Lines Matching refs:prm
310 PerReadMetrics& prm, // per-read metrics in extend() argument
362 prm.nSdFmops++; in extend()
386 prm.nSdFmops++; in extend()
427 prm.nSdFmops++; in extend()
451 prm.nSdFmops++; in extend()
505 PerReadMetrics& prm, // per-read metrics in prioritizeSATups() argument
587 prm, in prioritizeSATups()
787 PerReadMetrics& prm, // per-read metrics in extendSeeds()
817 prm.nEeFail = 0; in extendSeeds()
818 prm.nUgFail = 0; in extendSeeds()
819 prm.nDpFail = 0; in extendSeeds()
870 prm, // per-read metrics in extendSeeds()
912 if(prm.nExDps >= maxDp || prm.nMateDps >= maxDp) { in extendSeeds()
915 if(prm.nExUgs >= maxUg || prm.nMateUgs >= maxUg) { in extendSeeds()
918 if(prm.nExIters >= maxIters) { in extendSeeds()
921 prm.nExIters++; in extendSeeds()
931 gws_[i].advanceElement((TIndexOffU)elt, ebwtFw, ref, sa, gwstate_, wr, wlm, prm); in extendSeeds()
972 prm.nRedundants++; in extendSeeds()
1046 prm.nExUgs++; in extendSeeds()
1048 prm.nExUgFails++; in extendSeeds()
1049 prm.nUgFail++; in extendSeeds()
1050 if(prm.nUgFail >= maxUgStreak) { in extendSeeds()
1056 prm.nExUgFails++; in extendSeeds()
1057 prm.nUgFail++; // count this as failure in extendSeeds()
1058 if(prm.nUgFail >= maxUgStreak) { in extendSeeds()
1063 prm.nExUgSuccs++; in extendSeeds()
1064 prm.nUgLastSucc = prm.nExUgs-1; in extendSeeds()
1065 if(prm.nUgFail > prm.nUgFailStreak) { in extendSeeds()
1066 prm.nUgFailStreak = prm.nUgFail; in extendSeeds()
1068 prm.nUgFail = 0; in extendSeeds()
1141 prm.nExDps++; in extendSeeds()
1143 prm.nExDpFails++; in extendSeeds()
1144 prm.nDpFail++; in extendSeeds()
1145 if(prm.nDpFail >= maxDpStreak) { in extendSeeds()
1148 if(bestCell > std::numeric_limits<TAlScore>::min() && bestCell > prm.bestLtMinscMate1) { in extendSeeds()
1149 prm.bestLtMinscMate1 = bestCell; in extendSeeds()
1153 prm.nExDpSuccs++; in extendSeeds()
1154 prm.nDpLastSucc = prm.nExDps-1; in extendSeeds()
1155 if(prm.nDpFail > prm.nDpFailStreak) { in extendSeeds()
1156 prm.nDpFailStreak = prm.nDpFail; in extendSeeds()
1158 prm.nDpFail = 0; in extendSeeds()
1427 PerReadMetrics& prm, // per-read metrics in extendSeedsPaired()
1497 prm.nEeFail = 0; in extendSeedsPaired()
1498 prm.nUgFail = 0; in extendSeedsPaired()
1499 prm.nDpFail = 0; in extendSeedsPaired()
1557 prm, // per-read metrics in extendSeedsPaired()
1598 if(prm.nExDps >= maxDp || prm.nMateDps >= maxDp) { in extendSeedsPaired()
1601 if(prm.nExUgs >= maxUg || prm.nMateUgs >= maxUg) { in extendSeedsPaired()
1604 if(prm.nExIters >= maxIters) { in extendSeedsPaired()
1607 if(eeMode && prm.nEeFail >= maxEeStreak) { in extendSeedsPaired()
1610 if(!eeMode && prm.nDpFail >= maxDpStreak) { in extendSeedsPaired()
