String countsString() {
return mReadGroup
+ "\t"
+ mTotalReference
+ "\t"
+ mLengthDist.count()
+ "\t"
+ Utils.realFormat(mLengthDist.sum())
+ "\t"
+ Utils.realFormat(mLengthDist.sumSq())
+ "\t"
+ mFragmentSizeDist.count()
+ "\t"
+ Utils.realFormat(mFragmentSizeDist.sum())
+ "\t"
+ Utils.realFormat(mFragmentSizeDist.sumSq())
+ "\t"
+ mGapSizeDist.count()
+ "\t"
+ Utils.realFormat(mGapSizeDist.sum())
+ "\t"
+ Utils.realFormat(mGapSizeDist.sumSq())
+ "\t"
+ mMaxAlignment
+ "\t"
+ mProper
+ "\t"
+ mDiscordant
+ "\t"
+ mUnmated;
}
void add(ReadGroupStats stats) {
mLengthDist.add(stats.mLengthDist);
mFragmentSizeDist.add(stats.mFragmentSizeDist);
mGapSizeDist.add(stats.mGapSizeDist);
mMaxAlignment = Math.max(mMaxAlignment, stats.mMaxAlignment);
mProper += stats.mProper;
mDiscordant += stats.mDiscordant;
mUnmated += stats.mUnmated;
if (detectOverflow()) {
throw new NoTalkbackSlimException(
"Overflow detected in read group statistics calculation for read group: " + id());
}
}
void calculate() {
if (mLengthDist != null) {
mMeanLength = mLengthDist.count() > 1 ? mLengthDist.mean() : 0;
mFragmentStdDev = mFragmentSizeDist.count() > 1 ? mFragmentSizeDist.stdDev() + TINY : 0;
mFragmentMean = mFragmentSizeDist.count() > 1 ? mFragmentSizeDist.mean() : 0;
mGapStdDev = mGapSizeDist.count() > 1 ? mGapSizeDist.stdDev() + TINY : 0;
mGapMean = mGapSizeDist.count() > 1 ? mGapSizeDist.mean() : 0;
mProperRate = (double) (mProper + 1) / mTotalReference / 2.0 + TINY;
mDiscordantRate = (double) (mDiscordant + 1) / mTotalReference / 2.0 + TINY;
mUnmatedRate = (double) (mUnmated + 1) / mTotalReference / 2.0 + TINY;
mProperRandomRate = mDiscordantRate * mUnmatedRate;
// TODO we think this should be better:
// mProperRandomRate = mDiscordantRate * (2 * mGapStdDev / mTotalReference);
mAlignmentStartIgnored = (int) (mMeanLength * mAlignmentStartIgnoredFraction / 100);
}
}
boolean detectOverflow() {
return mProper < 0 || mDiscordant < 0 || mUnmatedRate < 0 || mLengthDist.count() < 0;
}
void addGapSize(int value) {
mGapSizeDist.add(value);
}
void addFragmentSize(int value) {
mFragmentSizeDist.add(value);
}
void addLength(int readlen) {
mLengthDist.add(readlen);
}
