- assert(seedLen >= OLEN && mld->getMinL() >= seedLen);
-
- memset(mw, 0, sizeof(double) * (M + 1));
- mw[0] = 1.0;
-
- for (int i = 1; i <= M; i++) {
- RefSeq& ref = refs->getRef(i);
- int totLen = ref.getTotLen();
- int fullLen = ref.getFullLen();
- int end = std::min(fullLen, totLen - gld->getMinL() + 1);
- double value = 0.0;
- int minL, maxL;
- int effL, pfpos;
-
- //seedPos is fpos here
- for (int seedPos = 0; seedPos < end; seedPos++)
- if (ref.getMask(seedPos)) {
- minL = gld->getMinL();
- maxL = std::min(gld->getMaxL(), totLen - seedPos);
- pfpos = seedPos;
- for (int fragLen = minL; fragLen <= maxL; fragLen++) {
- effL = std::min(fullLen, totLen - fragLen + 1);
- value += gld->getAdjustedProb(fragLen, totLen) * rspd->getAdjustedProb(pfpos, effL, fullLen);
+ assert(mld->getMinL() >= seedLen);
+
+ memset(mw, 0, sizeof(double) * (M + 1));
+ mw[0] = 1.0;
+
+ for (int i = 1; i <= M; i++) {
+ RefSeq& ref = refs->getRef(i);
+ int totLen = ref.getTotLen();
+ int fullLen = ref.getFullLen();
+ int end = std::min(fullLen, totLen - gld->getMinL() + 1);
+ double value = 0.0;
+ int minL, maxL;
+ int effL, pfpos;
+
+ //seedPos is fpos here
+ for (int seedPos = 0; seedPos < end; seedPos++)
+ if (ref.getMask(seedPos)) {
+ minL = gld->getMinL();
+ maxL = std::min(gld->getMaxL(), totLen - seedPos);
+ pfpos = seedPos;
+ for (int fragLen = minL; fragLen <= maxL; fragLen++) {
+ effL = std::min(fullLen, totLen - fragLen + 1);
+ value += gld->getAdjustedProb(fragLen, totLen) * rspd->getAdjustedProb(pfpos, effL, fullLen);
+ }
+ }
+
+ mw[i] = 1.0 - value;
+
+ if (mw[i] < 1e-8) {
+ //fprintf(stderr, "Warning: %dth reference sequence is masked for almost all positions!\n", i);
+ mw[i] = 0.0;
+ }