void norm_wins(int chrom_id, enum WINDOWTYPE wt, float *gclookup, float *gclookup_x){
int j;
int gc_index;
float new_depth;
struct window *win = NULL;
int win_cnt = 0;
float mean = 0.0;
float mean_x = 0.0;
switch (wt){
case LW:
win = chromosomes[chrom_id]->lw;
win_cnt = chromosomes[chrom_id]->lw_cnt;
mean = LW_MEAN;
mean_x = LW_MEAN_X;
break;
case SW:
win = chromosomes[chrom_id]->sw;
win_cnt = chromosomes[chrom_id]->sw_cnt;
mean = SW_MEAN;
mean_x = SW_MEAN_X;
break;
case CW:
win = chromosomes[chrom_id]->cw;
win_cnt = chromosomes[chrom_id]->cw_cnt;
mean = CW_MEAN;
mean_x = CW_MEAN_X;
break;
}
for (j=0; j<win_cnt; j++){
gc_index = win[j].gc * (float) GC_BIN;
if (isAutosome(win, j, chrom_id)){
if (MULTGC)
new_depth = gclookup[gc_index] * win[j].depth;
else
new_depth = win[j].depth - (gclookup[gc_index] - mean);
}
else{
if (MULTGC)
new_depth = gclookup_x[gc_index] * win[j].depth;
else
new_depth = win[j].depth - (gclookup_x[gc_index] - mean_x);
}
if (new_depth < 0) new_depth = 0;
win[j].depth = new_depth;
}
}
void calc_stat(enum WINDOWTYPE wt, float *gclookup, float *gclookup_x, char doClean, float *_max, float *_max_x, float *_min, float *_min_x){
int i, j, k;
float lw_var;
float lw_var_x;
int norm_win_cnt;
float max;
int norm_win_cnt_x;
float max_x;
float min;
float min_x;
int gc_index;
float gc_total[GC_BIN]; // total depth by GC
int gc_wincount[GC_BIN]; // count of windows with the given GC content
float gc_total_x[GC_BIN]; // total depth by GC
int gc_wincount_x[GC_BIN]; // count of windows with the given GC content
float MEAN = 0.0;
float MEAN_X = 0.0;
float maxcut, mincut;
float maxcut_x, mincut_x;
struct window *win = NULL;
float STD = 0.0;
float STD_X = 0.0;
float this_total = 0.0;
float this_total_x = 0.0;
float win_cnt;
lw_var = 0.0;
norm_win_cnt = 0;
lw_var_x = 0.0;
norm_win_cnt_x = 0;
win_cnt = 0;
for (i=0; i<GC_BIN; i++){
gc_total[i] = 0.0;
gclookup[i] = 0.0;
gc_wincount[i] = 0;
gc_total_x[i] = 0.0;
gclookup_x[i] = 0.0;
gc_wincount_x[i] = 0;
}
max = 0.0;
max_x = 0.0;
min = FLT_MAX;
min_x = FLT_MAX;
if (doClean){
for (i=0; i<num_chrom; i++){
switch (wt){
case LW:
win = chromosomes[i]->lw;
win_cnt = chromosomes[i]->lw_cnt;
MEAN = LW_MEAN;
MEAN_X = LW_MEAN_X;
STD = LW_STD;
STD_X = LW_STD_X;
break;
case SW:
win = chromosomes[i]->sw;
win_cnt = chromosomes[i]->sw_cnt;
MEAN = SW_MEAN;
MEAN_X = SW_MEAN_X;
STD = SW_STD;
STD_X = SW_STD_X;
break;
case CW:
win = chromosomes[i]->cw;
win_cnt = chromosomes[i]->cw_cnt;
MEAN = CW_MEAN;
MEAN_X = CW_MEAN_X;
STD = CW_STD;
STD_X = CW_STD_X;
break;
}
for (j=0; j<win_cnt; j++){
if (win[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
maxcut = MEAN + STDMULT * STD;
mincut = MEAN - STDMULT * STD;
