/dports/biology/bbmap/bbmap/current/assemble/ |
H A D | Shaver2.java | 82 assert(kmer.len>=kmer.kbig); in exploreAndMark() 85 …assert(countWithinLimits(kmer)) : "count="+getCount(kmer)+", minCount="+minCount+", maxCount="+max… in exploreAndMark() 96 kmer=tables.rightmostKmer(bb, kmer); in exploreAndMark() 102 kmer=tables.rightmostKmer(bb, kmer);//123 in exploreAndMark() 162 assert(bb.length()>=kmer.kbig && kmer.len>=kmer.kbig) : bb.length()+", "+kmer.len+", "+kmer.kbig; in explore() 505 assert(kmer.len()>=kbig) : kmer.len()+", "+kbig; in processKmer_high_leftLoop() 532 assert(kmer.len()>=kbig) : kmer.len()+", "+kbig; in processKmer_high_leftLoop() 610 kmer.clear(); in claim() 638 int getCount(Kmer kmer){return tables.getCount(kmer);} in getCount() argument 639 boolean claim(Kmer kmer, int id){return tables.claim(kmer, id);} in claim() argument [all …]
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H A D | Tadpole2.java | 122 public final int getCount(Kmer kmer){return tables.getCount(kmer);} in getCount() argument 127 final int findOwner(Kmer kmer){return tables.findOwner(kmer);} in findOwner() argument 130 final void release(Kmer kmer, int id){tables.release(kmer, id);} in release() argument 228 kmer=table.fillKmer(cell, kmer); in processCell() 903 kmer.clear(); in extendToRight() 905 kmer=tables.rightmostKmer(bb, kmer); in extendToRight() 906 if(kmer==null || kmer.len<kbig){return BAD_SEED;} in extendToRight() 1079 kmer.clear(); in extendToRight2() 1081 kmer=tables.rightmostKmer(bb, kmer); in extendToRight2() 1082 if(kmer==null || kmer.len<kbig){return 0;} in extendToRight2() [all …]
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/ |
H A D | kmer.c | 152 kmer->ints >>= 2; in shiftRight() 255 kmer->longs = 0; in clearKmer() 258 kmer->ints = 0; in clearKmer() 261 kmer->chars = 0; in clearKmer() 285 Kmer kmer; in testKmers() local 295 printKmer(&kmer); in testKmers() 297 clearKmer(&kmer); in testKmers() 298 printKmer(&kmer); in testKmers() 422 ++kmer->chars; in pushNucleotide() 436 ++kmer->chars; in pushNucleotide() [all …]
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H A D | splay.c | 168 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 177 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 184 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 200 copyKmers(&(newNode->kmer), kmer); in findOrInsertOccurenceInSplayTree() 214 copyKmers(&(newNode->kmer), kmer); in findOrInsertOccurenceInSplayTree() 227 copyKmers(&(newNode->kmer), kmer); in findOrInsertOccurenceInSplayTree() 256 copyKmers(&(newNode->kmer), kmer); in placeOccurenceInSplayTree() 270 copyKmers(&(newNode->kmer), kmer); in placeOccurenceInSplayTree() 283 copyKmers(&(newNode->kmer), kmer); in placeOccurenceInSplayTree() 368 copyKmers(&(newNode->kmer), kmer); in countOccurenceInSplayTree() [all …]
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/dports/biology/bbmap/bbmap/current/kmer/ |
H A D | HashArray.java | 1 package kmer; package 143 if(n==kmer){ in set() 150 array[cell]=kmer; in set() 175 if(n==kmer){ in set() 182 array[cell]=kmer; in set() 204 if(n==kmer){ in setIfNotPresent() 207 array[cell]=kmer; in setIfNotPresent() 345 return findKmer(kmer, kmerToCell(kmer)); in findKmer() 478 long kmer=array[i]; in fillHistogram() local 492 long kmer=array[i]; in fillHistogram() local [all …]
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H A D | HashBuffer.java | 1 package kmer; package 47 final int way=kmerToWay(kmer); in incrementAndReturnNumCreated() 66 final int way=kmerToWay(kmer); in set() 87 final int way=kmerToWay(kmer); in getValue() 93 final int way=kmerToWay(kmer); in getValues() 99 final int way=kmerToWay(kmer); in contains() 142 Object get(long kmer) { in get() argument 144 return tables[way].get(kmer); in get() 186 final long kmer=kmers[i]; in dumpBuffer_inner() local 187 if(kmer==prev){ in dumpBuffer_inner() [all …]
