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bam_draw_0.0.4.c
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bam_draw_0.0.4.c
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// gcc -g -O3 -Wall bam_draw_0.0.4.c -o bam_draw_0_0_4 .\samtools-0.1.19\libbam.a -I.\samtools-0.1.19 -L.\samtools-0.1.19 -mms-bitfields -IC:/MinGW/msys/1.0/include/cairo -IC:/MinGW/msys/1.0/include/glib-2.0 -IC:/MinGW/msys/1.0/lib/glib-2.0/include -IC:/MinGW/msys/1.0/include -IC:/MinGW/msys/1.0/include/freetype2 -IC:/MinGW/msys/1.0/include -IC:/MinGW/msys/1.0/include/libpng15 -LC:/MinGW/msys/1.0/lib -lcairo -lm -L. -lbam -Lwin32 -lz -lpthread -lws2_32
// gcc -g -O3 -Wall bam_draw_0.0.4.c -o bam_draw_0_0_4 ../hashtbl.a ./samtools-0.1.19/libbam.a -I./samtools-0.1.19 -L./samtools-0.1.19 $(pkg-config --cflags --libs cairo) -lpthread
#include <stdio.h>
#include <getopt.h>
#include <math.h>
#include <errno.h>
#include <sys/stat.h>
#include <time.h>
#include <sys/time.h>
#include <unistd.h>
#include <cairo.h>
#include <cairo-svg.h>
#include <cairo-pdf.h>
#include "sam.h"
#include "../hashtbl.h"
#include "hash-master/hash.h"
#define MAX_DEPTH 200
#define LEFT 50
#define TOP 50
#define EACH_READ_HEIGHT 5
#define EACH_WIG_HEIGHT 25
#define SCALE_WIDTH 16000
#define MAX_GENE_NUM 30000
#define MAX_CHR 64
typedef struct _data_buf_ {
samfile_t *fp;
bam_index_t *idx;
unsigned int max_depth;
double max_wig;
struct list **my_list ;
struct list **wig_list ;
struct list **Stack ;
} DataBuf;
typedef struct _region_ {
char *chromosome;
int32_t pos;
int32_t l_qseq;
int32_t qlen;
uint32_t end;
uint16_t n_cigar;
uint32_t *cigar;
char *qname;
char *qseq;
char strand;
} Region;
typedef struct _gtfLine_
{
char *seqname;
char *feature;
unsigned int start;
unsigned int end ;
char strand;
char frame;
char *attributes;
} GtfLine;
typedef struct _Gene_
{
unsigned int start;
unsigned int end ;
struct list *gtflist;
} Gene;
typedef struct _Chr_
{
unsigned int gene_count;
Gene *chr_gene;
} Chr;
typedef struct _GeneCluster_
{
unsigned int start;
unsigned int end ;
struct list *GeneList;
} GeneCluster;
typedef struct _ChrCluster_
{
unsigned int Cluster_count;
GeneCluster *chr_gene_cluster;
} ChrCluster;
typedef struct _wig_
{
int start;
int end;
double depth;
} Wig;
struct globalArgs_t {
char **infiles;
unsigned short numInfiles;
int overlap;
int window;
char *region;
char *outfile;
char *gtf;
int strand;
} globalArgs;
static int rgb[12][3]={
{255,255,255},
// {70, 130, 180},
{255, 140, 0},{160, 82, 45},{135, 206, 235},{107, 142, 35},{106, 90, 205},
{119, 136, 153},{218, 165, 32},{178, 34, 34},{255, 0, 255},{0, 255, 255},{0, 255, 0},
};
void display_usage(char * argv[]);
static inline long long usec(void);
static inline char *cal_GC(const uint8_t *seq,int32_t l_qseq,unsigned short *n_GC) ;
static inline int fetch_func(const bam1_t *b, void *data);
static inline void fill_item(const bam1_t *b,const bam1_core_t *c,uint32_t *cigar,char *qseq,Region *r,DataBuf *databuf);
static inline void parse_my_list(DataBuf *databuf,unsigned int j);
static inline unsigned int Stack_list(struct list *LIST,struct list **Stack);
static inline char *create_pdf(const char *chromosome,int beg,int end,const char *filename);
static inline void creat_pdf(DataBuf *databuf,unsigned short numInfiles,unsigned int *max_transcript_num,int *Width,int *Height);
static inline void draw_GeneList_rectangle(unsigned short transcript_num,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,int beg,int end);
static inline void draw_GeneList(GeneCluster *gene_cluster,unsigned short transcript_num,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,int beg,int end);
static inline void draw_region(struct list **Stack,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,unsigned int max_depth,int beg,int end,const char *filename) ;
static inline void free_cario(cairo_t *cr,cairo_surface_t *surface,char *filename);
static inline void Region_delete_int(void *DATA);
double tity_sam2wig(struct list *LIST,struct list *wig_list);
void Wig_delete_int(void *DATA);
