[BioC] report a possible bug of

[Martin Morgan]

On 02/28/2012 08:20 AM, wang peter wrote:
> hi all: i used ShortRead to trim some sequences
>
> 	max.mismatchs<- 0.25*1:nchar(DNAString(PCR2rc))

using 1:nchar(...) can be bad, e.g., when nchar() ==> 0

 > 1:0
[1] 1 0

use seq_len instead, so

   0.25 * seq_len(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

How can I reproduce this?


>
>
>> 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
>>
>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793