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H A D | KmerNode.java | 1 package kmer; package 36 if(kmer<pivot){ in increment() 39 }else if(kmer>pivot){ in increment() 100 if(kmer<pivot){ in set() 105 }else if(kmer>pivot){ in set() 124 if(kmer<pivot){ in setIfNotPresent() 127 }else if(kmer>pivot){ in setIfNotPresent() 136 KmerNode n=get(kmer); in getValue() 142 KmerNode n=get(kmer); in getValues() 186 if(kmer<pivot){return left==null ? this : left.getNodeOrParent(kmer);} in getNodeOrParent() [all …]
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H A D | HashForest.java | 1 package kmer; package 46 return (TWOD ? new KmerNode2D(kmer, val) : new KmerNode1D(kmer, val)); in makeNode() 67 n=makeNode(kmer, incr); in increment() 72 if(kmer<prev.pivot){ in increment() 80 n.increment(kmer, incr); in increment() 94 n=makeNode(kmer, incr); in incrementAndReturnNumCreated() 99 if(kmer<prev.pivot){ in incrementAndReturnNumCreated() 108 n.increment(kmer, incr); in incrementAndReturnNumCreated() 179 x=n.set(kmer, value); in set() 230 return get(kmer)!=null; in contains() [all …]
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H A D | KmerLink.java | 1 package kmer; package 38 int x=increment(kmer, incr); in incrementAndReturnNumCreated() 45 if(kmer==pivot){ in increment() 70 if(kmer==pivot){return 0;} in setIfNotPresent() 76 KmerLink get(long kmer){ in get() argument 90 KmerLink node=get(kmer); in contains() 151 KmerLink n=get(kmer); in setOwner() 165 KmerLink n=get(kmer); in clearOwner() 178 KmerLink n=get(kmer); in getOwner() 192 KmerLink n=get(kmer); in getValue() [all …]
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H A D | KmerTable.java | 1 package kmer; package 51 n=new KmerLink(kmer, incr); in increment() 75 n=new KmerLink(kmer, incr); in incrementAndReturnNumCreated() 98 x=n.set(kmer, value); in set() 125 public int getValue(long kmer){ in getValue() argument 126 int cell=(int)(kmer%prime); in getValue() 135 singleton[0]=getValue(kmer); in getValues() 141 KmerLink node=get(kmer); in contains() 184 return n.getOwner(kmer); in getOwner() 192 KmerLink get(long kmer){ in get() argument [all …]
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/dports/biology/velvet/velvet_1.2.10/src/ |
H A D | kmer.c | 275 kmer->ints >>= 2; in shiftRight() 378 kmer->longs = 0; in clearKmer() 381 kmer->ints = 0; in clearKmer() 384 kmer->chars = 0; in clearKmer() 469 kmer->ints <<= 2; in pushNucleotide() 498 if (++kmer->ints) in pushNucleotide() 502 ++kmer->chars; in pushNucleotide() 512 if (++kmer->ints) in pushNucleotide() 516 ++kmer->chars; in pushNucleotide() 526 ++kmer->chars; in pushNucleotide() [all …]
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H A D | splay.c | 38 Kmer kmer; member 136 while (compareKmers(kmer, &(T->kmer))) { in Splay() 137 if (compareKmers(kmer, &(T->kmer)) < 0) { in Splay() 183 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 190 if (compareKmers(kmer, &((*T)->kmer)) < 0) { in insertIntoTree() 192 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 199 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 215 copyKmers(&(newNode->kmer), kmer); in findOrInsertOccurenceInSplayTree() 227 if (compareKmers(kmer, &((*T)->kmer)) < 0) { in findOrInsertOccurenceInSplayTree() 229 copyKmers(&(newNode->kmer), kmer); in findOrInsertOccurenceInSplayTree() [all …]
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/ |
H A D | kmer.c | 275 kmer->ints >>= 2; in shiftRight() 378 kmer->longs = 0; in clearKmer() 381 kmer->ints = 0; in clearKmer() 384 kmer->chars = 0; in clearKmer() 469 kmer->ints <<= 2; in pushNucleotide() 498 if (++kmer->ints) in pushNucleotide() 502 ++kmer->chars; in pushNucleotide() 512 if (++kmer->ints) in pushNucleotide() 516 ++kmer->chars; in pushNucleotide() 526 ++kmer->chars; in pushNucleotide() [all …]