if (mincut < MEAN / 10.0) mincut = MEAN / 10.0;
/* if (maxcut - MEAN > MEAN - mincut)
maxcut = MEAN + (MEAN - mincut); */
if (win[j].depth > maxcut || win[j].depth < mincut){
/* Remove this window and its neighbors from controls */
win[j].isControl = 0;
if (wt != CW){
k = j;
while (k > 0 && win[k-1].end >= win[j].start){
win[--k].isControl = 0;
}
k = j;
while (k < win_cnt-1 && win[k+1].start <= win[j].end){
win[++k].isControl = 0;
}
}
else{
if (j > 0)
win[j-1].isControl = 0;
if (j < win_cnt-1)
win[j+1].isControl = 0;
}
}
else{
this_total += win[j].depth;
norm_win_cnt++;
}
} // if AUTOSOME
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
else{
maxcut_x = MEAN_X + 2 * STD_X;
mincut_x = MEAN_X - 2 * STD_X;
if (mincut_x < MEAN_X / 10.0) mincut_x = MEAN_X / 10.0;
if (win[j].depth > maxcut_x || win[j].depth < mincut_x){
/* Remove this window and its neighbors from controls */
win[j].isControl = 0;
if (wt != CW){
k = j;
while (k > 0 && win[k-1].end >= win[j].start){
win[--k].isControl = 0;
}
k = j;
while (k < win_cnt-1 && win[k+1].start <= win[j].end){
win[++k].isControl = 0;
}
}
else{
if (j > 0)
win[j-1].isControl = 0;
if (j < win_cnt-1)
win[j+1].isControl = 0;
}
}
else{
this_total_x += win[j].depth;
norm_win_cnt_x++;
}
} // if chrX
}
}
}
MEAN_X = this_total_x / norm_win_cnt_x;
MEAN = this_total / norm_win_cnt;
switch (wt){
case LW:
LW_MEAN = MEAN;
LW_MEAN_X = MEAN_X;
break;
case SW:
SW_MEAN = MEAN;
SW_MEAN_X = MEAN_X;
break;
case CW:
CW_MEAN = MEAN;
CW_MEAN_X = MEAN_X;
break;
}
} // do clean
this_total = 0.0;
norm_win_cnt = 0;
this_total_x = 0.0;
norm_win_cnt_x = 0;
for (i=0; i<num_chrom; i++){
switch (wt){
case LW:
win = chromosomes[i]->lw;
win_cnt = chromosomes[i]->lw_cnt;
break;
case SW:
win = chromosomes[i]->sw;
win_cnt = chromosomes[i]->sw_cnt;
break;
case CW:
win = chromosomes[i]->cw;
win_cnt = chromosomes[i]->cw_cnt;
break;
}
for (j=0; j<win_cnt; j++){
if (win[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
lw_var += (MEAN - win[j].depth) * (MEAN - win[j].depth);
norm_win_cnt++;
this_total += win[j].depth;
gc_index = win[j].gc * GC_BIN;
gc_total[gc_index] += win[j].depth;
gc_wincount[gc_index]++;
if (win[j].depth > max)
max = win[j].depth;
if (win[j].depth < min)
min = win[j].depth;
} // AUTOSOMES
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
else{ // if (strstr(chromosomes[i]->name, "chrX") && GENDER != FEMALE){
lw_var_x += (MEAN_X - win[j].depth) * (MEAN_X - win[j].depth);
norm_win_cnt_x++;
this_total_x += win[j].depth;
gc_index = win[j].gc * GC_BIN;
gc_total_x[gc_index] += win[j].depth;
gc_wincount_x[gc_index]++;
if (win[j].depth > max_x)
max_x = win[j].depth;
if (win[j].depth < min_x)
min_x = win[j].depth;
} // chrX
