Functions — github.com/Daniel-Liu-c0deb0t/UMICollapse

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Functions292 in github.com/Daniel-Liu-c0deb0t/UMICollapse

⨍ Functions 292◇ Types & classes 69

↓ 57 callersMethodget

(int idx)

src/umicollapse/util/BitSet.java:29

↓ 19 callersMethodumiDist

(BitSet a, BitSet b)

src/umicollapse/util/Utils.java:7

↓ 18 callersMethodclose

()

src/umicollapse/main/DeduplicateSAM.java:562

↓ 17 callersMethodequals

(Object o)

src/umicollapse/main/DeduplicateSAM.java:676

↓ 15 callersMethodcontains

(BitSet umi)

src/umicollapse/data/DataStructure.java:11

↓ 11 callersMethodcharSet

(BitSet a, int idx, int b)

src/umicollapse/util/Utils.java:21

↓ 10 callersMethodinit

(Map<BitSet, Integer> umiFreq, int umiLength, int maxEdits)

src/umicollapse/data/DataStructure.java:9

↓ 9 callersMethodget

(int idx)

src/umicollapse/data/Trie.java:153

↓ 9 callersMethodtoBitSet

(String s)

src/umicollapse/util/Utils.java:46

↓ 8 callersMethodapply

(Map<BitSet, ReadFreq> reads, DataStructure data, ClusterTracker tracker, int umiLength, int k, float percenta

src/umicollapse/algo/Algorithm.java:13

↓ 8 callersMethodget

(int i)

src/umicollapse/data/Ngram.java:109

↓ 7 callersMethodcharGet

(BitSet a, int idx)

src/umicollapse/util/Utils.java:35

↓ 7 callersMethodwrite

(SAMRecord record)

src/umicollapse/main/DeduplicateSAM.java:538

↓ 6 callersMethodtoString

(BitSet a, int length)

src/umicollapse/util/Utils.java:59

↓ 6 callersMethodumiPattern

(String sep)

src/umicollapse/util/SAMRead.java:28

↓ 5 callersMethodequals

(Object obj)

src/umicollapse/util/BitSet.java:61

↓ 5 callersMethodget

(int i)

src/umicollapse/data/SortNgramBKTree.java:218

↓ 5 callersMethodget

(int i)

src/umicollapse/data/NgramBKTree.java:206

↓ 5 callersMethodgetUMI

()

src/umicollapse/data/SortNgramBKTree.java:157

↓ 5 callersMethodgetUMI

()

src/umicollapse/data/FenwickBKTree.java:183

↓ 5 callersMethodgetUMI

()

src/umicollapse/data/NgramBKTree.java:145

↓ 5 callersMethodnear

(BitSet umi, int k, int maxFreq)

src/umicollapse/data/ParallelDataStructure.java:12

↓ 5 callersMethodremoveNear

(BitSet umi, int k, int maxFreq)

src/umicollapse/data/DataStructure.java:10

↓ 4 callersMethodaddAll

(Set<BitSet> s, Map<BitSet, ReadFreq> reads)

src/umicollapse/util/ClusterTracker.java:44

↓ 4 callersMethodcompareTo

(Object o)

src/umicollapse/main/DeduplicateSAM.java:706

↓ 4 callersMethodgetUMI

()

src/umicollapse/data/BKTree.java:153

↓ 4 callersMethodgetUMI

()

src/umicollapse/data/SortBKTree.java:162

↓ 4 callersMethodset

(int idx, boolean bit)

src/umicollapse/util/BitSet.java:34

↓ 4 callersMethodtest

(String a, String b)

src/test/TestBitSet.java:14

↓ 3 callersMethodclone

()

src/umicollapse/util/BitSet.java:97

↓ 3 callersMethodexists

()

src/umicollapse/data/BKTree.java:157

↓ 3 callersMethodexists

()

src/umicollapse/data/SortBKTree.java:166

↓ 3 callersMethodget

(int k)

src/umicollapse/data/SortNgramBKTree.java:189

↓ 3 callersMethodget

(int k)

src/umicollapse/data/FenwickBKTree.java:195

↓ 3 callersMethodget

(int k)

