void SaveScreen::SaveArea(int X1,int Y1,int X2,int Y2)
{
fix_coordinates(X1, Y1, X2, Y2);
m_X1=X1;
m_Y1=Y1;
m_X2=X2;
m_Y2=Y2;
ScreenBuf.allocate(height(), width());
SaveArea();
}
/* Pileup function for single end data.
Input:
1. int * plus_tags: the 5' ends of tags aligned to plus strand. Start from 0.
2. long l_plus_tags: number of plus tags.
3. int * minus_tags: the 3' ends of tags aligned to minus strand. Start from 0.
4. long l_minus_tags: number of minus tags.
5. int five_shift: shift value at 5' end to recover the DNA fragment
6. int three_shift: shift value at 3' end to recover the DNA fragment
7. int leftmost_coord: any coords smaller than it will be set to it
8. int rightmost_coord: any coords larger than it will be set to it
9. float scale_factor: scale factor on pileup
10. float baseline_value: the minimum value of pileup
Return:
1. PosVal *: position-value pairs in bedGraph fashion.
2. long * final_length: the final length for the returned array of PosVal.
Example of usage:
pileup = single_end_pileup ( {1,2,3}, 3, {2,3,4}, 3, 0, 3, 0, 20, 0.5, 1.0, &final_length );
for ( i = 0; i < final_length; i++ )
{
printf( "pos:%d value:%.2f\n", pileup[i].pos, pileup[i].value );
}
*/
struct PosVal * single_end_pileup( int * plus_tags, long l_plus_tags, int * minus_tags, long l_minus_tags, int five_shift, int three_shift, int leftmost_coord, int rightmost_coord, float scale_factor, float baseline_value, long * final_length )
{
long i_s, i_e, i;
int p, pre_p, pileup;
long l = l_plus_tags + l_minus_tags;
int * start_poss, * end_poss, * ptr_start_poss, * ptr_end_poss;
struct PosVal * pos_value_array;
start_poss = (int *) malloc( l * sizeof( int ) );
end_poss = (int *) malloc( l * sizeof( int ) );
ptr_start_poss = start_poss;
ptr_end_poss = end_poss;
for ( i = 0; i < l_plus_tags; i++ )
{
*ptr_start_poss = plus_tags[ i ] - five_shift; ptr_start_poss++;
*ptr_end_poss = plus_tags[ i ] + three_shift; ptr_end_poss++;
}
for ( i = 0; i < l_minus_tags; i++ )
{
*ptr_start_poss = minus_tags[ i ] - three_shift; ptr_start_poss++;
*ptr_end_poss = minus_tags[ i ] + five_shift; ptr_end_poss++;
}
qsort( start_poss, l, sizeof( int ), cmpfunc_simple );
qsort( end_poss, l, sizeof( int ), cmpfunc_simple );
// fix negative coordinations and those extends over end of chromosomes
start_poss = fix_coordinates ( start_poss, l, leftmost_coord, rightmost_coord );
end_poss = fix_coordinates ( end_poss, l, leftmost_coord, rightmost_coord );
pos_value_array = quick_pileup ( start_poss, end_poss, l, scale_factor, baseline_value, final_length );
// clean mem
free( start_poss );
free( end_poss );
return pos_value_array;
}
SaveScreen::SaveScreen(int X1,int Y1,int X2,int Y2)
{
fix_coordinates(X1, Y1, X2, Y2);
_OT(SysLog(L"[%p] SaveScreen::SaveScreen(X1=%i,Y1=%i,X2=%i,Y2=%i)",this,X1,Y1,X2,Y2));
SaveArea(X1,Y1,X2,Y2);
}
