void SGEdgeStatsVisitor::postvisit(StringGraph* /*pGraph*/)
{
printf("FoundOverlaps\n");
printCounts(foundCounts);
printf("\nPotentially Missing Overlaps\n\n");
printCounts(missingCounts);
}
int main(int argSize, char ** argArray)
{
unsigned firstArg = 1, files, i, totalLines = 0, totalWords = 0, totalCharacters = 0;
char operator = 'a';
FILE * filePointer;
Result * results, totalResults;
//Determine the operator, if any
if (argSize > 1 && argArray[1][0] == '-')
{
switch (argArray[1][1])
{
case 'l':
case 'w':
case 'c':
operator = argArray[1][1];
default:
firstArg = 2;
}
}
//Calculate the results from either input or files
if (firstArg == argSize)
{
files = 1;
results = (Result *)malloc(files * sizeof(Result));
results[0] = calculateCounts(stdin, "");
}
else
{
files = argSize - firstArg;
results = (Result *)malloc(files * sizeof(Result));
for (i = 0; i < files; i++)
{
filePointer = fopen(argArray[firstArg + i], "r");
results[i] = calculateCounts(filePointer, argArray[firstArg + i]);
}
}
//Output the results
for (i = 0; i < files; i++)
{
printCounts(results[i], operator);
totalLines += results[i].lines;
totalWords += results[i].words;
totalCharacters += results[i].characters;
}
//Print the total results if there are more than 1 files
if (files > 1)
{
totalResults.lines = totalLines;
totalResults.words = totalWords;
totalResults.characters = totalCharacters;
totalResults.fileName = "Total";
printCounts(totalResults, operator);
}
free(results);
return 0;
}
void print( const PlayerT & player )
{
if ( player.state_ )
{
std::cout << "<Player side=\"" << player.side_ << "\"";
std::cout << " unum=\"" << player.unum_ << "\"";
std::cout << " type=\"" << player.type_ << "\"";
if ( player.state_ != 1 ) std::cout << " mode=\"" << player.state_ << "\"";
std::cout << ">\n";
printPos( player.x_, player.y_ );
printVel( player.vx_, player.vy_ );
printAngles( player.body_, player.neck_ );
printView( player.view_width_, player.view_quality_ == 'h' );
printStamina( player.stamina_, player.effort_, player.recovery_ );
printCounts( player.kick_count_,
player.dash_count_,
player.turn_count_,
player.say_count_,
player.turn_neck_count_,
player.catch_count_,
player.move_count_,
player.change_view_count_ );
std::cout << "</Player>\n";
}
}
int hubTrackSettings(char *hubUrl, struct hash *totals)
/* Read hub trackDb files, noting settings used. If hubUrl is NULL, do this for
* all public hubs */
{
if (hubUrl != NULL)
return oneHubTrackSettings(hubUrl, totals);
// Get all urls from hubPublic table
struct sqlConnection *conn = hConnectCentral();
char query[1024];
// NOTE: don't bother with site-local names for these tables
/*
sqlSafef(query, sizeof(query), "select hubUrl from %s where hubUrl not in (select hubUrl from %s)\n",
defaultHubPublicTableName, defaultHubStatusTableName);
*/
sqlSafef(query, sizeof(query), "select hubUrl from %s where shortLabel not like '%%Test%%'",
defaultHubPublicTableName);
struct slName *hub, *hubs = sqlQuickList(conn, query);
int errs = 0;
for (hub = hubs; hub != NULL; hub = hub->next)
{
errs += oneHubTrackSettings(hub->name, totals);
}
if (totals)
printCounts(totals);
return errs;
}
void getCountMagic(char* word) {
int i;
int k;
int sizeword = strlen(word);
for (i = 0; i < sizeword; i++) {
k = word[i] - 97;
counts_magic[k]++;
}
counts_magic[14] = (counts_magic[14] * 0.5);
printCounts(counts_magic, 30);
return;
}
int main(int argc, char ** argv) {
//WRITE ME (plus add appropriate error checking!)
