Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KmerCountAbstract.java @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@68 | 1 package bloom; |
| jpayne@68 | 2 |
| jpayne@68 | 3 import shared.Shared; |
| jpayne@68 | 4 |
| jpayne@68 | 5 /** |
| jpayne@68 | 6 * @author Brian Bushnell |
| jpayne@68 | 7 * @date Dec 2, 2014 |
| jpayne@68 | 8 * |
| jpayne@68 | 9 */ |
| jpayne@68 | 10 public abstract class KmerCountAbstract { |
| jpayne@68 | 11 |
| jpayne@68 | 12 protected static final long[] transformToFrequency(int[] count){ |
| jpayne@68 | 13 long[] freq=new long[2000]; |
| jpayne@68 | 14 int max=freq.length-1; |
| jpayne@68 | 15 for(int i=0; i<count.length; i++){ |
| jpayne@68 | 16 int x=count[i]; |
| jpayne@68 | 17 x=min(x, max); |
| jpayne@68 | 18 freq[x]++; |
| jpayne@68 | 19 } |
| jpayne@68 | 20 return freq; |
| jpayne@68 | 21 } |
| jpayne@68 | 22 |
| jpayne@68 | 23 protected static final long sum(int[] array){ |
| jpayne@68 | 24 long x=0; |
| jpayne@68 | 25 for(int y : array){x+=y;} |
| jpayne@68 | 26 return x; |
| jpayne@68 | 27 } |
| jpayne@68 | 28 |
| jpayne@68 | 29 protected static final long sum(long[] array){ |
| jpayne@68 | 30 long x=0; |
| jpayne@68 | 31 for(long y : array){x+=y;} |
| jpayne@68 | 32 return x; |
| jpayne@68 | 33 } |
| jpayne@68 | 34 |
| jpayne@68 | 35 protected static final int min(int x, int y){return x<y ? x : y;} |
| jpayne@68 | 36 protected static final int max(int x, int y){return x>y ? x : y;} |
| jpayne@68 | 37 |
| jpayne@68 | 38 public static byte minQuality=6; |
| jpayne@68 | 39 public static long readsProcessed=0; |
| jpayne@68 | 40 public static long maxReads=-1; |
| jpayne@68 | 41 |
| jpayne@68 | 42 public static float minProb=0.5f; |
| jpayne@68 | 43 |
| jpayne@68 | 44 public static long keysCounted=0; |
| jpayne@68 | 45 public static long increments=0; |
| jpayne@68 | 46 |
| jpayne@68 | 47 public static final boolean verbose=false; |
| jpayne@68 | 48 public static boolean PREJOIN=false; |
| jpayne@68 | 49 public static boolean CANONICAL=false; |
| jpayne@68 | 50 public static boolean KEEP_DUPLICATE_KMERS=true; |
| jpayne@68 | 51 public static boolean SKETCH_MODE=false; |
| jpayne@68 | 52 public static boolean STORE_HASHED=false; |
| jpayne@68 | 53 public static boolean BUFFERED=false; |
| jpayne@68 | 54 public static int BUFFERLEN=3000; //Optimal is in the range of 2000-8000 for Clumpified 2x150bp data. |
| jpayne@68 | 55 // public static boolean SORT_SERIAL=false; //Not needed, see parallel sort flag |
| jpayne@68 | 56 |
| jpayne@68 | 57 public static int maxShortKmerLength=31; |
| jpayne@68 | 58 |
| jpayne@68 | 59 } |