int compare_hashed_key(const void *a, const void *b);
void draw_wig(struct list *wig_list,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,double max_wig,int beg,int end,const char *filename);
/*load GTF to a hash table*/
static inline void assign_gene_start_end(Gene *gene);
static inline GtfLine *readNextGtf(FILE *f,const char *buf);
struct hash *load_gtf(const char *infile);
static inline void data_delete_listT(void *DATA) ;
static inline void data_delete_hashT(void *DATA) ;
static inline void print_GtfList(struct list *gtfline_list);
static inline void print_gtf(struct hash *hash_gtf);
static inline int cmp_gene(const void *a, const void *b);
/*cluster GTF*/
static inline int overlap(unsigned int S1,unsigned int E1,unsigned int S2,unsigned int E2);
struct hash *cluster_gtf(struct hash *hash_gtf);
static inline void data_delete_list_GeneT(void *DATA);
static inline void data_delete_hash_clusterT(void *DATA);
/*binary search GeneList*/
static inline void print_GeneList(struct list *GeneList);
static inline int test_bsearch(struct hash *Clusterd_GTF,DataBuf *databuf,int ref,int beg,int end);
static inline int bsearch_04(ChrCluster *chrcluster,int x);
static inline int bsearch_draw(ChrCluster *chr_culster,int beg,int end,unsigned int *max_transcript_num);
static inline void draw_all_genes(struct hash *Clusterd_GTF,DataBuf *databuf,const char *current_dir,char *work_dir);
static inline void draw_a_region(struct hash *Clusterd_GTF,DataBuf *databuf);
long long usec(void) {
struct timeval tv;
gettimeofday(&tv,NULL);
return (((long long)tv.tv_sec)*1000000)+tv.tv_usec;
}
void display_usage(char * argv[]){
char *buffer=(char* )malloc(8092*sizeof(char));
const char* usage=
"\nCopyright (c) 2012-2013\n" \
"Contact: XiongXu <[email protected]> <[email protected]> \n" \
"Usage: %s [-w window_size] [-o overlap_size] [-g gtf_file][-r chr1:1-2000000] [-s 0] [-O OUTFILE] [-h] bamFile1 bamFile2 ..\n" \
"Discription:\n This program is used for drawing a region(less than 500kb)'s reads distribution with samtools indexed bam files.\n" \
"Example:\n %s -w 20000 -g /home/xuxiong/data/hg19/hg19.gtf -r chr1:1227764-1260067 -O out /share/work1/staff/xuxiong/twins/batch2/test_20131224/*_1224/accepted_hits.bam\n" \
"\n" \
" [-w window_size] = window size. default is 20000. [option]\n" \
" [-o overlap_size] = overlap size. default is 0. [option]\n" \
" [-g gtf_file] = gtf_infile [required]\n" \
" [-r] = region, default is whole genome.(chr1:1-20000) [option]\n" \
" [-s] = bool variant,strand or not, default is 0. [option]\n" \
" [-O OUTPUT_FILE] = OUTPUT file. default is 'out' [option]\n" \
" [-h] = This helpful help screen. [option]\n" \
" Infiles = bam format input file(s),at least 1 bam file. [required]\n" \
"\n";
sprintf(buffer,usage,argv[0],argv[0]);
printf("%s",buffer);
exit(1);
}
char *cal_GC(const uint8_t *seq,int32_t l_qseq,unsigned short *n_GC) {
char *temp_seq=(char *)malloc((l_qseq+1)*sizeof(char));
memset(temp_seq,0,l_qseq+1);
int32_t i=0;
int temp=0;
for (i=0;i<l_qseq ;i++ ) {
temp=bam1_seqi(seq, i);
switch (temp) {
case 1:
temp_seq[i]='A';
break;
case 2:
temp_seq[i]='C';
break;
case 4:
temp_seq[i]='G';
break;
case 8:
temp_seq[i]='T';
break;
case 15:
temp_seq[i]='N';
break;
default:
break;
}
if (temp == 2 || temp == 4) (*n_GC)++;
}
// fprintf(stderr,"%s %d\n",temp_seq,*n_GC);
return temp_seq;
}
int fetch_func(const bam1_t *b, void *data) {
DataBuf *databuf=(DataBuf *)data;
uint32_t *cigar = bam1_cigar(b);
const bam1_core_t *c = &b->core;
if (c->flag&BAM_FUNMAP) return 0;
// printf("%s\t%d\t%d\t%d\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%c\n",databuf->fp->header->target_name[c->tid],c->pos, bam_calend(c,cigar) ,c->pos + l,l,bam_cigar2qlen(c,cigar), bam1_qname(b), c->qual, c->bin,c->mtid,c->mpos,c->isize,(c->flag&BAM_FREVERSE)? '-' : '+');
unsigned short current_GC =0;
char *qseq=cal_GC(bam1_seq(b),c->l_qseq,¤t_GC);
Region *R=(Region *)malloc(sizeof(Region));
fill_item(b,c,cigar,qseq,R,databuf);
// printf("%s\n",((Region *)list_tail(*(databuf->my_list+c->tid)))->qname);
return 0;
}
