boolean isNormalCovered = normalDepth >= 8;
if (isTumorCovered) { tumorCovered++; }
if (isNormalCovered) { normalCovered++; }
if (isTumorCovered && isNormalCovered) {somaticCovered++; }
totalSites++;
<BUG>if (totalSites % 20000 == 0) {
out.println(String.format("%s:%d %d %d %d %d", context.getContig(), context.getPosition(), totalSites, tumorCovered, normalCovered, somaticCovered));
}
return 1;</BUG>
}

boolean isNormalCovered = normalDepth >= 8;
if (isTumorCovered) { tumorCovered++; }
if (isNormalCovered) { normalCovered++; }
if (isTumorCovered && isNormalCovered) {somaticCovered++; }
totalSites++;
StringBuilder sb = new StringBuilder();
sb.append(context.getContig()).append(" ");
sb.append(context.getPosition());
out.println(sb.toString());
return 1;
}
