[BioC] report a possible bug of

[wang peter]

hi all: i used ShortRead to trim some sequences

	max.mismatchs <- 0.25*1:nchar(DNAString(PCR2rc))
	trimmedCoords <- trimLRPatterns(Rpattern = PCR2rc, subject =
sread(highQuaReads), max.Rmismatch= max.mismatchs,
with.Rindels=T,ranges=T)
	trimmedReads <- narrow(highQuaReads, start=start(trimmedCoords),
end=end(trimmedCoords))

but it appear some null lines, but it is the first time to happen in
my exprience


@HWI-ST132:506:D0CNUABXX:3:1101:4456:1871 1:N:0:TTCACA

+

@HWI-ST132:506:D0CNUABXX:3:1101:4331:1931 1:N:0:TTCACA
GGTGGCTGTAGTTTAGTGGTAAGAATTCTACG
+
?<?DDD?D:<CDFFFG<FCFACGGIII at AEEH



> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
>

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