} // if control
} // inner for j
} // outer for i
MEAN_X = this_total_x / norm_win_cnt_x;
STD_X = sqrt(lw_var_x / norm_win_cnt_x);
MEAN = this_total / norm_win_cnt;
STD = sqrt(lw_var / norm_win_cnt);
switch (wt){
case LW:
LW_MEAN = MEAN;
LW_MEAN_X = MEAN_X;
LW_STD = STD;
LW_STD_X = STD_X;
break;
case SW:
SW_MEAN = MEAN;
SW_MEAN_X = MEAN_X;
SW_STD = STD;
SW_STD_X = STD_X;
break;
case CW:
CW_MEAN = MEAN;
CW_MEAN_X = MEAN_X;
CW_STD = STD;
CW_STD_X = STD_X;
break;
}
/* calculate the gclookup table */
for (i=0; i<GC_BIN; i++){
/* AUTOSOMES */
if (gc_wincount[i] == 0 || gc_total[i] == 0){
j=i-1;
while (j >= 0 && gc_total[j] == 0)
j--;
if (j >= 0 && (gc_total[j] == 0 || gc_wincount[j] == 0)){
j=i+1;
while (j < GC_BIN && gc_total[j] == 0) j++;
}
gc_total[i] = gc_total[j];
gc_wincount[i] = gc_wincount[j];
}
if (gc_total[i] != 0.0){
gclookup[i] = gc_total[i] / (float) gc_wincount[i];
if (MULTGC){
gclookup[i] = MEAN / gclookup[i];
if (gclookup[i] > MAX_GC_CORR)
gclookup[i] = MAX_GC_CORR;
else if (gclookup[i] < MIN_GC_CORR)
gclookup[i] = MIN_GC_CORR;
}
}
/* chrX */
if (GENDER != FEMALE){
if (gc_wincount_x[i] == 0 || gc_total_x[i] == 0){
j=i-1;
while (j >= 0 && gc_total_x[j] == 0)
j--;
if (j < 0) j = 0;
if (gc_total_x[j] == 0 || gc_wincount_x[j] == 0){
j=i+1;
while (j < GC_BIN && gc_total_x[j] == 0) j++;
}
gc_total_x[i] = gc_total_x[j];
gc_wincount_x[i] = gc_wincount_x[j];
}
if (gc_total_x[i] != 0.0){
gclookup_x[i] = gc_total_x[i] / (float) gc_wincount_x[i];
if (MULTGC){
gclookup_x[i] = MEAN_X / gclookup_x[i];
if (gclookup_x[i] > MAX_GC_CORR)
gclookup_x[i] = MAX_GC_CORR;
else if (gclookup_x[i] < MIN_GC_CORR)
gclookup_x[i] = MIN_GC_CORR;
}
}
}
}
*_max = max;
*_max_x = max_x;
*_min = min;
*_min_x = min_x;
}
void calc_stat(enum WINDOWTYPE wt, float *gclookup, float *gclookup_x, char doClean, float *_max, float *_max_x, float *_min, float *_min_x){
int i, j, k;
float lw_var;
float sw_var;
float cw_var;
float lw_total;
float sw_total;
float cw_total;
float lw_var_x;
float sw_var_x;
float cw_var_x;
float lw_total_x;
float sw_total_x;
float cw_total_x;
int win_cnt;
float max;
int win_cnt_x;
float max_x;
float min;
float min_x;
int gc_index;
float gc_total[GC_BIN]; // total depth by GC
int gc_wincount[GC_BIN]; // count of windows with the given GC content
float gc_total_x[GC_BIN]; // total depth by GC
int gc_wincount_x[GC_BIN]; // count of windows with the given GC content
float MEAN = 0.0;
float MEAN_X = 0.0;
float maxcut, mincut;
float maxcut_x, mincut_x;
lw_var = 0.0;
sw_var = 0.0;
cw_var = 0.0;
lw_total = 0.0;
sw_total = 0.0;
cw_total = 0.0;
win_cnt = 0;
lw_var_x = 0.0;
sw_var_x = 0.0;
cw_var_x = 0.0;
lw_total_x = 0.0;
sw_total_x = 0.0;
cw_total_x = 0.0;