void fill_item(const bam1_t *b,const bam1_core_t *c,uint32_t *cigar,char *qseq,Region *r,DataBuf *databuf){
r->chromosome=strdup(databuf->fp->header->target_name[c->tid]);
r->pos=c->pos;
r->l_qseq=c->l_qseq;
r->qlen=bam_cigar2qlen(c,cigar);
r->end=bam_calend(c,cigar);
r->cigar=malloc(sizeof(uint32_t)*c->n_cigar);
memcpy(r->cigar,cigar,c->n_cigar*sizeof(uint32_t));
r->n_cigar=c->n_cigar;
r->qname=strdup(bam1_qname(b));
r->qseq=qseq;
r->strand=(c->flag&BAM_FREVERSE)? '-' : '+';
list_push_back(*(databuf->my_list+c->tid), r);
}
void parse_my_list(DataBuf *databuf,unsigned int j){
databuf->max_depth=0;
databuf->max_wig=0;
if (!list_empty(*(databuf->my_list+j))) {
*(databuf->wig_list+j)=list_create(Wig_delete_int);
databuf->max_wig=tity_sam2wig(*(databuf->my_list+j),*(databuf->wig_list+j));
databuf->Stack=(struct list **)calloc(MAX_DEPTH,sizeof(struct list *));
databuf->max_depth = Stack_list(*(databuf->my_list+j),databuf->Stack);
}
else{
list_delete(*(databuf->my_list+j));
}
}
int compare_hashed_key(const void *a, const void *b) {
return atoi((*(ENTRY* const *)a)->key)-atoi((*(ENTRY* const *)b)->key);
}
void Wig_delete_int(void *DATA) {
free(DATA);
}
double tity_sam2wig(struct list *LIST,struct list *wig_list){
struct item *current, *next;
int i=0,l=0,j=0,prevkey=0;
double count=0;
HASHTBL *start = hashtbl_create((HSIZE)2*LIST->size, NULL);
HASHTBL *end = hashtbl_create((HSIZE)2*LIST->size, NULL);
char *buf=(char *)malloc(128*sizeof(char));
Region *r;
current = LIST->head;
while (current) {
next = current->next;
r = (Region *)current->data;
if (current) {
unsigned int temp_start= r->pos;
for (j = 0,l = 0; j < r->n_cigar; ++j) {
int op = r->cigar[j]&0xf;
if ( op == BAM_CDEL || op == BAM_CREF_SKIP){
l = r->cigar[j]>>4;
temp_start+=l;
}
else if (op == BAM_CMATCH ) {
l = r->cigar[j]>>4;
memset(buf,0,128*sizeof(char));
sprintf(buf,"%d",temp_start);
void *data=hashtbl_get(start,buf);
if (data==NULL) {
int *init=(int *)malloc(sizeof(int));
*init=1;
hashtbl_insert(start, buf, (void *)init);
}
else{
(*(int *)data)++;
}
temp_start+=l;
memset(buf,0,128*sizeof(char));
sprintf(buf,"%d",temp_start);
data=hashtbl_get(end,buf);
if (data==NULL) {
int *init=(int *)malloc(sizeof(int));
*init=1;
hashtbl_insert(end, buf, (void *)init);
}
else{
(*(int *)data)++;
}
}
}
}
current = next ;
}
free(buf);
char **all_keys=union_hashed_keys(start,end);
int all_keys_count=start->count+end->count;
double max_wig=0;
for (i = 0; i < all_keys_count; ++i) {
int pos=atoi(all_keys[i]);
if (pos==prevkey) continue;
if (prevkey) {
Wig *wig=(Wig *)malloc(sizeof(Wig));
wig->start=prevkey;
wig->end=pos;
wig->depth=count>0?(count>1?log(count)/log(2):0.5):0;
max_wig=wig->depth>max_wig?wig->depth:max_wig;
if (!list_empty(wig_list)) {
Wig *wig_last=(Wig *)list_tail(wig_list);
if (wig_last->end==prevkey && wig_last->depth == wig->depth) {
wig_last->end=pos;
free(wig);
}
else{
list_push_back(wig_list, wig);
}
}
else{
list_push_back(wig_list, wig);
}
}
prevkey=pos;
void *data=hashtbl_get(start,all_keys[i]);
if (data!=NULL) count+= *(int*)data;
data=hashtbl_get(end,all_keys[i]);
if (data!=NULL) count-= *(int*)data;
}
hashtbl_destroy(start,NULL);
hashtbl_destroy(end,NULL);
return max_wig;
}
unsigned int Stack_list(struct list *LIST,struct list **Stack){
struct item *current, *next;
Region *r;
unsigned int i=0;
if (!LIST) return 0;
unsigned int end=0;
/******************differentiate junction******************
while (1) {
end=0;
current = LIST->head;
*(Stack+i)=list_create(Region_delete_int);
while (current) {
next = current->next;
r = (Region *)current->data;
if (r->n_cigar>1) {
if (r->pos>end) {
list_push_back(*(Stack+i), r);
end=r->end;
if (current->next && current->prev) {
current->next->prev = current->prev;
current->prev->next = next;
}
else if (current->prev) {
LIST->tail->prev->next = NULL;
LIST->tail=current->prev;
}
else if (current->next){
LIST->head->next->prev = NULL;
LIST->head = next;
}
else{
LIST->tail->prev=NULL;
LIST->tail->next=NULL;
LIST->head->prev = NULL;
LIST->head->next = NULL;
LIST->head=current=LIST->tail;
}
if (current) {
LIST->size--;
}
}
}
current = next ;
}
