| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | BBIndex5.java | 633 final int baseChrom=baseChrom(chrom);
863 final int baseChrom=baseChrom(baseChrom_);
892 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1204 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1213 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1218 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1274 final int baseChrom=baseChrom(baseChrom_);
1325 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1670 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1722 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
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| H A D | BBIndexPacBio.java | 644 final int baseChrom=baseChrom(chrom);
869 final int baseChrom=baseChrom(baseChrom_);
898 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1188 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1197 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1202 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1258 final int baseChrom=baseChrom(baseChrom_);
1309 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1634 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1683 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
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| H A D | BBIndex.java | 668 final int baseChrom=baseChrom(chrom);
889 final int baseChrom=baseChrom(baseChrom_);
916 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1206 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1262 final int baseChrom=baseChrom(baseChrom_);
1313 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1673 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1755 final int baseChrom=baseChrom(baseChrom_); in camelWalk3() local
1804 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)); in camelWalk3()
2309 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
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| H A D | BBIndexAcc.java | 741 final int baseChrom=baseChrom(chrom);
951 final int baseChrom=baseChrom(baseChrom_);
978 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1272 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1281 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1286 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1342 final int baseChrom=baseChrom(baseChrom_);
1393 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1751 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1800 final int baseChrom=baseChrom(baseChrom_); in findMaxQscore2() local
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| H A D | IndexMaker4.java | 142 for(int i=baseChrom(minChrom); i<=maxChrom; i++){ in makeArrays()
173 Data.sysout.println("Indexing threads started for block "+baseChrom(minChrom)+"-"+maxChrom); in makeArrays()
184 Data.sysout.println("Indexing threads finished for block "+baseChrom(minChrom)+"-"+maxChrom); in makeArrays()
192 for(int i=baseChrom(minChrom); i<=maxChrom; i++){ in makeArrays()
354 int baseChrom=baseChrom(chrom); in fillArrays() local
410 assert(numberToChrom(number, baseChrom)==chrom); in fillArrays()
441 public final int numberToChrom(int number, int baseChrom){ in numberToChrom() argument
442 assert((baseChrom&CHROM_MASK_LOW)==0) : Integer.toHexString(number)+", baseChrom="+baseChrom; in numberToChrom()
443 assert(baseChrom>=0) : Integer.toHexString(number)+", baseChrom="+baseChrom; in numberToChrom()
448 out=out+(baseChrom&CHROM_MASK_HIGH); in numberToChrom()
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| H A D | BBIndexPacBioSkimmer.java | 718 final int baseChrom=baseChrom(chrom);
931 final int baseChrom=baseChrom(baseChrom_);
979 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1283 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1292 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1297 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1346 final int baseChrom=baseChrom(baseChrom_);
1367 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom));
1465 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
1474 assert(numberToChrom(a, baseChrom) == numberToChrom(a2, baseChrom)) :
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| H A D | IndexMaker5.java | 142 for(int i=baseChrom(minChrom); i<=maxChrom; i++){ in makeArrays()
192 for(int i=baseChrom(minChrom); i<=maxChrom; i++){ in makeArrays()
351 int baseChrom=baseChrom(chrom); in fillArrays() local
407 assert(numberToChrom(number, baseChrom)==chrom); in fillArrays()
438 public final int numberToChrom(int number, int baseChrom){ in numberToChrom() argument
439 assert((baseChrom&CHROM_MASK_LOW)==0) : Integer.toHexString(number)+", baseChrom="+baseChrom; in numberToChrom()
440 assert(baseChrom>=0) : Integer.toHexString(number)+", baseChrom="+baseChrom; in numberToChrom()
445 out=out+(baseChrom&CHROM_MASK_HIGH); in numberToChrom()
451 public final int baseChrom(int chrom){return Tools.max(0, chrom&CHROM_MASK_HIGH);} in baseChrom() method in IndexMaker5.BlockMaker
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