Package org.snpeff.fastq
Class FastqTrimmerAdrian
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- org.snpeff.fastq.FastqTrimmer
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- org.snpeff.fastq.FastqTrimmerMedian
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- org.snpeff.fastq.FastqTrimmerAdrian
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public class FastqTrimmerAdrian extends FastqTrimmerMedian
Trim fastq sequence when: - Median quality drops below a threshold (mean is calculated every 2 bases instead of every base) - Sequence length is at least 'minBases' From Adrian Platts ...Also the sliding window was not every base. It may be easier if I just clip out the vbscript (below) and you can let me know if there are major problems I was also conservative in not taking the frame in which the median dropped below 25 which means I never read the last 5 bases (which given the profile is probably not too bad a thing): [read loop] sa=s.readline() sb=s.readline() sc=s.readline() sd=s.readline() for x=0 to 103 step 2 for y=1 to 5 v(y)=asc(midb(sd,x+y,1))-64 next v.sort() if v(3)<25 then exit next x=x-5 all=all+108 if x>50 then t.write sa+EndOfLine.UNIX t.write left(sb,x)+EndOfLine.UNIX t.write sc+EndOfLine.UNIX t.write left(sd,x)+EndOfLine.UNIX tot=tot+x end if ... other stuff- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.fastq.FastqTrimmer
debug
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Constructor Summary
Constructors Constructor Description FastqTrimmerAdrian(int qualityThreshold, int minBases, int runningMedianLength)
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Method Summary
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Methods inherited from class org.snpeff.fastq.FastqTrimmer
trim
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