// =========================================================
// Convenience method for reporting merged blocks by strand
// =========================================================
void BedMerge::ReportStranded(string chrom, int start, int end,
const vector<string> &names, const vector<string> &scores,
int mergeCount, string strand)
{
if (_bed->isZeroBased == false) {start++;}
printf("%s\t%d\t%d", chrom.c_str(), start, end);
// just the merged intervals
if (_numEntries == false && _reportNames == false && _reportScores == false) {
printf("\t%s\n", strand.c_str());
}
// merged intervals and counts
else if (_numEntries == true && _reportNames == false && _reportScores == false) {
printf("\t%d\t%s\n", mergeCount, strand.c_str());
}
// merged intervals and names
else if (_numEntries == false && _reportNames == true && _reportScores == false) {
ReportMergedNames(names);
printf("\t%s\n", strand.c_str());
}
// merged intervals and scores
else if (_numEntries == false && _reportNames == false && _reportScores == true) {
ReportMergedScores(scores);
printf("\t%s\n", strand.c_str());
}
// merged intervals, names, and scores
else if (_numEntries == false && _reportNames == true && _reportScores == true) {
ReportMergedNames(names);
ReportMergedScores(scores);
printf("\t%s\n", strand.c_str());
}
}
// ===============================================
// Convenience method for reporting merged blocks
// ================================================
void BedMerge::Report(string chrom, int start,
int end, const vector<string> &names,
const vector<string> &scores, int mergeCount)
{
// ARQ: removed to force all output to be zero-based, BED format, reagrdless of input type
//if (_bed->isZeroBased == false) {start++;}
printf("%s\t%d\t%d", chrom.c_str(), start, end);
// just the merged intervals
if (_numEntries == false && _reportNames == false &&
_reportScores == false) {
printf("\n");
}
// merged intervals and counts
else if (_numEntries == true && _reportNames == false &&
_reportScores == false) {
printf("\t%d\n", mergeCount);
}
// merged intervals, counts, and scores
else if (_numEntries == true && _reportNames == false &&
_reportScores == true) {
printf("\t%d", mergeCount);
ReportMergedScores(scores);
printf("\n");
}
// merged intervals, counts, and names
else if (_numEntries == true && _reportNames == true &&
_reportScores == false) {
ReportMergedNames(names);
printf("\t%d\n", mergeCount);
}
// merged intervals, counts, names, and scores
else if (_numEntries == true && _reportNames == true &&
_reportScores == true) {
ReportMergedNames(names);
ReportMergedScores(scores);
printf("\t%d\n", mergeCount);
}
// merged intervals and names
else if (_numEntries == false && _reportNames == true &&
_reportScores == false) {
ReportMergedNames(names);
printf("\n");
}
// merged intervals and scores
else if (_numEntries == false && _reportNames == false &&
_reportScores == true) {
ReportMergedScores(scores);
printf("\n");
}
// merged intervals, names, and scores
else if (_numEntries == false && _reportNames == true &&
_reportScores == true) {
ReportMergedNames(names);
ReportMergedScores(scores);
printf("\n");
}
}
