int main(int argc, char *argv[])
{
// set some defaults
char *expDir = ".";
bool allreads = false;
bool unmappedReads = false;
bool lookup = false;
// process cmd line args
int argcc = 1;
while (argcc < argc) {
switch (argv[argcc][1]) {
case 'e': // set exp dir
argcc++;
expDir = argv[argcc];
break;
case 'a':
allreads = true;
break;
case 'u':
unmappedReads = true;
break;
case 'l':
argcc++;
lookup = true;
LookupInit(argv[argcc]);
break;
case 'L':
argcc++;
sscanf(argv[argcc], "%d", &lookupLimit);
break;
}
argcc++;
}
// crazy, but only way to get rows/cols right now is from mask.
Mask mask(1,1);
char maskPath[MAX_PATH_LENGTH];
sprintf(maskPath, "%s/bfmask.bin", expDir);
mask.SetMask(maskPath);
Histogram meanHist(1001, -1.0, 3.0);
Histogram stdevZeromerHist(1001, 0.0, 3.0);
Histogram stdevOnemerHist(1001, 0.0, 3.0);
Histogram avgZeromer(1001, -2.0, 1.0);
int w = mask.W();
int h = mask.H();
int validReads[w][h];
memset(validReads, 0, sizeof(validReads));
char blastFile[MAX_PATH_LENGTH];
sprintf(blastFile, "%s/keypass.rpt", expDir);
FILE *fp = fopen(blastFile, "r");
if (fp) {
char line[256];
while (fgets(line, sizeof(line), fp)) {
int row, col;
sscanf(line, "r%d|c%d", &row, &col);
char *ptr = strrchr(line, '|');
ptr++;
double qual;
int len;
sscanf(ptr, "%lf %d", &qual, &len);
validReads[col][row] = 0;
if (len > 50 && qual > 0.9) { // look at high quality reads
validReads[col][row] |= 1;
}
if (len > 30 && qual > 0.8) { // look at medium quality reads
validReads[col][row] |= 2;
}
if (len > 20 && !(validReads[col][row] & 4))
validReads[col][row] |= 4;
}
fclose(fp);
}
RawWells wells(expDir, "1.wells", mask.H(), mask.W());
wells.OpenForRead();
const WellData *data = NULL;
int numFlows = wells.NumFlows();
double measured[numFlows];
int keypassCount = 0;
int keypassFailCount = 0;
const int numFlowsInKey = 7;
int keypassLib[numFlowsInKey] = {1, 0, 1, 0, 0, 1, 0};
// int keypassLib[numFlowsInKey] = {0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1};
// const int numFlowsInKey = 11;
int i;
int zeromerCount = 0;
int onemerCount = 0;
double runningAvg0mer = 0.0;
double runningAvg1mer = 0.0;
double runningAvgN0mer = 0.0;
double runningAvgN1mer = 0.0;
int runningAvgCount = 0;
for(i=0;i<numFlowsInKey;i++) {
if (keypassLib[i] == 0)
zeromerCount++;
if (keypassLib[i] == 1)
onemerCount++;
}
while ((data = wells.ReadNextRegionData()) != NULL) {
// look for all live library reads
// 1 0 1 0 0 1 0 N - library TCAG key with TACG flow order
if (mask.Match(data->x, data->y, MaskLib)) {
bool useit = false;
if (unmappedReads && validReads[data->x][data->y] == 0)
useit = true;
else if (!unmappedReads && (allreads || (validReads[data->x][data->y] > 0))) // look at any (4), medium (2), or high(1) quality reads
useit = true;
if (lookup) {
useit = false;
if (LookupFind(data->y, data->x))
useit = true;
}
if (useit) {
// do simple keypass on raw well data:
// 1 - subtract avg 0-mer
// 2 - normalize to avg 1-mer
// 3 - threshold to generate vector, compare to 1st 7 flows of known
double avg0mer = 0.0;
for(i=0;i<numFlowsInKey;i++) {
if (keypassLib[i] == 0)
avg0mer += data->flowValues[i];
}
avg0mer /= zeromerCount;
double avg1mer = 0.0;
for(i=0;i<numFlowsInKey;i++) {
if (keypassLib[i] == 1)
avg1mer += data->flowValues[i];
}
avg1mer /= onemerCount;
// keep a running avg on 0-mer & 1-mer raw key signal
runningAvg0mer += avg0mer;
runningAvg1mer += avg1mer;
runningAvgCount++;
// key normalization...
avg0mer = 0.0; // force our algorithm to assume weka was right, and 0-mer on avg is already 0 !!! (need to think on this)
int flow;
for(flow=0;flow<numFlows;flow++) {
measured[flow] = data->flowValues[flow] - avg0mer;
}
double mult = 1.0/avg1mer;
for(flow=0;flow<numFlows;flow++) {
measured[flow] *= mult;
}
// calc avg normalized 0-mers & 1-mers
double avgN0mer = 0.0;
double avgN1mer = 0.0;
for(i=0;i<numFlowsInKey;i++) {
if (keypassLib[i] == 0)
avgN0mer += measured[i];
if (keypassLib[i] == 1)
avgN1mer += measured[i];
}
avgN0mer /= zeromerCount;
avgN1mer /= onemerCount;
runningAvgN0mer += avgN0mer;
runningAvgN1mer += avgN1mer;
// keypass...
