Searched refs:MAX_CALLED_QUALITY (Results 1 – 6 of 6) sorted by relevance
| /dports/biology/bbmap/bbmap/current/structures/ |
| H A D | Quantizer.java | 34 for(int i=0, max=Read.MAX_CALLED_QUALITY(); i<=max; i+=quant){ in setArray()
|
| /dports/biology/bbmap/bbmap/current/stream/ |
| H A D | Read.java | 3958 byte q2=(byte)Tools.min(q+5, MAX_CALLED_QUALITY); in aminoToNucleic()
4039 private static byte MAX_CALLED_QUALITY=41; field in Read
4043 public static byte[] qMap=makeQmap(MIN_CALLED_QUALITY, MAX_CALLED_QUALITY);
4046 public static byte MAX_CALLED_QUALITY(){return MAX_CALLED_QUALITY;} in MAX_CALLED_QUALITY() method in Read
4050 if(x!=MAX_CALLED_QUALITY){ in setMaxCalledQuality()
4051 MAX_CALLED_QUALITY=(byte)x; in setMaxCalledQuality()
4052 qMap=makeQmap(MIN_CALLED_QUALITY, MAX_CALLED_QUALITY); in setMaxCalledQuality()
4060 qMap=makeQmap(MIN_CALLED_QUALITY, MAX_CALLED_QUALITY); in setMinCalledQuality()
4065 return (byte)Tools.mid(MIN_CALLED_QUALITY, q, MAX_CALLED_QUALITY); in capQuality()
|
| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | QualityTools.java | 520 return (byte)Tools.mid(0, q, Read.MAX_CALLED_QUALITY());
|
| /dports/biology/bbmap/bbmap/current/clump/ |
| H A D | Clump.java | 130 double phred=(bminor==0 ? Read.MAX_CALLED_QUALITY() : -10*Math.log10(bratio)); in makeSimpleConsensus()
|
| /dports/biology/bbmap/bbmap/current/shared/ |
| H A D | ReadStats.java | 1075 final int qMin=Read.MIN_CALLED_QUALITY(), qMax=Read.MAX_CALLED_QUALITY(); in writeQualityAccuracyToFile()
|
| H A D | Parser.java | 1146 Read.setMaxCalledQuality(Tools.max(x, Read.MAX_CALLED_QUALITY())); in parseQualityAdjust()
|