int main(int argc, char **argv)
{
Base base(10);
AnotherBase anotherBase(20);
Derived derived(30, 40);
printBase(base);
printBase(derived);
printAnotherBase(anotherBase);
printAnotherBase(derived);
return 0;
}
void printModel(Game *game)
{
int i;
for(i=0; i<game->numRounds; i++) {
printBase(&flopsBase[i]);
}
}
void printModel(Game *game)
{
int i;
for(i=0; i<game->numRounds; i++) {
fprintf(stdout, "%d th round:\n", i);
printBase(&flopsBase[i]);
}
}
// o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o+o
void
Type::printType( std::ostream& out, Symbol *name, bool showBase, int level ) const
{
if (showBase) {
printBase(out,level);
if (name != NULL) out << " ";
}
printBefore(out,name,level);
printAfter(out);
}
void processIntToken( char* inStr, struct argsInfo info ){
long intToken;
int i;
ptrError = EINVAL;
// Convert string to long
intToken = strToLong(inStr, info.inputBase);
/* Check for non-integer errors */
if (errno == ptrError) {
(void) fprintf(stderr, STR_INT_ENDPTR_ERR, inStr,\
info.inputBase);
return;
}
/* Check for conversion errors */
if (errno) {
perror(inStr);
return;
}
/* Print English mode */
if (info.mode & E_FLAG) {
/* Check for negative numbers */
if (intToken < 0) {
(void) printf(STR_MINUS); // Print out minus sign
}
printEnglish(abs(intToken));
(void) printf(STR_NEWLINE);
}
/* Print out the numbers in the given bases*/
for (i = MIN_BASE; i <= MAX_BASE; i++) {
// Get the actual base value based on the given flags
int realBase = getRealBase(BASE_MASK(i) & info.outputBases);
switch (realBase) {
case 0:
break;
/* Print in binary representation*/
case 2:
printIntBinary(intToken);
break;
/* Print out prefix 0 and number in base 8 */
case 8:
/* Print out negative sign if negative number */
if (intToken < 0) {
(void) printf(STR_NEG_PREFIX);
}
(void) printf(STR_OCT_PREFIX);
printBase(abs(intToken), realBase);
(void) printf(STR_NEWLINE);
break;
/* Print out prefix 0x and number in base 16 */
case 16:
/* Print out negative sign if negative number */
if (intToken < 0) {
(void) printf(STR_NEG_PREFIX);
}
(void) printf(STR_HEX_PREFIX);
printBase(abs(intToken), realBase);
(void) printf(STR_NEWLINE);
break;
/* Print out number in given bases without prefixes */
default:
if (intToken < 0) {
(void) printf(STR_NEG_PREFIX);
}
printBase(abs(intToken), realBase);
(void) printf(STR_NEWLINE);
break;
}
}
}
//main processing function
// controlling flow for collecting data
// from each alignment
int processline(string line)
{
// variable definition
stringList columns, deletions, insertions, mismatchList;
string softclippedHead, softclippedTail;
numList baseCounter, deletionBaseCounter, insertionBaseCounter, mismatchBaseCounter;
numList headClippedBaseCounter, tailClippedBaseCounter;
string chrom, id, sequence,quality;
string deletionsString, insertionString, clippedString;
string XGfield = "A", NMfield, MDfield;
int numberOfMismatch, numberOfGapExtention;
string cigarString, MDline, cigarLine;
int i, seqlength, headClipped = 0, tailClipped = 0;
double averageQualityScore, head5Qual, end5Qual;
columns = split(line,'\t');
chrom = columns[2];
// only collect data from aligned reads
if (chrom != "*")
{
//define columns
id = columns[0];
cigarString = columns[5];
sequence = columns[9];
quality = columns[10];
seqlength = sequence.length();
baseCounter = getBaseCount(sequence); // collect base content
averageQualityScore = averageQual(quality); // whole sequence quality
head5Qual = averageQual(quality.substr(0,5)); // first 5 base quality
end5Qual = averageQual(quality.substr(seqlength-5,5)); //end 5 base quality
//define extra field
// for XG, NM and MD
findField(columns, XGfield, NMfield, MDfield);
//get field item
numberOfMismatch = atoi(extractField(NMfield).c_str());
if (XGfield.at(0) == 'X')
{
numberOfGapExtention = atoi(extractField(XGfield).c_str());
}
else
{
numberOfGapExtention = 0;
}
// creating a line using MDfield
MDline = processMD(MDfield, deletions);
cigarLine = processCigar(cigarString, headClipped, tailClipped);
mismatchList = insertionAndMismatch(cigarLine, MDline, sequence, insertions, softclippedHead, softclippedTail, id, numberOfMismatch);
mismatchBaseCounter = getMismatchCount(mismatchList);
int sumOfMismatch = std::accumulate(mismatchBaseCounter.begin(), mismatchBaseCounter.end(), 0);
//count deletion and insertion
deletionsString = concatString(deletions);
insertionString = concatString(insertions);
deletionBaseCounter = getBaseCount(deletionsString);
insertionBaseCounter = getBaseCount(insertionString);
headClippedBaseCounter = getBaseCount(softclippedHead);
tailClippedBaseCounter = getBaseCount(softclippedTail);
//assertions for verifying program
assert (softclippedTail.length() == tailClipped);
assert (softclippedHead.length() == headClipped);
assert(accumulate(baseCounter.begin(),baseCounter.end(),0) == seqlength);
//assert(sumOfMismatch + numberOfGapExtention == numberOfMismatch);
// print out result
cout << id << "\t";
//print out base counts
printBase(baseCounter) ;
cout << averageQualityScore << "\t" << head5Qual << "\t" << end5Qual << "\t";
cout << numberOfGapExtention << "\t" << numberOfMismatch - numberOfGapExtention << "\t";
//print mismatch
// AtoC, AtoT, AtoG, CtoA, CtoT, CtoG, GtoA, GtoT, GtoC, TtoA,TtoC, TtoG
printBase(mismatchBaseCounter);
// print out deletion
printBase(deletionBaseCounter) ;
printBase(insertionBaseCounter) ;
cout << headClipped << "\t" << tailClipped << "\t";
printBase(headClippedBaseCounter);
printBase(tailClippedBaseCounter);
cout << seqlength;
cout << '\n';
}
return 0;
}
void
testprintBase()
{
printf( "Testing printBase()\n\n" );
printf( "First line in each group below is the *expected* output.\n" );
printf( "Second line in each group is what *printBase* outputs.\n");
printf( "They should match exactly!\n" );
/*
* Test with 0.
*/
printf( "\nTesting with value 0 - should print:\n"
"0000 0000 0000 0000 0000 0000 0000 0000\n" );
printBase( 0 );
printf( "\n" );
/*
* Test with 1.
*/
printf( "\nTesting with value 1 - should print:\n"
"0000 0000 0000 0000 0000 0000 0000 0001\n" );
printBase( 1 );
printf( "\n" );
/*
* Test with -1.
*/
printf( "\nTesting with value -1 - should print:\n"
"1111 1111 1111 1111 1111 1111 1111 1111\n" );
printBase( -1 );
printf( "\n" );
/*
* Test with LONG_MAX.
*/
printf( "\nTesting with value LONG_MAX - should print:\n"
"0111 1111 1111 1111 1111 1111 1111 1111\n" );
printBase( LONG_MAX );
printf( "\n" );
/*
* Test with LONG_MIN.
*/
printf( "\nTesting with value LONG_MIN - should print:\n"
"1000 0000 0000 0000 0000 0000 0000 0000\n" );
printBase( LONG_MIN );
printf( "\n" );
}
