Searched refs:maskMiddle (Results 1 – 6 of 6) sorted by relevance
| /dports/biology/bbmap/bbmap/current/kmer/ |
| H A D | TableReader.java | 48 boolean maskMiddle=false; in main()
51 …erLockFree loader=new TableLoaderLockFree(tables, k, mink, speed, hdist, edist, rcomp, maskMiddle); in main()
73 TableReader tr=new TableReader(k, mink, speed, qskip, qhdist, rcomp, maskMiddle); in main()
94 middleMask=maskMiddle ? ~(3L<<(2*(k/2))) : -1L; in TableReader()
150 final int minlen2=(maskMiddle ? k/2 : k); in countKmerHits()
199 final int minlen2=(maskMiddle ? k/2 : k); in findBestMatch()
268 final int minlen2=(maskMiddle ? k/2 : k); in markBits()
312 assert(!maskMiddle && middleMask==-1) : maskMiddle+", "+middleMask+", k="+", mink="+mink; in markBits()
530 public final boolean maskMiddle=false; field in TableReader
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| H A D | TableLoaderLockFree.java | 55 boolean maskMiddle=false; in main()
58 …erLockFree loader=new TableLoaderLockFree(tables, k, mink, speed, hdist, edist, rcomp, maskMiddle); in main()
96 middleMask=maskMiddle ? ~(3L<<(2*(k/2))) : -1L; in TableLoaderLockFree()
731 public final boolean maskMiddle=false; field in TableLoaderLockFree
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | BBDuk2.java | 295 maskMiddle=Parse.parseBoolean(b); in BBDuk2()
640 if(maskMiddle){ in BBDuk2()
642 maskMiddle=false; in BBDuk2()
649 if(maskMiddle){ in BBDuk2()
651 maskMiddle=false; in BBDuk2()
664 if(maskMiddle){System.err.println("maskMiddle="+maskMiddle);} in BBDuk2()
2528 final int minlen2=(maskMiddle ? k/2 : k); in countSetKmers()
2588 final int minlen2=(maskMiddle ? k/2 : k); in findBestMatch()
2804 assert(!maskMiddle && middleMask==-1) : maskMiddle+", "+middleMask+", k="+", mink="+mink; in ktrim()
2977 assert(!maskMiddle && middleMask==-1) : maskMiddle+", "+middleMask+", k="+", mink="+mink; in kmask()
[all …]
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| H A D | SplitNexteraLMP.java | 125 maskMiddle=Parse.parseBoolean(b); in parseArgument()
203 …LoaderLockFree loader=new TableLoaderLockFree(tables, k, mink, 0, hdist, edist, rcomp, maskMiddle); in processInner()
218 reader=new TableReader(k, mink, 0, 0, 0, rcomp, maskMiddle); in processInner()
617 private boolean maskMiddle=false; field in SplitNexteraLMP
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| H A D | BBDuk.java | 308 maskMiddle=Parse.parseBoolean(b); in BBDuk()
764 if(maskMiddle){ in BBDuk()
766 maskMiddle=false; in BBDuk()
801 minlen2=(maskMiddle ? k/2 : k); in BBDuk()
816 if(maskMiddle){ in BBDuk()
818 maskMiddle=false; in BBDuk()
1648 sb.append("#Mask middle: "+maskMiddle+"\n"); in dukString()
3609 assert(!maskMiddle && middleMask==-1) : maskMiddle+", "+middleMask+", k="+", mink="+mink; in ktrim()
3780 assert(!maskMiddle && middleMask==-1) : maskMiddle+", "+middleMask+", k="+", mink="+mink; in kmask()
3963 assert(!maskMiddle && middleMask==-1) : maskMiddle+", "+middleMask+", k="+", mink="+mink; in ksplit()
[all …]
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| H A D | Seal.java | 250 maskMiddle=Parse.parseBoolean(b); in Seal()
525 middleMask=maskMiddle ? ~(3L<<(2*(k/2))) : -1L; in Seal()
2626 final int minlen2=(maskMiddle ? k/2 : k);
2676 final int minlen2=(maskMiddle ? k/2 : k);
2889 private boolean maskMiddle=true;
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