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H A D | splay.c | 38 Kmer kmer; member 136 while (compareKmers(kmer, &(T->kmer))) { in Splay() 137 if (compareKmers(kmer, &(T->kmer)) < 0) { in Splay() 183 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 190 if (compareKmers(kmer, &((*T)->kmer)) < 0) { in insertIntoTree() 192 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 199 copyKmers(&(newNode->kmer), kmer); in insertIntoTree() 215 copyKmers(&(newNode->kmer), kmer); in findOrInsertOccurenceInSplayTree() 227 if (compareKmers(kmer, &((*T)->kmer)) < 0) { in findOrInsertOccurenceInSplayTree() 229 copyKmers(&(newNode->kmer), kmer); in findOrInsertOccurenceInSplayTree() [all …]
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/dports/biology/bbmap/bbmap/current/ukmer/ |
H A D | HashArrayU.java | 185 assert(kmer.mult==mult && kmer.len>=kmer.kbig); in set() 247 int cell=findKmer(kmer); in getValue() 261 return getValue(kmer); in getCount() 284 kmer.fillArray2(); in fillKmer() 285 …ntln("Filled kmer "+kmer+": a1="+Arrays.toString(kmer.array1())+", a2="+Arrays.toString(kmer.array… in fillKmer() 286 return kmer; in fillKmer() 304 int cell=findKmer(kmer); in getValues() 352 …"+kmer+", array1="+Arrays.toString(kmer.array1())+", array2="+Arrays.toString(kmer.array2())+", ro… in setOwner() 407 return findKmer(kmer.key(), (int)(kmer.xor()%prime)); in findKmer() 606 long kmer=array0[i]; in fillHistogram() local [all …]
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H A D | KmerNodeU.java | 34 public final int increment(Kmer kmer){return increment(kmer.key());} in increment() argument 40 return left.increment(kmer); in increment() 43 return right.increment(kmer); in increment() 54 int x=increment(kmer); in incrementAndReturnNumCreated() 67 return left.set(kmer, value); in set() 97 KmerNodeU n=get(kmer); in getValue() 102 KmerNodeU n=get(kmer); in getValues() 107 KmerNodeU node=get(kmer); in contains() 314 KmerNodeU n=get(kmer); in setOwner() 328 KmerNodeU n=get(kmer); in clearOwner() [all …]
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H A D | HashBufferU.java | 24 kmer=new Kmer(kbig_); in HashBufferU() 25 mult=kmer.mult; in HashBufferU() 54 assert(kmer.mult==mult) : kmer.mult+"!="+mult+", kbig="+kmer.kbig+", k="+kmer.k; in incrementAndReturnNumCreated() 55 final int way=getWay(kmer); in incrementAndReturnNumCreated() 111 public final int getWay(Kmer kmer){return (int)(kmer.xor()%ways);} in getWay() argument 150 Object get(Kmer kmer) { in get() argument 156 Object get(long[] kmer) { in get() argument 194 kmer.fillArray2(); in dumpBuffer_inner() 195 if(verbose){System.err.println("Incrementing "+kmer+"; xor="+kmer.xor());} in dumpBuffer_inner() 207 kmer.fillArray2(); in dumpBuffer_inner() [all …]
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H A D | KmerTableSetU.java | 16 import kmer.DumpThread; 689 kmer.clear(); in regenerateCounts() 741 kmer.clear(); in regenerateCounts() 878 kmer.clear(); in rightmostKmer() 899 return kmer; in rightmostKmer() 907 kmer.clear(); in leftmostKmer() 928 return kmer; in leftmostKmer() 952 kmer.clear(); in calcCoverage() 1281 outstream.println("kmer: "+kmer+" (key==array1 ? "+(kmer.key()==kmer.array1())); in fillLeftCounts_safe() 1286 outstream.println("after: "+kmer+" (key==array1 ? "+(kmer.key()==kmer.array1())); in fillLeftCounts_safe() [all …]
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H A D | HashArrayU1D.java | 46 setKmer(kmer.key(), cell); in increment() 93 …", a1 "+Arrays.toString(kmer.array1())+", a2 "+Arrays.toString(kmer.array2())+", xor "+kmer.xor()+… in incrementAndReturnNumCreated() 275 assert(temp==kmer); in resize() 301 set(kmer, n.value()); in resize() 381 kmer=new Kmer(kbig); 393 fillKmer(i, kmer); 396 assert(kmer.len()>0) : kmer.len()+", "+value+", "+i+", "+values.length+"\n" 404 kn.fillKmer(kmer); 412 kmer.clearFast(); 418 public Kmer kmer(){return kmer;} [all …]