if (list_empty(*(Stack+i))) {
list_delete(*(Stack+i));
break;
}
if (++i > MAX_DEPTH) return i;
}
printf("i: %d\tlist_size: %d\n",i,list_size(LIST));
**********************************************************/
while (!list_empty(LIST)) {
end=0;
current = LIST->head;
*(Stack+i)=list_create(Region_delete_int);
while (current) {
next = current->next;
r = (Region *)current->data;
if (r->pos>end) {
list_push_back(*(Stack+i), r);
end=r->end;
if (current->next && current->prev) {
current->next->prev = current->prev;
current->prev->next = next;
}
else if (current->prev) {
LIST->tail->prev->next = NULL;
LIST->tail=current->prev;
}
else if (current->next){
LIST->head->next->prev = NULL;
LIST->head = next;
}
else{
LIST->tail->prev=NULL;
LIST->tail->next=NULL;
LIST->head->prev = NULL;
LIST->head->next = NULL;
LIST->head=current=LIST->tail;
}
if (current) {
free(current);
LIST->size--;
}
}
current = next ;
}
if (++i > MAX_DEPTH) break;
}
// printf("i: %d\tlist_size: %d\nDone stack list\n",i,list_size(LIST));
if (!list_empty(LIST)) {
list_delete(LIST);
}else{
free(LIST);
}
return i;
}
void creat_pdf(DataBuf *databuf,unsigned short numInfiles,unsigned int *max_transcript_num,int *Width,int *Height) {
float scale=1;
int i=0,each_transcript_height=20;
*Width = SCALE_WIDTH/scale + 2*LEFT;
*Height = TOP;
(*Height)+=(*max_transcript_num)*(each_transcript_height+5)+(*max_transcript_num>0?TOP:0);
for (i=0;i<numInfiles ;i++ ) {
(*Height)+=1.2*EACH_READ_HEIGHT*(databuf+i)->max_depth+((databuf+i)->max_depth>0?TOP:0);
(*Height)+=1.2*EACH_WIG_HEIGHT*(databuf+i)->max_wig+((databuf+i)->max_depth>0?TOP:0);
// printf("max_depth: %d\tmax_wig: %f\t%f\n",(databuf+i)->max_depth,(databuf+i)->max_wig,1.2*EACH_WIG_HEIGHT*(databuf+i)->max_wig+((databuf+i)->max_wig>0?TOP:0));
}
}
void draw_GeneList_rectangle(unsigned short transcript_num,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,int beg,int end){
float scale=1;
unsigned int each_transcript_height=20;
unsigned int Height = transcript_num*(each_transcript_height+5);
cairo_set_line_width(cr, 1);
cairo_set_source_rgb(cr,0,0,0);
cairo_rectangle(cr, LEFT,*current_top,SCALE_WIDTH/scale,Height);
cairo_stroke (cr);
(*current_top)+=Height+TOP;
}
void draw_GeneList(GeneCluster *gene_cluster,unsigned short transcript_num,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,int beg,int end) {
struct item *current, *next;
float scale=1;
unsigned int each_transcript_height=20;
float ratio= (float)SCALE_WIDTH/(end-beg)/scale;
float x=LEFT;
unsigned int y=*current_top;
current = (gene_cluster->GeneList)->head;
while (current) {
y+=5;
x=LEFT;
next=current->next;
Gene *current_gene=(Gene *)current->data;
int *current_color=(((GtfLine *)current_gene->gtflist->head->data)->strand == '+' ? rgb[1] : rgb[10]);
// printf("%u\t%u\n",current_gene->start,current_gene->end);
cairo_set_line_width(cr, 0.1);
cairo_set_source_rgb(cr,(double)current_color[0]/255,(double)current_color[1]/255,(double)current_color[2]/255);
struct item *current2,*next2;
current2=current_gene->gtflist->head;
while (current2) {
next2=current2->next;
GtfLine *gtfline=(GtfLine *)current2->data;
if (!strcmp(gtfline->feature,"exon")) {
cairo_rectangle(cr, (int)(x+(gtfline->start-beg)*ratio),y,(int)(gtfline->end-gtfline->start)*ratio,each_transcript_height);
cairo_fill(cr);
// fprintf(stderr,"%s\t%s\t%u\t%u\t%c\t%c\t%s\n",gtfline->seqname,gtfline->feature, gtfline->start, gtfline->end,gtfline->strand,gtfline->frame,gtfline->attributes);
}
current2=next2;
}
cairo_move_to(cr, (int)(x+(current_gene->start-beg)*ratio),y+each_transcript_height/2);
cairo_line_to (cr, (int)(x+(current_gene->end-beg)*ratio),y+each_transcript_height/2);
cairo_stroke (cr);
y+=each_transcript_height;
current=next;
}
}
void draw_wig(struct list *wig_list,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,double max_wig,int beg,int end,const char *filename) {
if (!wig_list) return;
struct item *current, *next;
float scale=1;
unsigned int Height = 1.2*max_wig*EACH_WIG_HEIGHT;
float ratio= (float)SCALE_WIDTH/(end-beg)/scale;
cairo_set_line_width (cr, 0.1);
