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Commit 76209a3d authored by Aaron's avatar Aaron
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80char cleanup of merge.

parent f27d4e7a
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src/mergeBed/mergeBed.cpp
+ 51
− 27
View file @ 76209a3d
......@@ -107,50 +107,59 @@ BedMerge::~BedMerge(void) {
// ===============================================
// 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)
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) {
if (_numEntries == false && _reportNames == false &&
_reportScores == false) {
printf("\n");
}
// merged intervals and counts
else if (_numEntries == true && _reportNames == false && _reportScores == false) {
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) {
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) {
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) {
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) {
else if (_numEntries == false && _reportNames == true &&
_reportScores == false) {
ReportMergedNames(names);
printf("\n");
}
// merged intervals and scores
else if (_numEntries == false && _reportNames == false && _reportScores == true) {
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) {
else if (_numEntries == false && _reportNames == true &&
_reportScores == true) {
ReportMergedNames(names);
ReportMergedScores(scores);
printf("\n");
......@@ -161,53 +170,62 @@ void BedMerge::Report(string chrom, int start, int end,
// =========================================================
// 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)
void BedMerge::ReportStranded(string chrom, int start,
int end, const vector<string> &names,
const vector<string> &scores, int mergeCount,
string strand)
{
// 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) {
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) {
else if (_numEntries == true && _reportNames == false &&
_reportScores == false) {
printf("\t%d\t%s\n", mergeCount, strand.c_str());
}
// merged intervals, counts, and scores
else if (_numEntries == true && _reportNames == false && _reportScores == true) {
else if (_numEntries == true && _reportNames == false &&
_reportScores == true) {
printf("\t%d", mergeCount);
ReportMergedScores(scores);
printf("\t%s\n", strand.c_str());
}
// merged intervals, counts, and names
else if (_numEntries == true && _reportNames == true && _reportScores == false) {
else if (_numEntries == true && _reportNames == true &&
_reportScores == false) {
ReportMergedNames(names);
printf("\t%d\t%s", mergeCount, strand.c_str());
printf("\n");
}
// merged intervals, counts, names, and scores
else if (_numEntries == true && _reportNames == true && _reportScores == true) {
else if (_numEntries == true && _reportNames == true &&
_reportScores == true) {
ReportMergedNames(names);
ReportMergedScores(scores);
printf("\t%s\t%d", strand.c_str(), mergeCount);
printf("\n");
}
// merged intervals and names
else if (_numEntries == false && _reportNames == true && _reportScores == false) {
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) {
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) {
else if (_numEntries == false && _reportNames == true &&
_reportScores == true) {
ReportMergedNames(names);
ReportMergedScores(scores);
printf("\t%s\n", strand.c_str());
......@@ -231,7 +249,9 @@ void BedMerge::MergeBed() {
if (_bed->_status != BED_VALID)
continue;
// new block, no overlap
if ( (((int) curr.start - end) > _maxDistance) || (curr.chrom != prev.chrom)) {
if ( (((int) curr.start - end) > _maxDistance) ||
(curr.chrom != prev.chrom))
{
if (start >= 0) {
Report(prev.chrom, start, end, names, scores, mergeCount);
// reset
......@@ -264,9 +284,9 @@ void BedMerge::MergeBed() {
}
// ==================================================================================
// ===============================================================================
// = Merge overlapping BED entries into a single entry, accounting for strandedness =
// ==================================================================================
// ================================================================================
void BedMerge::MergeBedStranded() {
// load the "B" bed file into a map so
......@@ -302,9 +322,12 @@ void BedMerge::MergeBedStranded() {
// is not on the current strand.
if (bedItr->strand != strands[s]) { continue; }
else { numOnStrand++; }
if ( (((int) bedItr->start - end) > _maxDistance) || (end < 0)) {
if ( (((int) bedItr->start - end) > _maxDistance) ||
(end < 0))
{
if (start >= 0) {
ReportStranded(chrom, start, end, names, scores, mergeCount, strands[s]);
ReportStranded(chrom, start, end, names,
scores, mergeCount, strands[s]);
// reset
mergeCount = 1;
names.clear();
......@@ -323,7 +346,8 @@ void BedMerge::MergeBedStranded() {
}
}
if (start >= 0) {
ReportStranded(chrom, start, end, names, scores, mergeCount, strands[s]);
ReportStranded(chrom, start, end, names,
scores, mergeCount, strands[s]);
}
}
}
......
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