public FeatureWrappedAlignment(BasicFeature f) {
this.readName = f.getName();
this.chr = f.getChr();
this.start = f.getStart();
this.end = f.getEnd();
strand = f.getStrand();
if (f.getExonCount() > 0) {
blocks = new AlignmentBlock[f.getExonCount()];
int i = 0;
for (Exon exon : f.getExons()) {
int length = exon.getLength();
byte[] seq = new byte[length];
blocks[i] = new AlignmentBlock(exon.getStart(), seq, seq, this);
i++;
}
}
}