cairo_set_source_rgb(cr,0,0,0);
cairo_rectangle(cr, LEFT,*current_top, SCALE_WIDTH/scale, Height);
cairo_stroke (cr);
float x=LEFT;
unsigned int y=*current_top;
int *current_color=rgb[3];
current = wig_list->head;
Wig *wig = (Wig *)current->data;
cairo_move_to(cr, (int)(x+(wig->start-beg+1)*ratio), (int)y);
while (current) {
next = current->next;
wig = (Wig *)current->data;
if (current) {
cairo_line_to(cr, (int)(x+(wig->start-beg+1)*ratio),(int)y + wig->depth * EACH_WIG_HEIGHT);
if (!wig->depth){
cairo_close_path (cr);
cairo_set_source_rgb(cr,(double)current_color[0]/255,(double)current_color[1]/255,(double)current_color[2]/255);
cairo_fill(cr);
cairo_move_to(cr,(int)(x+(wig->end-beg+1)*ratio), (int)y + wig->depth * EACH_WIG_HEIGHT);
}
else{
cairo_line_to (cr, (int)(x+(wig->end-beg+1)*ratio), (int)y + wig->depth * EACH_WIG_HEIGHT);
}
}
current = next ;
}
cairo_line_to (cr, (int)(x+(wig->end-beg+1)*ratio), (int)y);
cairo_close_path (cr);
cairo_set_source_rgb(cr,(double)current_color[0]/255,(double)current_color[1]/255,(double)current_color[2]/255);
cairo_fill(cr);
list_delete(wig_list);
(*current_top)+=Height+TOP;
}
void draw_region(struct list **Stack,cairo_surface_t *surface,cairo_t *cr,unsigned int *current_top,unsigned int max_depth,int beg,int end,const char *filename) {
unsigned int i=0,j=0,l=0;
struct item *current, *next;
Region *r;
float scale=1;
unsigned int Height = 1.2*max_depth*EACH_READ_HEIGHT;
float ratio= (float)SCALE_WIDTH/(end-beg)/scale;
cairo_set_line_width (cr, 1);
cairo_set_source_rgb(cr,0,0,0);
cairo_rectangle(cr, LEFT,*current_top, SCALE_WIDTH/scale, Height);
cairo_stroke (cr);
float x=LEFT;
unsigned int y=*current_top;
cairo_set_font_size (cr, 8);
cairo_select_font_face (cr, "Sans",CAIRO_FONT_SLANT_NORMAL, CAIRO_FONT_WEIGHT_NORMAL);
cairo_set_source_rgb (cr, 0, 0, 0);
cairo_move_to(cr, x,y-TOP/2);
cairo_show_text(cr, filename);
const double styleDotted[2]={1,1};
for (i=0;i<max_depth ;i++ ) {
x=LEFT;
y+=EACH_READ_HEIGHT;
if (list_empty(*(Stack+i))) break;
current = (*(Stack+i))->head;
while (current) {
next = current->next;
r = (Region *)current->data;
if (current) {
int *current_color= r->strand == '+' ? rgb[1] : rgb[10];
unsigned int temp_start= r->pos;
for (j = 0,l = 0; j < r->n_cigar; ++j) {
int op = r->cigar[j]&0xf;
if ( op == BAM_CDEL || op == BAM_CREF_SKIP){
l = r->cigar[j]>>4;
cairo_set_line_width (cr, 0.1);
cairo_set_dash (cr,styleDotted,2,0);
cairo_set_source_rgba (cr,(double)current_color[0]/255,(double)current_color[1]/255,(double)current_color[2]/255,0.4);
cairo_move_to(cr, (int)(x+(temp_start-beg+1)*ratio), (int)y);
cairo_line_to (cr, (int)(x+(temp_start+l-beg+1)*ratio), (int)y);
cairo_stroke (cr);
}
else if (op == BAM_CMATCH) {
l = r->cigar[j]>>4;
cairo_set_line_width (cr, 2);
cairo_set_dash (cr,styleDotted,0,0);
cairo_set_source_rgb(cr,(double)current_color[0]/255,(double)current_color[1]/255,(double)current_color[2]/255);
cairo_move_to(cr, (int)(x+(temp_start-beg+1)*ratio), (int)y);
cairo_line_to (cr, (int)(x+(temp_start+l-beg+1)*ratio), (int)y);
cairo_stroke (cr);
}
temp_start+=l;
}
// printf("%d\t%d\t%d\t%d\t#%d#\n",i,r->pos,r->end,(*(Stack+i))->size,r->n_cigar);
item_delete(*(Stack+i), current);
(*(Stack+i))->size--;
}
current = next ;
}
free(*(Stack+i));
}
(*current_top)+=Height+TOP;
free(Stack);
}
char *create_pdf(const char *chromosome,int beg,int end,const char *filename){
char *output=(char *)malloc(1024*sizeof(char));
memset(output,0,1024*sizeof(char));
sprintf(output,"%s_%s_%d_%d.pdf",filename,chromosome,beg,end);
return output;
}
void free_cario(cairo_t *cr,cairo_surface_t *surface,char *filename){
cairo_destroy (cr);
cairo_surface_destroy (surface);
free(filename);
}
void Region_delete_int(void *DATA) {
Region *R=(Region *)DATA;
free(R->cigar);
free(R->chromosome);
free(R->qname);
free(R->qseq);
free(R);
}
void data_delete_hashT(void *DATA) {
Gene *chr_gene=(Gene *)DATA;
free(chr_gene);
}
void data_delete_listT(void *DATA) {
GtfLine *gtfline=(GtfLine *)DATA;
free(gtfline->seqname);
free(gtfline->feature);
free(gtfline->attributes);
free(gtfline);
