put_edge(g,b,a);
}
}
}
return g;
}
#define SV_INIT_LIMIT 10000
vector_t *find_svs(vector_t *split_molecules, sv_type type, int chr){
int i,j,k;
vector_t *svs;
int num_threads = 1;
#ifdef _OPENMP
num_threads = omp_get_num_threads();
#endif
if(num_threads == 1){
svs = vector_init(sizeof(sv_t),SV_INIT_LIMIT);
splitmolecule_t *AB;
splitmolecule_t *CD;
for(i=0;i<split_molecules->size;i++){
AB = vector_get(split_molecules,i);
if(type&SV_DELETION){
sv_t *tmp = sv_init(AB,NULL,SV_DELETION);
tmp->chr = chr;
vector_soft_put(svs,tmp);
}
if(type&SV_TANDEM_DUPLICATION){
sv_t *tmp = sv_init(AB,NULL,SV_TANDEM_DUPLICATION);
tmp->chr = chr;
vector_soft_put(svs,tmp);
}
if(!(type & ( SV_INVERSION | SV_DIRECT_DUPLICATION | SV_INVERTED_DUPLICATION | SV_TRANSLOCATION | SV_INVERTED_TRANSLOCATION))){ continue;}
for(j=0;j<split_molecules->size;j++){
if(i==j){continue;}
CD = vector_get(split_molecules,j);
for(k=SV_INVERSION;k<SV_MAX_ID;k=k<<1){
if((k&type)==0){ continue;}
char orient = splitmolecule_indicates_sv(AB,CD,k);
if(orient){
sv_t *tmp = sv_init(AB,CD,k);
tmp->orientation = orient;
tmp->chr = chr;
vector_soft_put(svs,tmp);
}
}
}
}
}
else{
vector_t **osvs = malloc(sizeof(vector_t *) * num_threads);
for(i=0;i < num_threads;i++){
osvs[i]=vector_init(sizeof(sv_t),SV_INIT_LIMIT);
}
#pragma omp parallel for
for(i=0;i<split_molecules->size;i++){
splitmolecule_t *AB = vector_get(split_molecules,i);
if(type & SV_DELETION){
sv_t *tmp = sv_init(AB,NULL,SV_DELETION);
tmp->chr = chr;
vector_soft_put(osvs[omp_get_thread_num()],tmp);
}
if(type&SV_TANDEM_DUPLICATION){
sv_t *tmp = sv_init(AB,NULL,SV_TANDEM_DUPLICATION);
tmp->chr = chr;
vector_soft_put(osvs[omp_get_thread_num()],tmp);
}
if(!(type & ( SV_INVERSION | SV_DIRECT_DUPLICATION | SV_INVERTED_DUPLICATION| SV_TRANSLOCATION | SV_INVERTED_TRANSLOCATION))){ continue;}
for(j=0;j<split_molecules->size;j++){
if(i==j){continue;}
splitmolecule_t *CD = vector_get(split_molecules,j);
for(k=SV_INVERSION;k<SV_MAX_ID;k=k<<1){
if((k&type)==0){ continue;}
char orient = splitmolecule_indicates_sv(AB,CD,type);
if(orient){
sv_t *tmp = sv_init(AB,CD,type);
tmp->orientation = orient;
tmp->chr = chr;
vector_soft_put(osvs[omp_get_thread_num()],tmp);
}
}
}
}
size_t vsize = 0;
for(i=0;i<num_threads;i++){
vsize+=osvs[i]->size;
}
svs = vector_init(sizeof(sv_t),vsize);
for(i=0;i<num_threads;i++){
for(j=0;j<osvs[i]->size;j++){
vector_soft_put(svs,vector_get(osvs[i],j));
}
vector_tabularasa(osvs[i]);
vector_free(osvs[i]);
}
free(osvs);
}
return svs;
}
size_t scl_binary_searchdup(vector_t *intervals, splitmolecule_t *key){
if(intervals->size == 0){return -1;}
long first, last;
long mid = 0;
first =0;
last = intervals->size - 1;
int counter = 0;
while( first < last){
mid = (first + last)/2;
if(IDIS_VECTOR_GET(intervals,mid)->end1 < key->start1){
first = mid + 1;
}
else{
last = mid - 1;
}
counter ++;
}
return mid;
}
void update_tandem_duplication_supports_b(sv_t *dup, vector_t *mp_reads){
int j;
int mp_support = 0;
int midAB = scl_binary_search(mp_reads,&(dup->AB));
for(j=midAB;j<mp_reads->size;j++){
if(interval_pair_overlaps(&(dup->AB),vector_get(mp_reads,j),MAX_FRAG_SIZE)){
mp_support++;
}
if(dup->AB.end1 < IDIS_VECTOR_GET(mp_reads,j)->start1){
break;
}