win_cnt_x = 0;
for (i=0; i<GC_BIN; i++){
gc_total[i] = 0.0;
gclookup[i] = 0.0;
gc_wincount[i] = 0;
gc_total_x[i] = 0.0;
gclookup_x[i] = 0.0;
gc_wincount_x[i] = 0;
}
max = 0.0;
max_x = 0.0;
min = FLT_MAX;
min_x = FLT_MAX;
switch (wt){
case LW:
if (doClean){
for (i=0; i<num_chrom; i++){
for (j=0; j<chromosomes[i]->lw_cnt; j++){
if (chromosomes[i]->lw[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
maxcut = LW_MEAN + 2.5 * LW_STD;
mincut = LW_MEAN - 2.5 * LW_STD;
if (mincut < LW_MEAN / 10.0) mincut = LW_MEAN / 10.0;
if (maxcut - LW_MEAN > LW_MEAN - mincut)
maxcut = LW_MEAN + (LW_MEAN - mincut);
if (chromosomes[i]->lw[j].depth > maxcut || chromosomes[i]->lw[j].depth < mincut){
/* Remove this window and its neighbors from controls */
chromosomes[i]->lw[j].isControl = 0;
k = j;
while (k > 0 && chromosomes[i]->lw[k-1].end >= chromosomes[i]->lw[j].start){
chromosomes[i]->lw[--k].isControl = 0;
}
k = j;
while (k < chromosomes[i]->lw_cnt-1 && chromosomes[i]->lw[k+1].start <= chromosomes[i]->lw[j].end){
chromosomes[i]->lw[++k].isControl = 0;
}
}
else{
lw_total += chromosomes[i]->lw[j].depth;
win_cnt++;
}
} // if AUTOSOME
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
else{
maxcut_x = LW_MEAN_X + 2 * LW_STD_X;
mincut_x = LW_MEAN_X - 2 * LW_STD_X;
if (mincut_x < LW_MEAN_X / 10.0) mincut_x = LW_MEAN_X / 10.0;
if (chromosomes[i]->lw[j].depth > maxcut_x || chromosomes[i]->lw[j].depth < mincut_x){
/* Remove this window and its neighbors from controls */
chromosomes[i]->lw[j].isControl = 0;
k = j;
while (k > 0 && chromosomes[i]->lw[k-1].end >= chromosomes[i]->lw[j].start){
chromosomes[i]->lw[--k].isControl = 0;
}
k = j;
while (k < chromosomes[i]->lw_cnt-1 && chromosomes[i]->lw[k+1].start <= chromosomes[i]->lw[j].end){
chromosomes[i]->lw[++k].isControl = 0;
}
}
else{
lw_total_x += chromosomes[i]->lw[j].depth;
win_cnt_x++;
}
} // if chrX
}
}
}
LW_MEAN_X = lw_total_x / win_cnt_x;
LW_MEAN = lw_total / win_cnt;
} // do clean
lw_total = 0.0;
win_cnt = 0;
lw_total_x = 0.0;
win_cnt_x = 0;
for (i=0; i<num_chrom; i++){
for (j=0; j<chromosomes[i]->lw_cnt; j++){
if (chromosomes[i]->lw[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
lw_var += (LW_MEAN - chromosomes[i]->lw[j].depth) * (LW_MEAN - chromosomes[i]->lw[j].depth);
win_cnt++;
lw_total += chromosomes[i]->lw[j].depth;
gc_index = chromosomes[i]->lw[j].gc * GC_BIN;
gc_total[gc_index] += chromosomes[i]->lw[j].depth;
gc_wincount[gc_index]++;
if (chromosomes[i]->lw[j].depth > max)
max = chromosomes[i]->lw[j].depth;
if (chromosomes[i]->lw[j].depth < min)
min = chromosomes[i]->lw[j].depth;
} // AUTOSOMES
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
else{ // if (strstr(chromosomes[i]->name, "chrX") && GENDER != FEMALE){