}
GtfLine *readNextGtf(FILE *f,const char *buf){
GtfLine *gtfline=(GtfLine *)malloc(sizeof(GtfLine));
gtfline->seqname=(char *)calloc(128,sizeof(char));
gtfline->feature=(char *)calloc(128,sizeof(char));
gtfline->attributes=(char *)calloc(1024,sizeof(char));
sscanf(buf, "%s\t%*[^\t]\t%s\t%u\t%u\t%*[^\t]\t%c\t%c\t%*[^ ] \"%[^\"]",
gtfline->seqname,gtfline->feature, >fline->start, >fline->end,>fline->strand,>fline->frame,gtfline->attributes);
gtfline->seqname=realloc(gtfline->seqname,(strlen(gtfline->seqname)+1)*sizeof(char));
gtfline->feature=realloc(gtfline->feature,(strlen(gtfline->feature)+1)*sizeof(char));
gtfline->attributes=realloc(gtfline->attributes,(strlen(gtfline->attributes)+1)*sizeof(char));
// fprintf(stderr,"%s\t%s\t%u\t%u\t%c\t%c\t%s\n",
// gtfline->seqname,gtfline->feature, gtfline->start, gtfline->end,gtfline->strand,gtfline->frame,gtfline->attributes);
return gtfline;
}
struct hash *load_gtf(const char *infile){
FILE *f=fopen(infile,"r");
if(f == NULL) {
printf("Failed to open file (%s)", infile);
exit(1);
}
char *buf=(char *)calloc(1024,sizeof(char));
char *temp_seqname = "-";
char *temp_attributes = "-";
struct hash *hash_gtf = hash_create(data_delete_hashT, MAX_CHR);
unsigned int i=0;
Gene *temp_chr_gene=(Gene *)calloc(MAX_GENE_NUM,sizeof(Gene));
while (1) {
buf=fgets(buf,1024*sizeof(char),f);
if (feof(f)) break;
GtfLine *gtfline=readNextGtf(f,buf);
if (strcmp(temp_attributes,gtfline->attributes)) {
if (strcmp(temp_attributes,"-")) {
assign_gene_start_end(&temp_chr_gene[i++]);
}
if (strcmp(temp_seqname,gtfline->seqname)) {
// fprintf(stderr,"%u\n",i);
if (strcmp(temp_seqname,"-")) {
Chr *CHR=(Chr *)malloc(sizeof(Chr));
CHR->gene_count=i;
CHR->chr_gene=(Gene *)calloc(CHR->gene_count,sizeof(Gene));
memmove(CHR->chr_gene,temp_chr_gene,(CHR->gene_count)*sizeof(Gene));
hash_insert(hash_gtf,temp_seqname,CHR);
// fprintf(stderr,"%s: %d\n",temp_seqname,i);
}
i=0;
}
temp_chr_gene[i].gtflist=list_create(data_delete_listT);
list_push_back(temp_chr_gene[i].gtflist,gtfline);
}
else{
list_push_back(temp_chr_gene[i].gtflist,gtfline);
}
temp_seqname=gtfline->seqname;
temp_attributes=gtfline->attributes;
}
Chr *CHR=(Chr *)malloc(sizeof(Chr));
CHR->gene_count=++i;
CHR->chr_gene=(Gene *)calloc(CHR->gene_count,sizeof(Gene));
memmove(CHR->chr_gene,temp_chr_gene,(CHR->gene_count)*sizeof(Gene));
hash_insert(hash_gtf,temp_seqname,CHR);
// fprintf(stderr,"%s: %d",temp_seqname,i);
fclose(f);
free(temp_chr_gene);
return hash_gtf;
}
void assign_gene_start_end(Gene *gene){
struct item *current, *next,*prev;
current = gene->gtflist->head;
while (current) {
next = current->next;
GtfLine *temp_gtfline=(GtfLine *)current->data;
if (!strcmp(temp_gtfline->feature,"exon")) {
gene->start = temp_gtfline->start;
break;
}
current = next;
}
current = gene->gtflist->tail;
while (current) {
prev = current->prev;
GtfLine *temp_gtfline=(GtfLine *)current->data;
if (!strcmp(temp_gtfline->feature,"exon")) {
gene->end = temp_gtfline->end;
break;
}
current = prev;
}
}
void print_GtfList(struct list *gtfline_list){
struct item *current, *next;
current = gtfline_list->head;
while (current) {
next = current->next;
GtfLine *gtfline=(GtfLine *)current->data;
printf("%s\t%s\t%u\t%u\t%c\t%c\t%s\n",gtfline->seqname,gtfline->feature, gtfline->start, gtfline->end,gtfline->strand,gtfline->frame,gtfline->attributes);
current = next;
}
}
void print_gtf(struct hash *hash_gtf){
unsigned i=0,j=0;
struct item *current, *next;
fprintf(stdout,"%d\n",hash_gtf->key_count);
for (i=0;i<hash_gtf->size ;i++ ) {
struct list *list = (hash_gtf->table)[i];
// printf("bucket: %d\tlist_size: %d\n",i,list_size(list));
current = list->head;
while (current) {
next = current->next;
Chr *chr=(Chr *)((struct pair *)current->data)->value;
printf("%s: %u\n",(char *)((struct pair *)current->data)->key,chr->gene_count);
qsort(chr->chr_gene,chr->gene_count,sizeof(Gene),cmp_gene);
for (j=0;j< chr->gene_count;j++ ) {
Gene current_gene=chr->chr_gene[j];
printf("%u\t%u\n",current_gene.start,current_gene.end);
print_GtfList(current_gene.gtflist);
}
current = next;
}
}
}