src/umicollapse/data/NgramBKTree.java:177

↓ 3 callersMethodgetFreq

(int idx)

src/umicollapse/data/Trie.java:141

↓ 3 callersMethodgetUMI

()

src/umicollapse/data/ParallelFenwickBKTree.java:112

↓ 3 callersMethodgetUMI

()

src/umicollapse/data/ParallelBKTree.java:94

↓ 3 callersMethodgetUMI

()

src/umicollapse/util/SAMRead.java:32

↓ 3 callersMethodgetUMI

()

src/umicollapse/util/Read.java:31

↓ 3 callersMethodhashCode

()

src/umicollapse/main/DeduplicateSAM.java:698

↓ 3 callersMethodmerge

(Read a, Read b)

src/umicollapse/merge/Merge.java:6

↓ 3 callersMethodrandEdits

(String s, int k, Random rand)

src/test/TestUtils.java:52

↓ 3 callersMethodshouldTrack

()

src/umicollapse/util/ClusterTracker.java:32

↓ 3 callersMethodtrack

(BitSet unique, Read read)

src/umicollapse/util/ClusterTracker.java:53

↓ 2 callersMethodcharEquals

(BitSet a, int idx, int b)

src/umicollapse/util/Utils.java:12

↓ 2 callersMethoddeduplicateAndMerge

(File in, File out, Algo algo, Class<? extends Data> dataClass, Merge merge, int umiLengthParam, int k, float

src/umicollapse/main/DeduplicateSAM.java:37

↓ 2 callersMethodexists

(int idx)

src/umicollapse/data/Trie.java:133

↓ 2 callersMethodgenerateData

(int numRand, int numDup, int umiLength, int k, float percentage, Random rand)

src/test/TestUtils.java:23

↓ 2 callersMethodget

(int k)

src/umicollapse/data/ParallelFenwickBKTree.java:116

↓ 2 callersMethodget

(int k)

src/umicollapse/data/BKTree.java:189

↓ 2 callersMethodget

(int k)

src/umicollapse/data/SortBKTree.java:198

↓ 2 callersMethodgetAvgQual

()

src/umicollapse/util/Read.java:30

↓ 2 callersMethodgetFreq

()

src/umicollapse/data/SortNgramBKTree.java:181

↓ 2 callersMethodgetFreq

()

src/umicollapse/data/BKTree.java:181

↓ 2 callersMethodgetFreq

()

src/umicollapse/data/NgramBKTree.java:169

↓ 2 callersMethodgetFreq

()

src/umicollapse/data/SortBKTree.java:190

↓ 2 callersMethodgetFreq

()

src/umicollapse/util/ClusterTracker.java:89

↓ 2 callersMethodgetId

(BitSet umi)

src/umicollapse/util/ClusterTracker.java:66

↓ 2 callersMethodgetMapQual

()

src/umicollapse/util/SAMRead.java:58

↓ 2 callersMethodgetOffset

()

src/umicollapse/util/ClusterTracker.java:40

↓ 2 callersMethodgetRead

()

src/umicollapse/util/ClusterTracker.java:93

↓ 2 callersMethodgetRef

()

src/umicollapse/main/DeduplicateSAM.java:672

↓ 2 callersMethodgetStats

(int id)

src/umicollapse/util/ClusterTracker.java:70

↓ 2 callersMethodgetUMI

()

src/umicollapse/util/FASTQRead.java:43

↓ 2 callersMethodgetUMILength

()

src/umicollapse/util/SAMRead.java:40

↓ 2 callersMethodminFreq

(int k)

src/umicollapse/data/SortNgramBKTree.java:185

↓ 2 callersMethodminFreq

(int k)

src/umicollapse/data/BKTree.java:185

↓ 2 callersMethodminFreq

(int k)

src/umicollapse/data/NgramBKTree.java:173

↓ 2 callersMethodminFreq

(int k)

src/umicollapse/data/SortBKTree.java:194

↓ 2 callersMethodrandUMI

(int n, Random rand)