if(mp_support > MAX_SUPPORT){ break;}
}
dup->supports[1] = mp_support;
dup->supports[0] = mp_support;
}
void update_deletion_supports_b(sv_t *del, vector_t *pm_reads){
int j;
int pm_support;
int midAB;
pm_support = 0;
midAB = scl_binary_search(pm_reads,&(del->AB));
for(j=midAB;j<pm_reads->size;j++){
if(interval_pair_overlaps(&(del->AB),vector_get(pm_reads,j),MAX_FRAG_SIZE)){//CLONE_MEAN)){
pm_support++;
}
if(del->AB.end1 < IDIS_VECTOR_GET(pm_reads,j)->start1){
break;
}
if(pm_support > MAX_SUPPORT){ break;}
}
del->supports[1] = pm_support;
del->supports[0] = pm_support;
}
void update_deletion_supports(vector_t *dels, vector_t *pm_reads){
int i,j;
int pm_support;
int midAB;
qsort(pm_reads->items,pm_reads->size,sizeof(interval_discordant *),interval_pair_comp);
for(i=0;i<dels->size;i++){
pm_support = 0;
midAB = scl_binary_search(pm_reads,&(SV_VECTOR_GET(dels,i)->AB));
for(j=midAB;j<pm_reads->size;j++){
if(interval_pair_overlaps(&(SV_VECTOR_GET(dels,i)->AB),vector_get(pm_reads,j),CLONE_MEAN)){
pm_support++;
}
if(SV_VECTOR_GET(dels,i)->AB.end1 < IDIS_VECTOR_GET(pm_reads,j)->start1){
break;
}
if(pm_support > MAX_SUPPORT){ break;}
}
SV_VECTOR_GET(dels,i)->supports[1] = pm_support;
SV_VECTOR_GET(dels,i)->supports[0] = pm_support;
}
}
void update_duplication_supports_b(sv_t *dup, vector_t *pm_reads, vector_t *mp_reads){
int j;
int pm_support;
int mp_support;
int midAB;
int midCD;
pm_support = 0;
mp_support = 0;
if(dup->orientation == DUP_FORW_COPY){
midAB = scl_binary_search(pm_reads,&(dup->CD));
midCD = scl_binary_search(mp_reads,&(dup->AB));
for(j=midAB;j<pm_reads->size;j++){
// printf("midAB: %d, j %d",midAB,j);
if(interval_pair_overlaps(&(dup->CD),vector_get(pm_reads,j),CLONE_MEAN)){
pm_support++;
}
// printf("\n");
if(dup->CD.end1 < IDIS_VECTOR_GET(pm_reads,j)->start1){
break;
}
if(pm_support > MAX_SUPPORT){ break;}
}
for(j=midCD;j<mp_reads->size;j++){
if(interval_pair_overlaps(&(dup->AB),vector_get(mp_reads,j),CLONE_MEAN)){
mp_support++;
}
if(dup->AB.end1 < IDIS_VECTOR_GET(mp_reads,j)->start1){
break;
}
if(mp_support > MAX_SUPPORT){ break;}
}
}
else if(dup->orientation == DUP_BACK_COPY){
midAB = scl_binary_search(pm_reads,&(dup->AB));
midCD = scl_binary_search(mp_reads,&(dup->CD));
for(j=midAB;j<pm_reads->size;j++){
if(interval_pair_overlaps(&(dup->AB),vector_get(pm_reads,j),CLONE_MEAN)){
pm_support++;
}
if(dup->AB.end1 < IDIS_VECTOR_GET(pm_reads,j)->start1){
break;
}
if(pm_support > MAX_SUPPORT){ break;}
}
for(j=midCD;j<mp_reads->size;j++){
if(interval_pair_overlaps(&(dup->CD),vector_get(mp_reads,j),CLONE_MEAN)){
mp_support++;
}
if(dup->CD.end1 < IDIS_VECTOR_GET(mp_reads,j)->start1){
break;
}
if(mp_support > MAX_SUPPORT){ break;}
}
}
dup->supports[0] = mp_support;
dup->supports[1] = pm_support;
}
void update_duplication_supports(vector_t *dups, vector_t *pm_reads, vector_t *mp_reads){
int i,j;
int pm_support;
int mp_support;
int midAB;
int midCD;
qsort(pm_reads->items,pm_reads->size,sizeof(interval_discordant *),interval_pair_comp);
qsort(mp_reads->items,mp_reads->size,sizeof(interval_discordant *),interval_pair_comp);
for(i=0;i<dups->size;i++){
pm_support = 0;
mp_support = 0;
if(SV_VECTOR_GET(dups,i)->orientation == DUP_FORW_COPY){
midAB = scl_binary_search(pm_reads,&(SV_VECTOR_GET(dups,i)->CD));