1613 if(!eeMode && prm.nUgFail >= maxUgStreak) { in extendSeedsPaired()
1622 prm.nExIters++; in extendSeedsPaired()
1632 gws_[i].advanceElement((TIndexOffU)elt, ebwtFw, ref, sa, gwstate_, wr, wlm, prm); in extendSeedsPaired()
1672 prm.nRedundants++; in extendSeedsPaired()
1738 prm.nExEes++; in extendSeedsPaired()
1739 prm.nEeFail++; // say it's failed until proven successful in extendSeedsPaired()
1740 prm.nExEeFails++; in extendSeedsPaired()
1755 prm.nExUgs++; in extendSeedsPaired()
1756 prm.nUgFail++; // say it's failed until proven successful in extendSeedsPaired()
1757 prm.nExUgFails++; in extendSeedsPaired()
1836 prm.nExDps++; in extendSeedsPaired()
1837 prm.nDpFail++; // failed until proven successful in extendSeedsPaired()
1838 prm.nExDpFails++; // failed until proven successful in extendSeedsPaired()
1840 TAlScore bestLast = anchor1 ? prm.bestLtMinscMate1 : prm.bestLtMinscMate2; in extendSeedsPaired()
1843 prm.bestLtMinscMate1 = bestCell; in extendSeedsPaired()
1845 prm.bestLtMinscMate2 = bestCell; in extendSeedsPaired()
2080 prm.nMateDps++; in extendSeedsPaired()
2083 TAlScore bestLast = anchor1 ? prm.bestLtMinscMate2 : prm.bestLtMinscMate1; in extendSeedsPaired()
2086 prm.bestLtMinscMate2 = bestCell; in extendSeedsPaired()
2088 prm.bestLtMinscMate1 = bestCell; in extendSeedsPaired()
2356 prm.nMateDpSuccs++; in extendSeedsPaired()
2362 assert_gt(prm.nUgFail, 0); in extendSeedsPaired()
2363 assert_gt(prm.nExUgFails, 0); in extendSeedsPaired()
2364 prm.nExUgFails--; in extendSeedsPaired()
2365 prm.nExUgSuccs++; in extendSeedsPaired()
2366 prm.nUgLastSucc = prm.nExUgs-1; in extendSeedsPaired()
2367 if(prm.nUgFail > prm.nUgFailStreak) { in extendSeedsPaired()
2368 prm.nUgFailStreak = prm.nUgFail; in extendSeedsPaired()
2370 prm.nUgFail = 0; in extendSeedsPaired()
2372 assert_gt(prm.nEeFail, 0); in extendSeedsPaired()
2373 assert_gt(prm.nExEeFails, 0); in extendSeedsPaired()
2374 prm.nExEeFails--; in extendSeedsPaired()
2375 prm.nExEeSuccs++; in extendSeedsPaired()
2376 prm.nEeLastSucc = prm.nExEes-1; in extendSeedsPaired()
2377 if(prm.nEeFail > prm.nEeFailStreak) { in extendSeedsPaired()
2378 prm.nEeFailStreak = prm.nEeFail; in extendSeedsPaired()
2380 prm.nEeFail = 0; in extendSeedsPaired()
2382 assert_gt(prm.nDpFail, 0); in extendSeedsPaired()
2383 assert_gt(prm.nExDpFails, 0); in extendSeedsPaired()
2384 prm.nExDpFails--; in extendSeedsPaired()
2385 prm.nExDpSuccs++; in extendSeedsPaired()
2386 prm.nDpLastSucc = prm.nExDps-1; in extendSeedsPaired()
2387 if(prm.nDpFail > prm.nDpFailStreak) { in extendSeedsPaired()
2388 prm.nDpFailStreak = prm.nDpFail; in extendSeedsPaired()
2390 prm.nDpFail = 0; in extendSeedsPaired()
2393 prm.nMateDpFails++; in extendSeedsPaired()