int cmp_gene(const void *a, const void *b){
Gene *c=(Gene *)a;
Gene *d=(Gene *)b;
if (c->start!=d->start) {
return c->start-d->start;
}
else{
return c->end-d->end;
}
}
void data_delete_hash_clusterT(void *DATA) {
ChrCluster *chrcluster=(ChrCluster *)DATA;
free(chrcluster);
}
void data_delete_list_GeneT(void *DATA) {
Gene *gene=(Gene *)DATA;
list_delete(gene->gtflist);
free(gene);
}
int overlap(unsigned int S1,unsigned int E1,unsigned int S2,unsigned int E2){
return E1>=S2?1:0;
}
struct hash *cluster_gtf(struct hash *hash_gtf) {
struct hash *hash_cluster_gtf=hash_create(data_delete_hash_clusterT, MAX_CHR);
unsigned i=0,j=0;
struct item *current, *next;
for (i=0;i<hash_gtf->size ;i++ ) {
struct list *list = (hash_gtf->table)[i];
current = list->head;
while (current) {
next = current->next;
Chr *chr=(Chr *)((struct pair *)current->data)->value;
// printf("%s: %u\n",(char *)((struct pair *)current->data)->key,chr->gene_count);
qsort(chr->chr_gene,chr->gene_count,sizeof(Gene),cmp_gene);
unsigned int cluster_index=0;
GeneCluster *chr_gene_cluster=(GeneCluster *)calloc(MAX_GENE_NUM,sizeof(GeneCluster));
chr_gene_cluster[cluster_index].start=0;
chr_gene_cluster[cluster_index].end=0;
for (j=0;j< chr->gene_count;j++ ) {
if (!overlap(chr_gene_cluster[cluster_index].start,chr_gene_cluster[cluster_index].end,chr->chr_gene[j].start,chr->chr_gene[j].end)) {
if (!list_empty(chr_gene_cluster[cluster_index].GeneList)) cluster_index++;
chr_gene_cluster[cluster_index].GeneList=list_create(data_delete_list_GeneT);
list_push_back(chr_gene_cluster[cluster_index].GeneList,&chr->chr_gene[j]);
chr_gene_cluster[cluster_index].start=((Gene *)chr_gene_cluster[cluster_index].GeneList->head->data)->start;
}
else{
list_push_back(chr_gene_cluster[cluster_index].GeneList,&chr->chr_gene[j]);
}
chr_gene_cluster[cluster_index].end=chr_gene_cluster[cluster_index].end>((Gene *)chr_gene_cluster[cluster_index].GeneList->tail->data)->end?chr_gene_cluster[cluster_index].end:((Gene *)chr_gene_cluster[cluster_index].GeneList->tail->data)->end;
}
ChrCluster *chr_culster=(ChrCluster *)malloc(sizeof(ChrCluster));
chr_culster->Cluster_count=cluster_index+1;
// fprintf(stderr,"%s\t%u\n",(char *)((struct pair *)current->data)->key,chr_culster->Cluster_count);
chr_culster->chr_gene_cluster=(GeneCluster *)calloc(chr_culster->Cluster_count,sizeof(GeneCluster));
memmove(chr_culster->chr_gene_cluster,chr_gene_cluster,chr_culster->Cluster_count*sizeof(GeneCluster));
hash_insert(hash_cluster_gtf,((struct pair *)current->data)->key,chr_culster);
free(chr_gene_cluster);
current = next;
}
}
return hash_cluster_gtf;
}
int bsearch_04(ChrCluster *chrcluster,int x) {
int lo = 0;
int hi = chrcluster->Cluster_count - 1;
while(lo <= hi){
int mid = (hi + lo) / 2;
// int mid = (hi + lo) >> 1;
if(x < chrcluster->chr_gene_cluster[mid].start)
hi = mid - 1;
else if(x > chrcluster->chr_gene_cluster[mid+1].start)
lo = mid + 1;
else if (x >=chrcluster->chr_gene_cluster[mid].start && x <=chrcluster->chr_gene_cluster[mid+1].start) {
return mid;
}
}
return -1;
}
void print_GeneList(struct list *GeneList){
struct item *current, *next;
if (!GeneList) return;
printf("GeneListSize: %d\n",list_size(GeneList));
current = GeneList->head;
while (current) {
next = current->next;
Gene *current_gene=(Gene *)current->data;
printf("Gene_start: %u\tGene_end: %u\n",current_gene->start,current_gene->end);
print_GtfList(current_gene->gtflist);
current = next;
}
}
int test_bsearch(struct hash *Clusterd_GTF,DataBuf *databuf,int ref,int beg,int end) {
ChrCluster *chr_culster=(ChrCluster *)hash_find(Clusterd_GTF, databuf->fp->header->target_name[ref]);
int gene_cluster_index=bsearch_04(chr_culster,beg);
if (gene_cluster_index>0) {
printf("gene_cluster_index: %d\tgene_cluster_start: %u\tgene_cluster_end: %u\n",gene_cluster_index,chr_culster->chr_gene_cluster[gene_cluster_index].start,chr_culster->chr_gene_cluster[gene_cluster_index].end);
print_GeneList(chr_culster->chr_gene_cluster[gene_cluster_index].GeneList);
while (chr_culster->chr_gene_cluster[gene_cluster_index].end <end) {
