Searched refs:retainSemiperfect (Results 1 – 3 of 3) sorted by relevance
| /dports/biology/bbmap/bbmap/current/var/ |
| H A D | GenerateVarlets3.java | 268 final boolean retainSemiperfect=maxDistFromDefined!=0;
284 SiteR head=toImperfectSites(s, retainSemiperfect);
309 public SiteR toImperfectSites(String s, boolean retainSemiperfect){
323 if(ssr.perfect || (ssr.semiperfect && !retainSemiperfect)){retain=false;}
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| /dports/biology/bbmap/bbmap/current/shared/ |
| H A D | Tools.java | 1449 …ist(ArrayList<SiteScore> ssl, float fractionOfMax, boolean retainPaired, boolean retainSemiperfect,
1466 …trimSitesBelowCutoff(ssl, cutoff, retainPaired, retainSemiperfect, minSitesToRetain, maxSitesToRet…
1471 …iteListByMax(ArrayList<SiteScore> ssl, int cutoff, boolean retainPaired, boolean retainSemiperfect,
1477 …trimSitesBelowCutoff(ssl, cutoff, retainPaired, retainSemiperfect, minSitesToRetain, maxSitesToRet…
1908 …sBelowCutoff(ArrayList<SiteScore> ssl, int cutoff, boolean retainPaired, boolean retainSemiperfect, in trimSitesBelowCutoff() argument
1924 if(!retainSemiperfect || !ss.semiperfect){ in trimSitesBelowCutoff()
1938 if(!retainSemiperfect || !ss.semiperfect){ in trimSitesBelowCutoff()
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| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | AbstractMapThread.java | 1413 …stAdvanced(ArrayList<SiteScore> list, boolean retainPaired, boolean retainSemiperfect, int maxScor… in trimListAdvanced() argument
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