midCD = scl_binary_search(mp_reads,&(SV_VECTOR_GET(dups,i)->AB));
for(j=midAB;j<pm_reads->size;j++){
// printf("midAB: %d, j %d",midAB,j);
if(interval_pair_overlaps(&(SV_VECTOR_GET(dups,i)->CD),vector_get(pm_reads,j),MAX_FRAG_SIZE)){
pm_support++;
}
// printf("\n");
if(SV_VECTOR_GET(dups,i)->CD.end1 < IDIS_VECTOR_GET(pm_reads,j)->start1){
break;
}
if(pm_support > MAX_SUPPORT){ break;}
}
for(j=midCD;j<mp_reads->size;j++){
if(interval_pair_overlaps(&(SV_VECTOR_GET(dups,i)->AB),vector_get(mp_reads,j),MAX_FRAG_SIZE)){
mp_support++;
}
if(SV_VECTOR_GET(dups,i)->AB.end1 < IDIS_VECTOR_GET(mp_reads,j)->start1){
break;
}
if(mp_support > MAX_SUPPORT){ break;}
}
}
else if(SV_VECTOR_GET(dups,i)->orientation == DUP_BACK_COPY){
midAB = scl_binary_search(pm_reads,&(SV_VECTOR_GET(dups,i)->AB));
midCD = scl_binary_search(mp_reads,&(SV_VECTOR_GET(dups,i)->CD));
for(j=midAB;j<pm_reads->size;j++){
if(interval_pair_overlaps(&(SV_VECTOR_GET(dups,i)->AB),vector_get(pm_reads,j),MAX_FRAG_SIZE)){
pm_support++;
}
if(SV_VECTOR_GET(dups,i)->AB.end1 < IDIS_VECTOR_GET(pm_reads,j)->start1){
break;
}
if(pm_support > MAX_SUPPORT){ break;}
}
for(j=midCD;j<mp_reads->size;j++){
if(interval_pair_overlaps(&(SV_VECTOR_GET(dups,i)->CD),vector_get(mp_reads,j),MAX_FRAG_SIZE)){
mp_support++;
}
if(SV_VECTOR_GET(dups,i)->CD.end1 < IDIS_VECTOR_GET(mp_reads,j)->start1){
break;
}
if(mp_support > MAX_SUPPORT){ break;}
}
}
SV_VECTOR_GET(dups,i)->supports[0] = mp_support;
SV_VECTOR_GET(dups,i)->supports[1] = pm_support;
}
}
void update_inversion_supports_b(sv_t *inv, vector_t *pp_reads, vector_t *mm_reads){
int j;
int pp_support;
int mm_support;
int midAB;
int midCD;
pp_support = 0;
mm_support = 0;
midAB = scl_binary_search(pp_reads,&(inv->AB));
midCD = scl_binary_search(mm_reads,&(inv->CD));
for(j=midAB;j<pp_reads->size;j++){
if(interval_pair_overlaps(&(inv->AB),vector_get(pp_reads,j),CLONE_MEAN/2)){
pp_support++;
}
if(inv->AB.end1 < IDIS_VECTOR_GET(pp_reads,j)->start1){
break;
}
if(pp_support > MAX_SUPPORT){ break;}
}
for(j=midCD;j<mm_reads->size;j++){
if(interval_pair_overlaps(&(inv->CD),vector_get(mm_reads,j),CLONE_MEAN/2)){
mm_support++;
}
if(inv->CD.end1 < IDIS_VECTOR_GET(mm_reads,j)->start1){
break;
}
if(mm_support > MAX_SUPPORT){ break;}
}
inv->supports[0] = pp_support;
inv->supports[1] = mm_support;
}
void update_inversion_supports(vector_t *inversions, vector_t *pp_reads, vector_t *mm_reads){
int i,j;
int pp_support;
int mm_support;
int midAB;
int midCD;
qsort(pp_reads->items,pp_reads->size,sizeof(interval_discordant *),interval_pair_comp);
qsort(mm_reads->items,mm_reads->size,sizeof(interval_discordant *),interval_pair_comp);
for(i=0;i<inversions->size;i++){
pp_support = 0;
mm_support = 0;
midAB = scl_binary_search(pp_reads,&(SV_VECTOR_GET(inversions,i)->AB));
midCD = scl_binary_search(mm_reads,&(SV_VECTOR_GET(inversions,i)->CD));
for(j=midAB;j<pp_reads->size;j++){
if(interval_pair_overlaps(&(SV_VECTOR_GET(inversions,i)->AB),vector_get(pp_reads,j),CLONE_MEAN)){
pp_support++;
}
if(SV_VECTOR_GET(inversions,i)->AB.end1 < IDIS_VECTOR_GET(pp_reads,j)->start1){
break;
}
if(pp_support > MAX_SUPPORT){ break;}
}
for(j=midCD;j<mm_reads->size;j++){