print_GeneList(chr_culster->chr_gene_cluster[++gene_cluster_index].GeneList);
}
}
return gene_cluster_index;
}
int bsearch_draw(ChrCluster *chr_culster,int beg,int end,unsigned int *max_transcript_num) {
int gene_cluster_index=bsearch_04(chr_culster,beg);
if (gene_cluster_index>0) {
int i=gene_cluster_index;
*max_transcript_num=list_size(chr_culster->chr_gene_cluster[i].GeneList);
while (chr_culster->chr_gene_cluster[i].end <end) {
int current_list_size = list_size(chr_culster->chr_gene_cluster[++i].GeneList);
if (current_list_size>*max_transcript_num) {
*max_transcript_num=current_list_size;
}
}
printf("max_transcript_num: %u\n",*max_transcript_num);
}
return gene_cluster_index;
}
void draw_a_region(struct hash *Clusterd_GTF,DataBuf *databuf){
int ref, beg, end,i,boolen=0;
unsigned int current_top=50;
// printf("%s\t%d\t%d\n",databuf->fp->header->target_name[ref],beg,end);
for (i=0;i<globalArgs.numInfiles ;i++ ) {
ref=0;beg=0;end=0;
bam_parse_region((databuf+i)->fp->header, globalArgs.region, &ref, &beg, &end);
if (ref < 0) {
printf("bam2bed: Invalid region %s\n", globalArgs.region);
exit(1);
}
*((databuf+i)->my_list+ref)=list_create(Region_delete_int);
bam_fetch((databuf+i)->fp->x.bam, (databuf+i)->idx, ref, beg, end, (databuf+i), fetch_func);
printf("%s read count in this region: %d\n",*(globalArgs.infiles+i),list_size(*((databuf+i)->my_list+ref)));
if (!list_empty(*((databuf+i)->my_list+ref))) boolen=1;
parse_my_list(databuf+i,ref);
}
if (boolen) {
unsigned int max_transcript_num=0;
// int gene_cluster_index = test_bsearch(Clusterd_GTF,databuf,ref,beg,end);
// printf("Done binary search GTF at %.3f sec\n",(double)(usec()-begin)/CLOCKS_PER_SEC);
ChrCluster *chr_culster=(ChrCluster *)hash_find(Clusterd_GTF, databuf->fp->header->target_name[ref]);
int gene_cluster_index=bsearch_draw(chr_culster,beg,end,&max_transcript_num);
char *outfile=create_pdf(databuf->fp->header->target_name[ref],++beg,end,globalArgs.outfile);
int Width=0;
int Height=0;
creat_pdf(databuf,globalArgs.numInfiles,&max_transcript_num, &Width, &Height);
cairo_surface_t *surface = cairo_pdf_surface_create(outfile, Width, Height);
cairo_t *cr = cairo_create(surface);
if (gene_cluster_index>0) {
draw_GeneList(&chr_culster->chr_gene_cluster[gene_cluster_index],max_transcript_num,surface,cr,¤t_top,beg,end);
while (chr_culster->chr_gene_cluster[gene_cluster_index].end <end) {
draw_GeneList(&(chr_culster->chr_gene_cluster[++gene_cluster_index]),max_transcript_num,surface,cr,¤t_top,beg,end);
}
draw_GeneList_rectangle(max_transcript_num,surface,cr,¤t_top,beg,end);
}
for (i=0;i<globalArgs.numInfiles ;i++ ) {
if ((databuf+i)->max_depth>0) {
draw_region((databuf+i)->Stack,surface,cr,¤t_top,(databuf+i)->max_depth,beg,end,*(globalArgs.infiles+i));
draw_wig(*((databuf+i)->wig_list+ref),surface,cr,¤t_top,(databuf+i)->max_wig,beg,end,*(globalArgs.infiles+i));
}
}
free_cario(cr,surface,outfile);
}
}
void draw_all_genes(struct hash *Clusterd_GTF,DataBuf *databuf,const char *current_dir,char *work_dir){
unsigned int i,j,m=0;
for (j=0;j<databuf->fp->header->n_targets ;j++ ) {
sprintf(work_dir,"%s/%s",current_dir,databuf->fp->header->target_name[j]);
mkdir(work_dir,0750);
int status=chdir(work_dir);
if (status) exit(0);
ChrCluster *chr_culster=(ChrCluster *)hash_find(Clusterd_GTF, databuf->fp->header->target_name[j]);
if (chr_culster==NULL) continue;
printf("%s\t%u\n",databuf->fp->header->target_name[j],chr_culster->Cluster_count);
for (m=0;m<chr_culster->Cluster_count ;m++ ) {
int boolen=0;
for (i=0;i<globalArgs.numInfiles ;i++ ) {
*((databuf+i)->my_list+j)=list_create(Region_delete_int);
bam_fetch((databuf+i)->fp->x.bam, (databuf+i)->idx,j,chr_culster->chr_gene_cluster[m].start,chr_culster->chr_gene_cluster[m].end,(databuf+i), fetch_func);
printf("%u\t%s read count in this region: %d\n",m+1,*(globalArgs.infiles+i),list_size(*((databuf+i)->my_list+j)));
if (!list_empty(*((databuf+i)->my_list+j))) boolen=1;
parse_my_list(databuf+i,j);
}
if (boolen) {
unsigned int max_transcript_num=list_size(chr_culster->chr_gene_cluster[m].GeneList);
unsigned int current_top=50;