lw_var_x += (LW_MEAN_X - chromosomes[i]->lw[j].depth) * (LW_MEAN_X - chromosomes[i]->lw[j].depth);
win_cnt_x++;
lw_total_x += chromosomes[i]->lw[j].depth;
gc_index = chromosomes[i]->lw[j].gc * GC_BIN;
gc_total_x[gc_index] += chromosomes[i]->lw[j].depth;
gc_wincount_x[gc_index]++;
if (chromosomes[i]->lw[j].depth > max_x)
max_x = chromosomes[i]->lw[j].depth;
if (chromosomes[i]->lw[j].depth < min_x)
min_x = chromosomes[i]->lw[j].depth;
} // chrX
} // if control
} // outer for
} // if (!doClean)
LW_MEAN_X = lw_total_x / win_cnt_x;
LW_STD_X = sqrt(lw_var_x / win_cnt_x);
LW_MEAN = lw_total / win_cnt;
LW_STD = sqrt(lw_var / win_cnt);
MEAN = LW_MEAN;
MEAN_X = LW_MEAN_X;
break;
case SW:
if (doClean){
for (i=0; i<num_chrom; i++){
for (j=0; j<chromosomes[i]->sw_cnt; j++){
if (chromosomes[i]->sw[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
maxcut = SW_MEAN + 2.5 * SW_STD;
mincut = SW_MEAN - 2.5 * SW_STD;
if (mincut < SW_MEAN / 10.0) mincut = SW_MEAN / 10.0;
if (maxcut - SW_MEAN > SW_MEAN - mincut)
maxcut = SW_MEAN + (SW_MEAN - mincut);
if (chromosomes[i]->sw[j].depth > maxcut || chromosomes[i]->sw[j].depth < mincut){
/* Remove this window and its neighbors from controls */
chromosomes[i]->sw[j].isControl = 0;
k = j;
while (k > 0 && chromosomes[i]->sw[k-1].end >= chromosomes[i]->sw[j].start){
chromosomes[i]->sw[--k].isControl = 0;
}
k = j;
while (k < chromosomes[i]->sw_cnt-1 && chromosomes[i]->sw[k+1].start <= chromosomes[i]->sw[j].end){
chromosomes[i]->sw[++k].isControl = 0;
}
}
else{
sw_total += chromosomes[i]->sw[j].depth;
win_cnt++;
}
} // if AUTOSOME
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
else{
maxcut_x = SW_MEAN_X + 2 * SW_STD_X;
mincut_x = SW_MEAN_X - 2 * SW_STD_X;
if (mincut_x < SW_MEAN_X / 10.0) mincut_x = SW_MEAN_X / 10.0;
if (chromosomes[i]->sw[j].depth > maxcut_x || chromosomes[i]->sw[j].depth < mincut_x){
/* Remove this window and its neighbors from controls */
chromosomes[i]->sw[j].isControl = 0;
k = j;
while (k > 0 && chromosomes[i]->sw[k-1].end >= chromosomes[i]->sw[j].start){
chromosomes[i]->sw[--k].isControl = 0;
}
k = j;
while (k < chromosomes[i]->sw_cnt-1 && chromosomes[i]->sw[k+1].start <= chromosomes[i]->sw[j].end){
chromosomes[i]->sw[++k].isControl = 0;
}
}
else{
sw_total_x += chromosomes[i]->sw[j].depth;
win_cnt_x++;
}
} // if chrX
}
}
}
SW_MEAN_X = sw_total_x / win_cnt_x;
SW_MEAN = sw_total / win_cnt;
} // do clean
sw_total = 0.0;
win_cnt = 0;
sw_total_x = 0.0;
win_cnt_x = 0;
for (i=0; i<num_chrom; i++){
for (j=0; j<chromosomes[i]->sw_cnt; j++){
if (chromosomes[i]->sw[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
sw_var += (SW_MEAN - chromosomes[i]->sw[j].depth) * (SW_MEAN - chromosomes[i]->sw[j].depth);