if(interval_pair_overlaps(&(SV_VECTOR_GET(inversions,i)->CD),vector_get(mm_reads,j),CLONE_MEAN)){
mm_support++;
}
if(SV_VECTOR_GET(inversions,i)->CD.end1 < IDIS_VECTOR_GET(mm_reads,j)->start1){
break;
}
if(mm_support > MAX_SUPPORT){ break;}
}
SV_VECTOR_GET(inversions,i)->supports[0] = pp_support;
SV_VECTOR_GET(inversions,i)->supports[1] = mm_support;
}
}
void update_sv_supports_b(vector_t *svs, bam_vector_pack *reads){
int i;
qsort(reads->pp_discordants->items,reads->pp_discordants->size,sizeof(interval_discordant *),interval_pair_comp);
qsort(reads->mm_discordants->items,reads->mm_discordants->size,sizeof(interval_discordant *),interval_pair_comp);
qsort(reads->pm_discordants->items,reads->pm_discordants->size,sizeof(interval_discordant *),interval_pair_comp);
qsort(reads->mp_discordants->items,reads->mp_discordants->size,sizeof(interval_discordant *),interval_pair_comp);
for(i=0;i<svs->size;i++){
sv_t *sv = vector_get(svs,i);
switch(sv->type){
case SV_INVERSION:
update_inversion_supports_b(sv,reads->pp_discordants,reads->mm_discordants);
break;
case SV_DIRECT_DUPLICATION:
update_duplication_supports_b(sv,reads->pm_discordants,reads->mp_discordants);
break;
case SV_INVERTED_DUPLICATION:
update_duplication_supports_b(sv,reads->pp_discordants,reads->mm_discordants);
break;
case SV_TANDEM_DUPLICATION:
update_tandem_duplication_supports_b(sv,reads->mp_discordants);
break;
case SV_TRANSLOCATION:
update_duplication_supports_b(sv,reads->pm_discordants,reads->mp_discordants);
break;
case SV_INVERTED_TRANSLOCATION:
update_duplication_supports_b(sv,reads->pp_discordants,reads->mm_discordants);
break;
case SV_DELETION:
update_deletion_supports_b(sv,reads->pm_discordants);
break;
default:
fprintf(stderr,"Unknown SV type ordinal %d\n",sv->type);
VALOR_LOG("Unknown SV type ordinal %d\n",sv->type);
exit(-1);
}
}
}
void update_sv_supports(vector_t *svs, bam_vector_pack *reads ,sv_type type){
switch(type){
case SV_INVERSION:
update_inversion_supports(svs,reads->pp_discordants,reads->mm_discordants);
break;
case SV_DIRECT_DUPLICATION:
update_duplication_supports(svs,reads->pm_discordants,reads->mp_discordants);
break;
case SV_INVERTED_DUPLICATION:
update_duplication_supports(svs,reads->pp_discordants,reads->mm_discordants);
break;
case SV_DELETION:
update_deletion_supports(svs,reads->pm_discordants);
break;
case SV_TRANSLOCATION:
update_duplication_supports(svs,reads->pm_discordants,reads->mp_discordants);
break;
case SV_INVERTED_TRANSLOCATION:
update_duplication_supports(svs,reads->pp_discordants,reads->mm_discordants);
break;
default:
fprintf(stderr,"Unknown SV type ordinal %d\n",type);
VALOR_LOG("Unknown SV type ordinal %d\n",type);
exit(-1);
}
}
//TODO is this revers?
splitmolecule_t *inversion_reduce_breakpoints(sv_t *inv){
splitmolecule_t *sc = getMem(sizeof(splitmolecule_t));
sc->start1 = inv->AB.end1;
sc->end1 = inv->CD.start1;
sc->start2 = inv->AB.end2;
sc->end2 = inv->CD.start2;
return sc;
}
splitmolecule_t *duplication_reduce_breakpoints(sv_t *dup){
splitmolecule_t *sc = getMem(sizeof(splitmolecule_t));
if(dup->orientation == DUP_FORW_COPY){
sc->start1 = dup->AB.start1;
sc->end1 = dup->CD.end1;
sc->start2 = dup->AB.end2;
sc->end2 = dup->CD.start2;
} else if(dup->orientation == DUP_BACK_COPY){