[BioC] report a possble bug in shortread

[Wang Peter]

i read the fastq file and let the function identify the quality score

		if(iteration==1)#
		{
			score_sys = data.class(quality(reads));	
		}
		if(score_sys =="SFastqQuality")#Phred+64
		{
		  do something
		}
		if(score_sys =="FastqQuality")#Phred+33
		{
		 do something
		}


but the score_sys=SFastqQuality, the data is Phred+33

see the quality line
HHHHHHHHHHHHHHHHHHGHHHHHHDDCDD#?CCBCDDDCHEHHHHHHHHHHHFH7

-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
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