/**
* Count number of bases, for a given chromosome and marker type
*
* @param mtype
* @param chr
* @param markers
* @return
*/
void countBases(String mtype, Chromosome chr, Markers markers) {
String chrName = chr.getChromosomeName();
if (verbose) System.err.print(" " + chrName);
// Initialize
byte busy[] = new byte[chr.size()];
for (int i = 0; i < busy.length; i++) busy[i] = 0;
for (Marker m : markers) {
// Same marker type & same chromo? Count bases
if (m.getChromosomeName().equals(chrName) && markerTypes.isType(m, mtype)) {
for (int i = m.getStart(); i <= m.getEnd(); i++) busy[i] = 1;
}
}
int latest = 0;
for (int i = 0; i < busy.length; i++) {
// Transition? Count another marker
if ((i > 0) && (busy[i] != 0) && (busy[i - 1] == 0)) {
if ((i - latest) <= readLength)
countBases.inc(mtype, i - latest); // Intervals are less than one read away? Unify them
else countMarkers.inc(mtype);
}
// Base busy? Count another base
if (busy[i] != 0) {
countBases.inc(mtype);
latest = i;
}
}
}
