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Script for filtering alignments with deficient properties (rqs,gaps, mismatches). The script generates a new .SAM file from the input SAM file, where only alignments are contained that fulfill certain quality thresholds. nm = numberOfMisMatches rq = readqualityscore MQ = mappingquality
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| counter1 = 0 | |||
| counter2 = 0 | |||
| __package__ = None | |||
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 Reads a .fastqfile and filters them for certain quality values. If an alignment is equally good or better as the threshold it will be written to the filtered .SAM file. input: fastq file output: fastq dictionary key = readid; value = qualstr 
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 Calculates the number of gaps / mistmatches from an HTSeq alngt. object. 
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 Calculates the number of gaps / mistmatches from an HTSeq alngt. object. 
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 Function for filtering a given sam file. The alignments are evaluated individually in regard to RQS,mismatches and gaps. The input needs to be sorted. | 
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