if (argc == 1){
fprintf(stderr, "Please input a valid File!\n");
exit (EXIT_FAILURE);
}
FILE * file1 = fopen(argv[1], "r");
if (file1 == NULL){
fprintf(stderr, "File does not exist!\n");
exit (EXIT_FAILURE);
}
if (fclose(file1) != 0){
fprintf(stderr, "Failed to close file!\n");
exit (EXIT_FAILURE);
}
//read the key/value pairs from the file named by argv[1] (call the result kv)
kvarray_t * kvs = readKVs(argv[1]);
//count from 2 to argc (call the number you count i)
for (int i = 2; i < argc; i++) {
//count the values that appear in the file named by argv[i], using kv as the key/value pair
// (call this result c)
FILE * file2 = fopen(argv[i], "r");
if (file2 == NULL){
fprintf(stderr, "File does not exist!\n");
exit (EXIT_FAILURE);
}
if (fclose(file2) != 0){
fprintf(stderr, "Failed to close file!\n");
}
counts_t * c = countFile(argv[i], kvs);
//compute the output file name from argv[i] (call this outName)
char * outName = computeOutputFileName(argv[i]);
//open the file named by outName (call that f)
FILE * f = fopen(outName,"w");
//print the counts from c into the FILE f
printCounts(c,f);
//close f
fclose(f);
//free the memory for outName and c
free(outName);
freeCounts(c);
}
//free the memory for kv
freeKVs(kvs);
return EXIT_SUCCESS;
}
void getCount(char* word) {
int i;
int sizeword = strlen(word);
for (i = 0; i < sizeword; i++) {
char letter = word[i];
switch(letter) {
case 'f': counts[0]++; break;
case 'a': counts[1]++; break;
case 'c': counts[2]++; break;
case 'e': counts[3]++; break;
case 'b': counts[4]++; break;
case 'o': counts[5] = (counts[5] + 0.5); break;
case 'k': counts[6]++; break;
default: break;
}
}
printCounts(counts, 7);
return;
}
int oneHubTrackSettings(char *hubUrl, struct hash *totals)
/* Read hub trackDb files, noting settings used */
{
struct trackHub *hub = NULL;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
hub = trackHubOpen(hubUrl, "hub_0");
errCatchEnd(errCatch);
errCatchFree(&errCatch);
if (hub == NULL)
return 1;
printf("%s (%s)\n", hubUrl, hub->shortLabel);
struct trackHubGenome *genome;
struct hash *counts;
if (totals)
counts = totals;
else
counts = newHash(0);
struct hashEl *el;
for (genome = hub->genomeList; genome != NULL; genome = genome->next)
{
struct trackDb *tdb, *tdbs = trackHubTracksForGenome(hub, genome);
for (tdb = tdbs; tdb != NULL; tdb = tdb->next)
{
struct hashCookie cookie = hashFirst(trackDbHashSettings(tdb));
verbose(2, " track: %s\n", tdb->shortLabel);
while ((el = hashNext(&cookie)) != NULL)
{
int count = hashIntValDefault(counts, el->name, 0);
count++;
hashReplace(counts, el->name, intToPt(count));
}
}
}
if (!totals)
printCounts(counts);
trackHubClose(&hub);
return 0;
}
// If there is a simple undefeated Condorcet winner, that is enough. Return the winner.
static int VRR_plainCondorcet( VRR* it, int winnersLength, NameVote** winnersP, int** defeatCountP ) {
int* defeatCount;
int i;
defeatCount = (int*)malloc( sizeof(int)*it->numc );
assert( defeatCount != NULL );
if ( debug ) {
printCounts( stdout, it );
}
countDefeats( it, defeatCount );
for ( i = 0; i < it->numc; i++ ) {
if ( defeatCount[i] == 0 ) {
// winner
VRR_makeWinners( it, defeatCount );
free( defeatCount );
return VRR_returnWinners( it, winnersLength, winnersP );
}
}
*defeatCountP = defeatCount;
return -1;
}
VOID Fini(INT32 code, VOID *v)
{
UINT32 status = 0;
if (icount[0] != icount[1])
{
out << "***Mismatch in total instructions : Before " << dec << icount[0] <<
" After " << dec << icount[1] << endl;
status = 1;
}
UINT32 expectedCounts[5];
for (UINT32 i=0; i<5; i++)
expectedCounts[i] = 0;
for (UINT32 j=0; j<=icount[0]; j++)
{
for (UINT32 i=0; i<5; i++)
{
if (j & (1<<i))
{
expectedCounts[i]++;
}
}
}
for (UINT32 i=0; i<5; i++)
{
if (icountBits[i] != expectedCounts[i])
{
out << "*** Bit counts failed : " << dec << i << " expected " << expectedCounts[i] <<
" see " <<icountBits[i] << endl;
}
}
printCounts();
out.close();
_exit(status);
}
int main(int argc, char ** argv) {
int i;
if(argc<=2)
{
fprintf(stderr,"The no. of inputs are less");
return EXIT_FAILURE;
}
kvarray_t *kv=readKVs(argv[1]);
if(kv->length==-1)
{
printf("Couldn't open file!");
return EXIT_FAILURE;
}
if(kv->length==-2)
{
printf("Couldn't close file");
return EXIT_FAILURE;
}
//WRITE ME (plus add appropriate error checking!)