src/test/TestUtils.java:43

↓ 2 callersMethodrecursiveRemoveNear

(BitSet umi, int idx, Node currNode, int k, int maxFreq, BitSet currStr, Set<BitSet> res)

src/umicollapse/data/Trie.java:44

↓ 2 callersMethodrecursiveRemoveNear

(BitSet umi, Node curr, int k, Set<BitSet> res)

src/umicollapse/data/FenwickBKTree.java:66

↓ 2 callersMethodrecursiveRemoveNear

(BitSet umi, Node curr, int k, int maxFreq, Set<BitSet> res)

src/umicollapse/data/BKTree.java:47

↓ 2 callersMethodrecursiveRemoveNear

(BitSet umi, Node curr, int k, int maxFreq, Set<BitSet> res)

src/umicollapse/data/SortBKTree.java:56

↓ 2 callersMethodrecursiveRemoveNearBKTree

(BitSet umi, Node curr, int k, int maxFreq, Set<BitSet> res)

src/umicollapse/data/SortNgramBKTree.java:77

↓ 2 callersMethodrecursiveRemoveNearBKTree

(BitSet umi, Node curr, int k, int maxFreq, Set<BitSet> res)

src/umicollapse/data/NgramBKTree.java:65

↓ 2 callersMethodsetDefaultUMIPattern

(String sep)

src/umicollapse/util/SAMRead.java:24

↓ 2 callersMethodsetExists

(boolean exists)

src/umicollapse/data/Trie.java:137

↓ 2 callersMethodsetFreq

(int freq)

src/umicollapse/data/Trie.java:149

↓ 2 callersMethodsetMatches

(Set<BitSet> a, Set<BitSet> b)

src/test/TestUtils.java:16

↓ 2 callersMethodsetMinFreq

(int minFreq)

src/umicollapse/data/SortNgramBKTree.java:173

↓ 2 callersMethodsetMinFreq

(int minFreq)

src/umicollapse/data/BKTree.java:173

↓ 2 callersMethodsetMinFreq

(int minFreq)

src/umicollapse/data/NgramBKTree.java:161

↓ 2 callersMethodsetMinFreq

(int minFreq)

src/umicollapse/data/SortBKTree.java:182

↓ 2 callersMethodsetOffset

(int offset)

src/umicollapse/util/ClusterTracker.java:36

↓ 2 callersMethodsubtreeExists

(int k)

src/umicollapse/data/SortNgramBKTree.java:169

↓ 2 callersMethodsubtreeExists

(int k)

src/umicollapse/data/FenwickBKTree.java:191

↓ 2 callersMethodsubtreeExists

(int k)

src/umicollapse/data/BKTree.java:169

↓ 2 callersMethodsubtreeExists

(int k)

src/umicollapse/data/NgramBKTree.java:157

↓ 2 callersMethodsubtreeExists

(int k)

src/umicollapse/data/SortBKTree.java:178

↓ 2 callersMethodtest

(String[] umiList, int k, ParallelDataStructure baseline, ParallelDataStructure[] data)

src/test/TestParallelDataStructures.java:27

↓ 2 callersMethodtest

(String[] umiList, int k, DataStructure baseline, DataStructure[] data)

src/test/TestDataStructures.java:34

↓ 2 callersMethodtoPhred33ByteArray

(String q)

src/umicollapse/util/Utils.java:69

↓ 2 callersMethodtoSAMRecord

()

src/umicollapse/util/SAMRead.java:62

↓ 2 callersMethodwriteReversed

(boolean fullPass)

src/umicollapse/main/DeduplicateSAM.java:569

↓ 1 callersMethodbitCountXOR

(BitSet o)

src/umicollapse/util/BitSet.java:50

↓ 1 callersMethodcharSetNBit

(BitSet a, int idx)

src/umicollapse/util/Utils.java:28

↓ 1 callersMethoddeduplicateAndMergeTwoPass

(File in, File out, Algo algo, Class<? extends Data> dataClass, Merge merge, int umiLengthParam, int k, float

src/umicollapse/main/DeduplicateSAM.java:276

↓ 1 callersMethoddepth

(Node curr)

src/umicollapse/data/FenwickBKTree.java:136

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