zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Removing many unused functions of unquestionable purpose

This commit is contained in:
Mark DePristo 2011-09-02 08:42:01 -04:00
parent 827fe6130c
commit c3ea96d856
1 changed files with 10 additions and 91 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

101
public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
View File

@ -9,14 +9,17 @@ import net.sf.samtools.SAMUtils;
* @author Kiran Garimella
*/
public class QualityUtils {
public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
public final static double MIN_REASONABLE_ERROR = 0.0001;
public final static byte MAX_REASONABLE_Q_SCORE = 40;
public final static byte MIN_USABLE_Q_SCORE = 6;
public final static int MAPPING_QUALITY_UNAVAILABLE = 255;
private static double qualToErrorProbCache[] = new double[256];
static {
for (byte i = 0; i < 256; i++) qualToErrorProbCache[i] = qualToErrorProbRaw(i);
}
/**
* Private constructor. No instantiating this class!
*/
@ -33,10 +36,6 @@ public class QualityUtils {
return 1.0 - qualToErrorProb(qual);
}
static public double qualToProb(int qual) {
return qualToProb( (double)qual );
}
static public double qualToProb(double qual) {
return 1.0 - Math.pow(10.0, qual/(-10.0));
}
@ -48,10 +47,14 @@ public class QualityUtils {
* @param qual a quality score (0-40)
* @return a probability (0.0-1.0)
*/
static public double qualToErrorProb(byte qual) {
static public double qualToErrorProbRaw(byte qual) {
return Math.pow(10.0, ((double) qual)/-10.0);
}
static public double qualToErrorProb(byte qual) {
return qualToErrorProbCache[qual];
}
/**
* Convert a probability to a quality score. Note, this is capped at Q40.
*
@ -110,88 +113,4 @@ public class QualityUtils {
//return (byte) Math.min(qual, maxQual);
return (byte) Math.max(Math.min(qual, maxQual), 1);
}
/**
* Compress a base and a probability into a single byte so that it can be output in a SAMRecord's SQ field.
* Note: the highest probability this function can encode is 64%, so this function should only never be used on the best base hypothesis.
* Another note: the probability encoded here gets rounded to the nearest 1%.
*
* @param baseIndex the base index
* @param prob the base probability
* @return a byte containing the index and the probability
*/
static public byte baseAndProbToCompressedQuality(int baseIndex, double prob) {
byte compressedQual = 0;
compressedQual = (byte) baseIndex;
byte cprob = (byte) (100.0*prob);
byte qualmask = (byte) 252;
compressedQual += ((cprob << 2) & qualmask);
return compressedQual;
}
/**
* From a compressed base, extract the base index (0:A, 1:C, 2:G, 3:T)
*
* @param compressedQual the compressed quality score, as returned by baseAndProbToCompressedQuality
* @return base index
*/
static public int compressedQualityToBaseIndex(byte compressedQual) {
return (int) (compressedQual & 0x3);
}
/**
* From a compressed base, extract the base probability
*
* @param compressedQual the compressed quality score, as returned by baseAndProbToCompressedQuality
* @return the probability
*/
static public double compressedQualityToProb(byte compressedQual) {
// Because java natives are signed, extra care must be taken to avoid
// shifting a 1 into the sign bit in the implicit promotion of 2 to an int.
int x2 = ((int) compressedQual) & 0xff;
x2 = (x2 >>> 2);
return ((double) x2)/100.0;
}
/**
* Return the complement of a compressed quality
*
* @param compressedQual the compressed quality score (as returned by baseAndProbToCompressedQuality)
* @return the complementary compressed quality
*/
static public byte complementCompressedQuality(byte compressedQual) {
int baseIndex = compressedQualityToBaseIndex(compressedQual);
double prob = compressedQualityToProb(compressedQual);
return baseAndProbToCompressedQuality(BaseUtils.complementIndex(baseIndex), prob);
}
/**
* Return the reverse complement of a byte array of compressed qualities
*
* @param compressedQuals a byte array of compressed quality scores
* @return the reverse complement of the byte array
*/
static public byte[] reverseComplementCompressedQualityArray(byte[] compressedQuals) {
byte[] rcCompressedQuals = new byte[compressedQuals.length];
for (int pos = 0; pos < compressedQuals.length; pos++) {
rcCompressedQuals[compressedQuals.length - pos - 1] = complementCompressedQuality(compressedQuals[pos]);
}
return rcCompressedQuals;
}
/**
* Return the reverse of a byte array of qualities (compressed or otherwise)
* @param quals the array of bytes to be reversed
* @return the reverse of the quality array
*/
static public byte[] reverseQualityArray( byte[] quals ) {
return Utils.reverse(quals); // no sense in duplicating functionality
}
}