//read the key/value pairs from the file named by argv[1] (call the result kv)
for(i=2;i<argc;i++) {
counts_t *c=countFile(argv[i],kv); //count the values that appear in the file named by argv[i], using kv as the key/value pair
// (call this result c)
char *outName = computeOutputFileName(argv[i]);//compute the output file name from argv[i] (call this outName)
FILE *f = fopen(outName,"w");//open the file named by outName (call that f)
printCounts(c,f);//print the counts from c into the FILE f
if(fclose(f)!=0)
{
fprintf(stderr,"Couldn't close file!");
return EXIT_FAILURE;
}//close f
free(outName);
freeCounts(c); //free the memory for outName and c
}
freeKVs(kv); //free the memory for kv
return EXIT_SUCCESS;
}
int main(int argSize, char ** argArray)
{
unsigned firstArg = 1, files, i, totalLines = 0, totalWords = 0, totalCharacters = 0;
int process, descriptors[2];
char operator = 'a';
FILE * filePointer;
Result result, totalResults;
//Set up the pipe
pipe(descriptors);
//Determine the operator, if any
if (argSize > 1 && argArray[1][0] == '-')
{
switch (argArray[1][1])
{
case 'l':
case 'w':
case 'c':
operator = argArray[1][1];
default:
firstArg = 2;
}
}
//Calculate the results from either input or files
if (firstArg == argSize)
{
files = 1;
process = fork();
if (process == 0)
{
result = calculateCounts(stdin, "");
write(descriptors[1], &result, sizeof(result));
exit(0);
}
}
else
{
files = argSize - firstArg;
for (i = 0; i < files; i++)
{
process = fork();
if (process == 0)
{
filePointer = fopen(argArray[firstArg + i], "r");
result = calculateCounts(filePointer, argArray[firstArg + i]);
write(descriptors[1], &result, sizeof(result));
exit(0);
}
}
}
wait(0);
//Output the results
for (i = 0; i < files; i++)
{
read(descriptors[0], &result, sizeof(result));
printCounts(result, operator);
totalLines += result.lines;
totalWords += result.words;
totalCharacters += result.characters;
}
//Print the total results if there are more than 1 files
if (files > 1)
{
totalResults.lines = totalLines;
totalResults.words = totalWords;
totalResults.characters = totalCharacters;
totalResults.fileName = "Total";
printCounts(totalResults, operator);
}
return 0;
}
void abcCounts::print(funkyPars *pars){
if(pars->numSites==0)
return;
if(dumpCounts)
printCounts(header->target_name[pars->refId],pars->posi,pars->counts,pars->numSites,pars->nInd,bpos,bbin,dumpCounts,pars->keepSites);
if(bbin.l>0)
aio::bgzf_write(oFileCountsBin,bbin.s,bbin.l);bbin.l=0;
if(bpos.l>0)
aio::bgzf_write(oFileCountsPos,bpos.s,bpos.l);bpos.l=0;
if(doQsDist)
countQs(pars->chk,qsDist,pars->keepSites,minQ);
if(doDepth!=0){
assert(pars->counts!=NULL);
for(int s=0;s<pars->numSites;s++) {
if(pars->keepSites[s]==0)
continue;
for(int i=0;i<pars->nInd;i++){
int sum=0;
for(int a=0;a<4;a++)
sum+=pars->counts[s][i*4+a];
if(sum>maxDepth){
sum=maxDepth;
}
depthCount[i][sum]++;
}
}
//thorfinn below
for(int s=0;s<pars->numSites;s++) {
if(pars->keepSites[s]==0)
continue;
int sum=0;
for(int i=0;i<4*pars->nInd;i++){
sum+=pars->counts[s][i];
if(sum>maxDepth){
sum=maxDepth;
}
}
globCount[sum]++;
}
}
if(iCounts==1){
for(int s=0;s<pars->numSites;s++) {
if(pars->keepSites[s]==0)
continue;
int cnt[4];
for(int i=0;i<4;i++)
cnt[i] = pars->counts[s][i];
int p = pars->posi[s]+1;
aio::bgzf_write(oFileIcounts,&p,sizeof(int)); // new
aio::bgzf_write(oFileIcounts,cnt,sizeof(int)*4); // new
}
}
if(iCounts==2){
for(int s=0;s<pars->chk->nSites;s++){
// fprintf(stderr,"TT: %d %d\n",pars->chk->nd[s][0].l2,pars->chk->nd[s][0].deletion);
if(pars->keepSites[s]==0||pars->chk->nd==NULL||pars->chk->nd[s][0]->l2||pars->chk->nd[s][0]->deletion)
continue;
int count[4]={0,0,0,0};
//loop over persample reads
for(int l=0;pars->chk->nd[s][0]&&l<pars->chk->nd[s][0]->l;l++){
int allele = refToInt[pars->chk->nd[s][0]->seq[l]];
int tmp=lookup[pars->chk->nd[s][0]->seq[l]];
#if 0
fprintf(stderr,"l:%d b:%c qs:%d\n",l,pars->chk->nd[s][0].seq[l],pars->chk->nd[s][0].qs[l]);
#endif
if(allele==4)//skip of 'n'/'N'
continue;
if(qfileFname&&pars->chk->nd[s][0]->qs[l]<=qCutoff[tmp]) //skip if we are using qscores and we are below
continue;
// if q score bin to sample from: count if sampled
if(pars->chk->nd[s][0]->qs[l]==qCutoff[tmp]+1){
double x =drand48();
//fprintf(stderr,"skipping\n");
if(x>=fCutoff[tmp])
count[tmp%5]++;
}else // if in q score bigger: always count
count[tmp%5]++;
}
if(1||count[0]+ count[1]+count[2]+count[3]){
int p = pars->posi[s]+1;
aio::bgzf_write(oFileIcounts,&p,sizeof(int)); // new
aio::bgzf_write(oFileIcounts,count,sizeof(int)*4); // new
}
}
}
}