win_cnt++;
sw_total += chromosomes[i]->sw[j].depth;
gc_index = chromosomes[i]->sw[j].gc * GC_BIN;
gc_total[gc_index] += chromosomes[i]->sw[j].depth;
gc_wincount[gc_index]++;
if (chromosomes[i]->sw[j].depth > max)
max = chromosomes[i]->sw[j].depth;
if (chromosomes[i]->sw[j].depth < min)
min = chromosomes[i]->sw[j].depth;
} // AUTOSOMES
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
// if (strstr(chromosomes[i]->name, "chrX") && GENDER != FEMALE){
else{
sw_var_x += (SW_MEAN_X - chromosomes[i]->sw[j].depth) * (SW_MEAN_X - chromosomes[i]->sw[j].depth);
win_cnt_x++;
sw_total_x += chromosomes[i]->sw[j].depth;
gc_index = chromosomes[i]->sw[j].gc * GC_BIN;
gc_total_x[gc_index] += chromosomes[i]->sw[j].depth;
gc_wincount_x[gc_index]++;
if (chromosomes[i]->sw[j].depth > max_x)
max_x = chromosomes[i]->sw[j].depth;
if (chromosomes[i]->sw[j].depth < min_x)
min_x = chromosomes[i]->sw[j].depth;
} // chrX
} // if control
} // outer for
} // if (!doClean)
SW_MEAN_X = sw_total_x / win_cnt_x;
SW_STD_X = sqrt(sw_var_x / win_cnt_x);
SW_MEAN = sw_total / win_cnt;
SW_STD = sqrt(sw_var / win_cnt);
MEAN = SW_MEAN;
MEAN_X = SW_MEAN_X;
break;
case CW:
if (doClean){
for (i=0; i<num_chrom; i++){
for (j=0; j<chromosomes[i]->cw_cnt; j++){
if (chromosomes[i]->cw[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
maxcut = CW_MEAN + 2.5 * CW_STD;
mincut = CW_MEAN - 2.5 * CW_STD;
if (mincut < CW_MEAN / 10.0) mincut = CW_MEAN / 10.0;
if (maxcut - CW_MEAN > CW_MEAN - mincut)
maxcut = CW_MEAN + (CW_MEAN - mincut);
if (chromosomes[i]->cw[j].depth > maxcut || chromosomes[i]->cw[j].depth < mincut){
/* Remove this window and its neighbors from controls */
chromosomes[i]->cw[j].isControl = 0;
if (j > 0)
chromosomes[i]->cw[j-1].isControl = 0;
if (j < chromosomes[i]->cw_cnt-1)
chromosomes[i]->cw[j+1].isControl = 0;
}
else{
cw_total += chromosomes[i]->cw[j].depth;
win_cnt++;
}
} // if AUTOSOME
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
//if (strstr(chromosomes[i]->name, "chrX") && GENDER != FEMALE){
else{
maxcut_x = CW_MEAN_X + 2 * CW_STD_X;
mincut_x = CW_MEAN_X - 2 * CW_STD_X;
if (mincut_x < CW_MEAN_X / 10.0) mincut_x = CW_MEAN_X / 10.0;
if (chromosomes[i]->cw[j].depth > maxcut_x || chromosomes[i]->cw[j].depth < mincut_x){
/* Remove this window and its neighbors from controls */
chromosomes[i]->cw[j].isControl = 0;
if (j > 0)
chromosomes[i]->cw[j-1].isControl = 0;
if (j < chromosomes[i]->cw_cnt-1)
chromosomes[i]->cw[j+1].isControl = 0;
}
else{
cw_total_x += chromosomes[i]->cw[j].depth;
win_cnt_x++;
}
} // if chrX
}
}
}
CW_MEAN_X = cw_total_x / win_cnt_x;
CW_MEAN = cw_total / win_cnt;
} // do clean
cw_total = 0.0;
