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/dports/biology/bbmap/bbmap/current/assemble/
H A DShaver2.java82 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
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H A DTadpole2.java122 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()
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-v0.3.1/src/
H A Dkmer.c152 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()
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H A Dsplay.c168 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()
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/dports/biology/bbmap/bbmap/current/kmer/
H A DHashArray.java1 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
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H A DHashBuffer.java1 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()
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H A DKmerNode.java1 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()
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H A DHashForest.java1 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()
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H A DKmerLink.java1 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()
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H A DKmerTable.java1 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
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/dports/biology/velvet/velvet_1.2.10/src/
H A Dkmer.c275 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()
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H A Dsplay.c38 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()
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/dports/biology/velvet/velvet_1.2.10/contrib/MetaVelvet-1.2.01/Velvet-1.1.06/
H A Dkmer.c275 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()
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H A Dsplay.c38 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()
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/dports/biology/bbmap/bbmap/current/ukmer/
H A DHashArrayU.java185 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
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H A DKmerNodeU.java34 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()
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H A DHashBufferU.java24 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()
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H A DKmerTableSetU.java16 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()
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H A DHashArrayU1D.java46 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;}
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H A DHashForestU.java47 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()
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/dports/biology/wise/wise2.4.1/src/dnaindex/
H A Dkmer_hash.c115 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()
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H A Dkmer_hash.dy17 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;
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/dports/biology/vsearch/vsearch-2.17.1/src/
H A Dunique.cc74 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()
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/dports/biology/mmseqs2/MMseqs2-13-45111/src/linclust/
H A DKmerIndex.h41 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
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DKMerCounter.java36 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()
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