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H A D | HashForestU.java | 47 private KmerNodeU makeNode(Kmer kmer, int val){return makeNode(kmer.key(), val);} in makeNode() argument 48 private KmerNodeU makeNode(Kmer kmer, int[] vals){return makeNode(kmer.key(), vals);} in makeNode() argument 51 return (TWOD ? new KmerNodeU2D(kmer, val) : new KmerNodeU1D(kmer, val)); in makeNode() 88 n=makeNode(kmer, 1); in increment() 101 n.increment(kmer); in increment() 134 n=makeNode(kmer, 1); in incrementAndReturnNumCreated() 148 n.increment(kmer); in incrementAndReturnNumCreated() 219 x=n.set(kmer, value); in set() 233 x=n.set(kmer, vals); in set() 256 return getValue(kmer.key(), kmer.xor()); in getValue() [all …]
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/dports/biology/wise/wise2.4.1/src/dnaindex/ |
H A D | kmer_hash.c | 115 kmer_t hash = kmer; in hash_kmer() 160 if(khb->kmer[i] == kmer){ in retrieve_by_kmer_KmerHashIndex() 181 if( kmer == -1 ) { in next_filled_kmer_KmerHashIndex() 197 if( kmer == khb->kmer[i] ) { in next_filled_kmer_KmerHashIndex() 215 return khb->kmer[i+1]; in next_filled_kmer_KmerHashIndex() 231 if(kmer > khi->max_kmer) khi->max_kmer = kmer; in insert_by_kmer_KmerHashIndex() 232 if(kmer < khi->min_kmer) khi->min_kmer = kmer; in insert_by_kmer_KmerHashIndex() 243 if(khb->kmer == NULL){ in insert_by_kmer_KmerHashIndex() 256 khb->kmer = (kmer_t*)realloc(khb->kmer, sizeof(kmer_t)*(khb->buflen*2)); in insert_by_kmer_KmerHashIndex() 264 khb->kmer[khb->length] = kmer; in insert_by_kmer_KmerHashIndex() [all …]
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H A D | kmer_hash.dy | 17 kmer_t *kmer; 150 kmer <<= 5; 152 kmer <<= 5; 154 kmer <<= 5; 156 kmer <<= 5; 186 if(khb->kmer[i] == kmer){ 222 if( kmer == khb->kmer[i] ) { 255 if(kmer > khi->max_kmer) khi->max_kmer = kmer; 256 if(kmer < khi->min_kmer) khi->min_kmer = kmer; 288 khb->kmer[khb->length] = kmer; [all …]
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/dports/biology/vsearch/vsearch-2.17.1/src/ |
H A D | unique.cc | 74 unsigned int kmer; member 173 uint64_t kmer = 0; in unique_count_bitmap() local 191 kmer <<= 2ULL; in unique_count_bitmap() 203 kmer <<= 2ULL; in unique_count_bitmap() 205 kmer &= mask; in unique_count_bitmap() 277 kmer <<= 2ULL; in unique_count_hash() 289 kmer <<= 2ULL; in unique_count_hash() 291 kmer &= mask; in unique_count_hash() 297 while((uh->hash[j].count) && (uh->hash[j].kmer != kmer)) { in unique_count_hash() 306 uh->hash[j].kmer = kmer; in unique_count_hash() [all …]
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/linclust/ |
H A D | KmerIndex.h | 41 size_t kmer; member 46 kmer(kmer), id(id), pos(pos), seqLen(seqLen) {} in KmerEntry() 85 size_t kmer; in getNextEntry() local 90 kmer = entryOffsetPos*indexGridResolution + kmer; in getNextEntry() 91 kmer = (isReverse) ? kmer : BIT_SET(kmer, 63); in getNextEntry() 100 size_t getGridPosition(size_t kmer){ in getGridPosition() argument 101 return kmer / indexGridResolution; in getGridPosition() 104 size_t getKmerStartRange(size_t kmer) { in getKmerStartRange() argument 125 bool needsFlush(const size_t kmer){ in needsFlush() argument 214 KmerEntry kmer = getNextEntry<TYPE>(); in printIndex() local [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
H A D | KMerCounter.java | 36 public int getKmerCount(final Kmer kmer) { in getKmerCount() argument 37 Utils.nonNull(kmer, "kmer cannot be null"); in getKmerCount() 59 result.add(countedKmer.kmer); in getKmersWithCountsAtLeast() 79 …Utils.validateArg(kmer.length() == kmerLength, () -> "bad kmer length " + kmer + " expected size "… in addKmer() 99 final Kmer kmer; field in KMerCounter.CountedKmer 102 private CountedKmer(final Kmer kmer) { in CountedKmer() argument 103 this.kmer = kmer; in CountedKmer() 107 return kmer; in getKmer() 117 "kmer='" + kmer + '\'' + in toString() 135 for ( final String kmer : kmers ) { in addKmers() [all …]
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