win_cnt = 0;
cw_total_x = 0.0;
win_cnt_x = 0;
for (i=0; i<num_chrom; i++){
for (j=0; j<chromosomes[i]->cw_cnt; j++){
if (chromosomes[i]->cw[j].isControl == 1){
/* AUTOSOMES -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
if (isAutosome(NULL, -1, i)){
cw_var += (CW_MEAN - chromosomes[i]->cw[j].depth) * (CW_MEAN - chromosomes[i]->cw[j].depth);
win_cnt++;
cw_total += chromosomes[i]->cw[j].depth;
gc_index = chromosomes[i]->cw[j].gc * GC_BIN;
gc_total[gc_index] += chromosomes[i]->cw[j].depth;
gc_wincount[gc_index]++;
if (chromosomes[i]->cw[j].depth > max)
max = chromosomes[i]->cw[j].depth;
if (chromosomes[i]->cw[j].depth < min)
min = chromosomes[i]->cw[j].depth;
} // AUTOSOMES
/* chrX -- NOTE: chrY is NOT a control; it is prefiltered, no need to check for it here */
else{
cw_var_x += (CW_MEAN_X - chromosomes[i]->cw[j].depth) * (CW_MEAN_X - chromosomes[i]->cw[j].depth);
win_cnt_x++;
cw_total_x += chromosomes[i]->cw[j].depth;
gc_index = chromosomes[i]->cw[j].gc * GC_BIN;
gc_total_x[gc_index] += chromosomes[i]->cw[j].depth;
gc_wincount_x[gc_index]++;
if (chromosomes[i]->cw[j].depth > max_x)
max_x = chromosomes[i]->cw[j].depth;
if (chromosomes[i]->cw[j].depth < min_x)
min_x = chromosomes[i]->cw[j].depth;
} // chrX
} // if control
} // outer for
} // if (!doClean)
CW_MEAN_X = cw_total_x / win_cnt_x;
CW_STD_X = sqrt(cw_var_x / win_cnt_x);
CW_MEAN = cw_total / win_cnt;
CW_STD = sqrt(cw_var / win_cnt);
MEAN = CW_MEAN;
MEAN_X = CW_MEAN_X;
break;
}
/* calculate the gclookup table */
for (i=0; i<GC_BIN; i++){
/* AUTOSOMES */
if (gc_wincount[i] == 0 || gc_total[i] == 0){
j=i-1;
while (j >= 0 && gc_total[j] == 0)
j--;
if (gc_total[j] == 0 || gc_wincount[j] == 0){
j=i+1;
while (j < GC_BIN && gc_total[j] == 0) j++;
}
gc_total[i] = gc_total[j];
gc_wincount[i] = gc_wincount[j];
}
if (gc_total[i] != 0.0){
gclookup[i] = gc_total[i] / (float) gc_wincount[i];
if (MULTGC){
gclookup[i] = MEAN / gclookup[i];
if (gclookup[i] > MAX_GC_CORR)
gclookup[i] = MAX_GC_CORR;
else if (gclookup[i] < MIN_GC_CORR)
gclookup[i] = MIN_GC_CORR;
}
}
/* chrX */
if (GENDER != FEMALE){
if (gc_wincount_x[i] == 0 || gc_total_x[i] == 0){
j=i-1;
while (j >= 0 && gc_total_x[j] == 0)
j--;
if (gc_total_x[j] == 0 || gc_wincount_x[j] == 0){
j=i+1;
while (j < GC_BIN && gc_total_x[j] == 0) j++;
}
gc_total_x[i] = gc_total_x[j];
gc_wincount_x[i] = gc_wincount_x[j];
}
if (gc_total_x[i] != 0.0){
gclookup_x[i] = gc_total_x[i] / (float) gc_wincount_x[i];
if (MULTGC){
gclookup_x[i] = MEAN_X / gclookup_x[i];
if (gclookup_x[i] > MAX_GC_CORR)
gclookup_x[i] = MAX_GC_CORR;
else if (gclookup_x[i] < MIN_GC_CORR)
gclookup_x[i] = MIN_GC_CORR;
}
}
}
}
*_max = max;
*_max_x = max_x;
*_min = min;
*_min_x = min_x;
}