selex
Class SeqRead
java.lang.Object
selex.SeqRead
- public class SeqRead
- extends java.lang.Object
Container for information related to a particular sequencing read.
Constructor Summary |
SeqRead(java.lang.String sequence,
java.lang.String seqComment,
java.lang.String quality,
java.lang.String qualComment,
SelexParams aSP,
SeqFiles aSF)
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Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SeqRead
public SeqRead(java.lang.String sequence,
java.lang.String seqComment,
java.lang.String quality,
java.lang.String qualComment,
SelexParams aSP,
SeqFiles aSF)
checkEstimateNumSubSeqs
public boolean checkEstimateNumSubSeqs()
printSeqRead
public void printSeqRead()
makeSubSeqs
public boolean makeSubSeqs()
findEnds
public java.util.ArrayList findEnds()
extractSegs
public int[][] extractSegs(java.util.ArrayList ends)
removeLowQualitySegs
public java.util.ArrayList removeLowQualitySegs(int[][] segs)
removeOddSizedSegs
public java.util.ArrayList removeOddSizedSegs(java.util.ArrayList segs)
checkSeqQuality
public static boolean checkSeqQuality(int[] qualityScores,
int minNumHighQualBases,
int minQualScore)
- Examines an int[] for a continuous stretch of scores
getNumStretchesGoodQuality
public static int getNumStretchesGoodQuality(int[] qualityScores,
int qualCutOff,
int seqLength)
- Counts the number of stretches of scores above a cut off in an int[]. Useful for estimating the
number of concatinated selex oligos that should be found in a sequence read