int keypassVec[numFlowsInKey];
bool keypass = true;
for(flow=0;flow<numFlowsInKey;flow++) {
keypassVec[flow] = (int)(measured[flow]+0.5);
if (keypassVec[flow] != keypassLib[flow])
keypass = false;
}
if (keypass) {
keypassCount++;
} else {
keypassFailCount++;
}
// now, lets generate a few metrics and see how they correlate to mapped reads, interest is in mixed fragments
// metric1 - the dist between the avg 0-mer and the avg 1-mer - for this, we can usually call the read without cafie corrections for around 40 flows, so we go ahead and do that, then avg the 0-mer and 1-mer signals, then report the mean dist, and the stdev on the 0-mers and 1-mers
int numTestFlows = 12;
double onemerSig[40];
double zeromerSig[40];
int onemerCount = 0;
int zeromerCount = 0;
int base;
for(flow=numFlowsInKey+1;flow<numTestFlows+numFlowsInKey+1;flow++) { // note we ignore the key
base = (int)(measured[flow]+0.5);
if (base == 0) {
zeromerSig[zeromerCount] = measured[flow];
zeromerCount++;
avgZeromer.Add(measured[flow]);
}
if (base == 1) {
onemerSig[onemerCount] = measured[flow];
onemerCount++;
}
}
// if we have sane counts, calc metrics for this read
double avgZeroMer = 0.0;
double avgOneMer = 0.0;
double onemerStdev = 0.0;
double zeromerStdev = 0.0;
if (zeromerCount > 2 && onemerCount > 2) {
int k;
for(k=0;k<zeromerCount;k++) {
avgZeroMer += zeromerSig[k];
}
avgZeroMer /= (double)zeromerCount;
for(k=0;k<onemerCount;k++) {
avgOneMer += onemerSig[k];
}
avgOneMer /= (double)onemerCount;
double delta = 0.0;
for(k=0;k<zeromerCount;k++) {
delta = avgZeroMer - zeromerSig[k];
zeromerStdev += delta*delta;
}
zeromerStdev = sqrt(zeromerStdev);
for(k=0;k<onemerCount;k++) {
delta = avgOneMer - onemerSig[k];
onemerStdev += delta*delta;
}
onemerStdev = sqrt(onemerStdev);
meanHist.Add(avgOneMer - avgZeroMer);
stdevZeromerHist.Add(zeromerStdev);
stdevOnemerHist.Add(onemerStdev);
}
}
}
}
wells.Close();
// dump some stats
printf("Reads: pass/fail/all %d/%d/%d\n", keypassCount, keypassFailCount, keypassCount + keypassFailCount);
printf("Avg signals in key: Raw: 0-mer: %.4lf 1-mer: %.4lf Norm: 0-mer: %.4lf 1-mer: %.4lf\n",
runningAvg0mer/runningAvgCount, runningAvg1mer/runningAvgCount, runningAvgN0mer/runningAvgCount, runningAvgN1mer/runningAvgCount);
meanHist.Dump("AvgDist.txt", 1);
stdevZeromerHist.Dump("ZeromerStdev.txt", 1);
stdevOnemerHist.Dump("OnemerStdev.txt", 1);
avgZeromer.Dump("Avg0mer.txt", 1);
}
void
RTFInit ()
{
int i;
RTFColor *cp;
RTFFont *fp;
RTFStyle *sp;
RTFStyleElt *eltList, *ep;
rtfClass = -1;
pushedClass = -1;
pushedChar = EOF;
rtfLineNum = 0;
rtfLinePos = 0;
prevChar = EOF;
bumpLine = 0;
if (rtfTextBuf == (char *) NULL) /* initialize text buffers */
{
rtfTextBuf = RTFAlloc (rtfBufSiz);
pushedTextBuf = RTFAlloc (rtfBufSiz);
if (rtfTextBuf == (char *) NULL
|| pushedTextBuf == (char *) NULL)
RTFPanic ("Cannot allocate text buffers.");
rtfTextBuf[0] = pushedTextBuf[0] = '\0';
}
RTFFree (inputName);
RTFFree (outputName);
inputName = outputName = (char *) NULL;
/* initialize control symbol lookup table */
LookupInit ();
for (i = 0; i < rtfMaxClass; i++)
RTFSetClassCallback (i, (RTFFuncPtr) NULL);
for (i = 0; i < rtfMaxDestination; i++)
RTFSetDestinationCallback (i, (RTFFuncPtr) NULL);
/* install built-in destination readers */
RTFSetDestinationCallback (rtfFontTbl, ReadFontTbl);
RTFSetDestinationCallback (rtfColorTbl, ReadColorTbl);
RTFSetDestinationCallback (rtfStyleSheet, ReadStyleSheet);
RTFSetDestinationCallback (rtfInfo, ReadInfoGroup);
RTFSetDestinationCallback (rtfPict, ReadPictGroup);
RTFSetDestinationCallback (rtfObject, ReadObjGroup);
RTFSetReadHook ((RTFFuncPtr) NULL);
/* dump old lists if necessary */
while (fontList != (RTFFont *) NULL)
{
fp = fontList->rtfNextFont;
RTFFree (fontList->rtfFName);
RTFFree ((char *) fontList);
fontList = fp;
}
while (colorList != (RTFColor *) NULL)
{
cp = colorList->rtfNextColor;
RTFFree ((char *) colorList);
colorList = cp;
}
while (styleList != (RTFStyle *) NULL)
{
sp = styleList->rtfNextStyle;
eltList = styleList->rtfSSEList;
while (eltList != (RTFStyleElt *) NULL)
{
ep = eltList->rtfNextSE;
RTFFree (eltList->rtfSEText);
RTFFree ((char *) eltList);
eltList = ep;
}
RTFFree (styleList->rtfSName);
RTFFree ((char *) styleList);
styleList = sp;
}
CharSetInit ();
csTop = 0;
}