Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KmerCountAbstract.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package bloom;
2
3 import shared.Shared;
4
5 /**
6 * @author Brian Bushnell
7 * @date Dec 2, 2014
8 *
9 */
10 public abstract class KmerCountAbstract {
11
12 protected static final long[] transformToFrequency(int[] count){
13 long[] freq=new long[2000];
14 int max=freq.length-1;
15 for(int i=0; i<count.length; i++){
16 int x=count[i];
17 x=min(x, max);
18 freq[x]++;
19 }
20 return freq;
21 }
22
23 protected static final long sum(int[] array){
24 long x=0;
25 for(int y : array){x+=y;}
26 return x;
27 }
28
29 protected static final long sum(long[] array){
30 long x=0;
31 for(long y : array){x+=y;}
32 return x;
33 }
34
35 protected static final int min(int x, int y){return x<y ? x : y;}
36 protected static final int max(int x, int y){return x>y ? x : y;}
37
38 public static byte minQuality=6;
39 public static long readsProcessed=0;
40 public static long maxReads=-1;
41
42 public static float minProb=0.5f;
43
44 public static long keysCounted=0;
45 public static long increments=0;
46
47 public static final boolean verbose=false;
48 public static boolean PREJOIN=false;
49 public static boolean CANONICAL=false;
50 public static boolean KEEP_DUPLICATE_KMERS=true;
51 public static boolean SKETCH_MODE=false;
52 public static boolean STORE_HASHED=false;
53 public static boolean BUFFERED=false;
54 public static int BUFFERLEN=3000; //Optimal is in the range of 2000-8000 for Clumpified 2x150bp data.
55 // public static boolean SORT_SERIAL=false; //Not needed, see parallel sort flag
56
57 public static int maxShortKmerLength=31;
58
59 }